Starting phenix.real_space_refine on Sat Jun 7 11:30:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287.map" model { file = "/net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flu_29287/06_2025/8flu_29287_neut.cif" } resolution = 2.76 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= -0.002 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5577 2.51 5 N 1518 2.21 5 O 1576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8725 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1793 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2528 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 50 Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 382 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 956 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "P" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 271 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "R" Number of atoms: 2790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2790 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 351} Chain breaks: 3 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'HIS:plan': 2, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 5.90, per 1000 atoms: 0.68 Number of scatterers: 8725 At special positions: 0 Unit cell: (74.62, 95.12, 168.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1576 8.00 N 1518 7.00 C 5577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 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: 2.23 Conformation dependent library (CDL) restraints added in 995.0 milliseconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 44.3% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.534A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.548A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.103A pdb=" N ASP A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.810A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.573A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.578A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'P' and resid 2 through 32 removed outlier: 3.717A pdb=" N ASP P 17 " --> pdb=" O LYS P 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 54 Processing helix chain 'R' and resid 169 through 174 removed outlier: 3.743A pdb=" N LYS R 172 " --> pdb=" O GLU R 169 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE R 173 " --> pdb=" O CYS R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.840A pdb=" N ARG R 181 " --> pdb=" O GLU R 177 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.841A pdb=" N SER R 246 " --> pdb=" O ALA R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 278 through 311 removed outlier: 3.503A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 316 through 347 removed outlier: 3.585A pdb=" N TYR R 320 " --> pdb=" O SER R 316 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N TRP R 322 " --> pdb=" O LYS R 318 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY R 323 " --> pdb=" O LYS R 319 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LEU R 331 " --> pdb=" O PHE R 327 " (cutoff:3.500A) Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.809A pdb=" N LYS R 359 " --> pdb=" O SER R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 391 Proline residue: R 366 - end of helix removed outlier: 3.531A pdb=" N ASN R 380 " --> pdb=" O ILE R 376 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL R 384 " --> pdb=" O ASN R 380 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 418 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 434 through 460 removed outlier: 3.971A pdb=" N SER R 449 " --> pdb=" O MET R 445 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 463 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.407A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.388A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.557A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.606A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.205A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.520A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.556A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.287A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 111 through 112 Processing sheet with id=AB3, first strand: chain 'R' and resid 126 through 130 489 hydrogen bonds defined for protein. 1380 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: 2.54 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2836 1.34 - 1.46: 1836 1.46 - 1.58: 4173 1.58 - 1.70: 0 1.70 - 1.81: 75 Bond restraints: 8920 Sorted by residual: bond pdb=" CA SER B 316 " pdb=" CB SER B 316 " ideal model delta sigma weight residual 1.536 1.483 0.053 1.42e-02 4.96e+03 1.37e+01 bond pdb=" CA SER B 275 " pdb=" CB SER B 275 " ideal model delta sigma weight residual 1.534 1.483 0.051 1.64e-02 3.72e+03 9.57e+00 bond pdb=" N VAL R 432 " pdb=" CA VAL R 432 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.30e-02 5.92e+03 8.11e+00 bond pdb=" N GLN P 6 " pdb=" CA GLN P 6 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.19e-02 7.06e+03 7.91e+00 bond pdb=" N ARG B 314 " pdb=" CA ARG B 314 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.28e-02 6.10e+03 7.90e+00 ... (remaining 8915 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 11429 1.39 - 2.78: 571 2.78 - 4.17: 95 4.17 - 5.57: 30 5.57 - 6.96: 2 Bond angle restraints: 12127 Sorted by residual: angle pdb=" N LYS P 13 " pdb=" CA LYS P 13 " pdb=" C LYS P 13 " ideal model delta sigma weight residual 112.38 107.34 5.04 1.22e+00 6.72e-01 1.71e+01 angle pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" O GLY B 272 " ideal model delta sigma weight residual 121.64 118.03 3.61 9.20e-01 1.18e+00 1.54e+01 angle pdb=" N TYR B 59 " pdb=" CA TYR B 59 " pdb=" C TYR B 59 " ideal model delta sigma weight residual 113.28 108.72 4.56 1.22e+00 6.72e-01 1.40e+01 angle pdb=" CA THR R 430 " pdb=" C THR R 430 " pdb=" O THR R 430 " ideal model delta sigma weight residual 121.81 117.60 4.21 1.18e+00 7.18e-01 1.28e+01 angle pdb=" N THR B 274 " pdb=" CA THR B 274 " pdb=" C THR B 274 " ideal model delta sigma weight residual 113.97 109.51 4.46 1.28e+00 6.10e-01 1.21e+01 ... (remaining 12122 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 4814 17.66 - 35.32: 329 35.32 - 52.98: 47 52.98 - 70.64: 17 70.64 - 88.30: 8 Dihedral angle restraints: 5215 sinusoidal: 1899 harmonic: 3316 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 156.00 24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA PHE R 314 " pdb=" C PHE R 314 " pdb=" N PHE R 315 " pdb=" CA PHE R 315 " ideal model delta harmonic sigma weight residual -180.00 -159.66 -20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 127.08 -34.08 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 5212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1038 0.047 - 0.094: 255 0.094 - 0.141: 62 0.141 - 0.188: 9 0.188 - 0.235: 3 Chirality restraints: 1367 Sorted by residual: chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS P 13 " pdb=" N LYS P 13 " pdb=" C LYS P 13 " pdb=" CB LYS P 13 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1364 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 325 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO A 326 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 55 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C LEU B 55 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU B 55 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 56 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 428 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C PRO R 428 " 0.037 2.00e-02 2.50e+03 pdb=" O PRO R 428 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR R 429 " -0.012 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1520 2.76 - 3.29: 8941 3.29 - 3.83: 15852 3.83 - 4.36: 19131 4.36 - 4.90: 31893 Nonbonded interactions: 77337 Sorted by model distance: nonbonded pdb=" OD1 ASP A 274 " pdb=" ND2 ASN A 278 " model vdw 2.223 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.236 3.040 nonbonded pdb=" O PHE A 315 " pdb=" NH2 ARG A 336 " model vdw 2.249 3.120 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.249 3.040 nonbonded pdb=" OE2 GLU P 4 " pdb=" OH TYR R 195 " model vdw 2.250 3.040 ... (remaining 77332 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=0.00 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.470 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.004 0.053 8926 Z= 0.255 Angle : 0.697 6.957 12139 Z= 0.439 Chirality : 0.045 0.235 1367 Planarity : 0.004 0.073 1544 Dihedral : 13.281 88.298 3053 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.04 % Favored : 96.87 % Rotamer: Outliers : 0.35 % Allowed : 0.46 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.25), residues: 1119 helix: 1.61 (0.25), residues: 428 sheet: -0.68 (0.32), residues: 209 loop : -0.15 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS B 266 PHE 0.014 0.002 PHE R 314 TYR 0.014 0.001 TYR R 459 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.14074 ( 489) hydrogen bonds : angle 6.51501 ( 1380) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.13029 ( 12) covalent geometry : bond 0.00425 ( 8920) covalent geometry : angle 0.69624 (12127) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 170 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6085 (ttpp) cc_final: 0.5495 (tttt) REVERT: N 83 MET cc_start: 0.6321 (mtm) cc_final: 0.5300 (mtm) REVERT: R 36 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: R 221 TYR cc_start: 0.7269 (t80) cc_final: 0.6913 (t80) outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 1.5233 time to fit residues: 279.3556 Evaluate side-chains 116 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain R residue 36 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 156 GLN B 220 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 6 GLN ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 220 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.214679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.173383 restraints weight = 9922.920| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.84 r_work: 0.4062 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3953 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8926 Z= 0.156 Angle : 0.609 10.736 12139 Z= 0.328 Chirality : 0.043 0.221 1367 Planarity : 0.004 0.056 1544 Dihedral : 5.674 85.328 1236 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 9.71 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.98 (0.25), residues: 1119 helix: 2.22 (0.25), residues: 432 sheet: -0.79 (0.31), residues: 212 loop : -0.05 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.010 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.034 0.002 TYR R 191 ARG 0.004 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 489) hydrogen bonds : angle 4.87152 ( 1380) SS BOND : bond 0.00239 ( 6) SS BOND : angle 2.55754 ( 12) covalent geometry : bond 0.00339 ( 8920) covalent geometry : angle 0.60426 (12127) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.957 Fit side-chains REVERT: A 53 LYS cc_start: 0.6357 (ttpp) cc_final: 0.5621 (ttpt) REVERT: A 208 PHE cc_start: 0.7631 (m-80) cc_final: 0.7316 (m-10) REVERT: A 373 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.7058 (mmm-85) REVERT: B 44 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.5815 (mp-120) REVERT: B 170 ASP cc_start: 0.7943 (t70) cc_final: 0.7702 (p0) REVERT: B 175 GLN cc_start: 0.7262 (mm110) cc_final: 0.6377 (pt0) REVERT: G 50 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.5869 (mp) REVERT: N 83 MET cc_start: 0.6820 (mtm) cc_final: 0.5995 (mtm) REVERT: R 180 GLU cc_start: 0.6091 (tp30) cc_final: 0.5390 (mt-10) REVERT: R 221 TYR cc_start: 0.7331 (t80) cc_final: 0.6850 (t80) REVERT: R 438 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7175 (mm-40) outliers start: 21 outliers final: 5 residues processed: 142 average time/residue: 1.4080 time to fit residues: 212.9361 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 4 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 62 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN P 10 GLN R 37 GLN R 380 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 448 ASN ** 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 = 0.4534 r_free = 0.4534 target = 0.213857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.172808 restraints weight = 10065.684| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 1.82 r_work: 0.4053 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8926 Z= 0.153 Angle : 0.576 10.163 12139 Z= 0.309 Chirality : 0.042 0.238 1367 Planarity : 0.004 0.047 1544 Dihedral : 4.804 35.801 1231 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.08 % Allowed : 13.29 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.97 (0.26), residues: 1119 helix: 2.23 (0.24), residues: 437 sheet: -0.89 (0.31), residues: 216 loop : -0.03 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 14 HIS 0.008 0.001 HIS A 357 PHE 0.015 0.002 PHE B 199 TYR 0.030 0.002 TYR R 191 ARG 0.005 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 489) hydrogen bonds : angle 4.71780 ( 1380) SS BOND : bond 0.00226 ( 6) SS BOND : angle 2.09620 ( 12) covalent geometry : bond 0.00338 ( 8920) covalent geometry : angle 0.57210 (12127) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.963 Fit side-chains REVERT: A 27 GLU cc_start: 0.7169 (tp30) cc_final: 0.6731 (tp30) REVERT: A 53 LYS cc_start: 0.6370 (ttpp) cc_final: 0.5669 (ttpt) REVERT: A 373 ARG cc_start: 0.7361 (mmt-90) cc_final: 0.7075 (mmm-85) REVERT: A 392 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7441 (mt-10) REVERT: B 87 THR cc_start: 0.7821 (t) cc_final: 0.7464 (m) REVERT: B 170 ASP cc_start: 0.7975 (t70) cc_final: 0.7710 (p0) REVERT: B 175 GLN cc_start: 0.7298 (mm110) cc_final: 0.6345 (pt0) REVERT: B 197 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6691 (mpp80) REVERT: B 219 ARG cc_start: 0.7748 (mtp-110) cc_final: 0.7209 (mmt-90) REVERT: B 280 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7709 (mtpt) REVERT: G 50 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.5822 (mp) REVERT: N 83 MET cc_start: 0.6835 (mtm) cc_final: 0.6251 (mtm) REVERT: R 180 GLU cc_start: 0.6127 (tp30) cc_final: 0.5359 (mp0) REVERT: R 181 ARG cc_start: 0.6485 (ttp-110) cc_final: 0.6285 (ttp-110) REVERT: R 182 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7252 (tm-30) REVERT: R 195 TYR cc_start: 0.8280 (m-80) cc_final: 0.7912 (m-80) REVERT: R 221 TYR cc_start: 0.7224 (t80) cc_final: 0.6766 (t80) REVERT: R 438 GLN cc_start: 0.7478 (OUTLIER) cc_final: 0.7146 (mm-40) outliers start: 18 outliers final: 6 residues processed: 135 average time/residue: 1.2739 time to fit residues: 182.9336 Evaluate side-chains 127 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 117 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 0.3980 chunk 77 optimal weight: 0.0030 chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.0270 chunk 80 optimal weight: 8.9990 overall best weight: 0.3848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 44 GLN B 220 GLN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 420 HIS R 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.216331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.175562 restraints weight = 9992.175| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.84 r_work: 0.4081 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3968 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8926 Z= 0.121 Angle : 0.530 10.086 12139 Z= 0.286 Chirality : 0.041 0.248 1367 Planarity : 0.003 0.042 1544 Dihedral : 4.635 33.651 1231 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.31 % Allowed : 14.22 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.07 (0.26), residues: 1119 helix: 2.35 (0.24), residues: 437 sheet: -0.85 (0.31), residues: 216 loop : -0.01 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP P 14 HIS 0.007 0.001 HIS A 357 PHE 0.016 0.001 PHE A 222 TYR 0.029 0.001 TYR R 191 ARG 0.004 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 489) hydrogen bonds : angle 4.57940 ( 1380) SS BOND : bond 0.00119 ( 6) SS BOND : angle 1.63141 ( 12) covalent geometry : bond 0.00255 ( 8920) covalent geometry : angle 0.52824 (12127) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.866 Fit side-chains REVERT: A 27 GLU cc_start: 0.7043 (tp30) cc_final: 0.6661 (tp30) REVERT: A 53 LYS cc_start: 0.6259 (ttpp) cc_final: 0.5722 (ttpt) REVERT: A 208 PHE cc_start: 0.7560 (m-80) cc_final: 0.7212 (m-10) REVERT: A 390 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.6037 (pt0) REVERT: A 392 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7401 (mt-10) REVERT: B 87 THR cc_start: 0.7709 (t) cc_final: 0.7391 (m) REVERT: B 170 ASP cc_start: 0.8013 (t70) cc_final: 0.7767 (p0) REVERT: B 219 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7193 (mmt-90) REVERT: B 280 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7678 (mtpt) REVERT: G 50 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.5782 (mp) REVERT: N 83 MET cc_start: 0.6727 (mtm) cc_final: 0.6265 (mtm) REVERT: R 180 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5407 (mp0) REVERT: R 221 TYR cc_start: 0.7213 (t80) cc_final: 0.6795 (t80) REVERT: R 438 GLN cc_start: 0.7453 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: R 467 GLN cc_start: 0.7579 (tp40) cc_final: 0.6947 (tm-30) outliers start: 20 outliers final: 8 residues processed: 132 average time/residue: 1.2831 time to fit residues: 180.6565 Evaluate side-chains 124 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 438 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 97 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 0.0030 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** R 374 ASN ** 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 = 0.4546 r_free = 0.4546 target = 0.215145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.174370 restraints weight = 9926.921| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.77 r_work: 0.4068 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3955 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8926 Z= 0.147 Angle : 0.546 9.622 12139 Z= 0.295 Chirality : 0.042 0.267 1367 Planarity : 0.004 0.047 1544 Dihedral : 4.626 33.980 1231 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.01 % Allowed : 14.34 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.16 (0.26), residues: 1119 helix: 2.40 (0.24), residues: 437 sheet: -0.62 (0.32), residues: 216 loop : -0.03 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 14 HIS 0.008 0.001 HIS A 362 PHE 0.022 0.002 PHE A 222 TYR 0.027 0.002 TYR R 191 ARG 0.004 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 489) hydrogen bonds : angle 4.55523 ( 1380) SS BOND : bond 0.00600 ( 6) SS BOND : angle 1.79353 ( 12) covalent geometry : bond 0.00325 ( 8920) covalent geometry : angle 0.54290 (12127) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7027 (tp30) cc_final: 0.6644 (tp30) REVERT: A 53 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5504 (ttpt) REVERT: A 208 PHE cc_start: 0.7555 (m-80) cc_final: 0.7206 (m-10) REVERT: B 87 THR cc_start: 0.7761 (t) cc_final: 0.7439 (m) REVERT: B 170 ASP cc_start: 0.7958 (t70) cc_final: 0.7747 (p0) REVERT: B 175 GLN cc_start: 0.7284 (mm110) cc_final: 0.6329 (pt0) REVERT: B 219 ARG cc_start: 0.7710 (mtp-110) cc_final: 0.7188 (mmt-90) REVERT: B 280 LYS cc_start: 0.7923 (OUTLIER) cc_final: 0.7654 (mtpt) REVERT: G 50 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5751 (mp) REVERT: N 83 MET cc_start: 0.6810 (mtm) cc_final: 0.6360 (mtm) REVERT: R 180 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5517 (mp0) REVERT: R 221 TYR cc_start: 0.7224 (t80) cc_final: 0.6788 (t80) REVERT: R 391 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6837 (mt-10) REVERT: R 463 ASN cc_start: 0.8029 (t0) cc_final: 0.7761 (t0) REVERT: R 467 GLN cc_start: 0.7550 (tp40) cc_final: 0.7006 (tm-30) outliers start: 26 outliers final: 10 residues processed: 130 average time/residue: 1.1947 time to fit residues: 166.0626 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 115 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 391 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 44 GLN ** R 374 ASN ** 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 = 0.4536 r_free = 0.4536 target = 0.214153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.172072 restraints weight = 9826.760| |-----------------------------------------------------------------------------| r_work (start): 0.4134 rms_B_bonded: 1.85 r_work: 0.4049 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3935 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8926 Z= 0.156 Angle : 0.558 8.702 12139 Z= 0.301 Chirality : 0.042 0.284 1367 Planarity : 0.004 0.049 1544 Dihedral : 4.645 32.255 1231 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.01 % Allowed : 15.14 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.14 (0.26), residues: 1119 helix: 2.38 (0.24), residues: 438 sheet: -0.68 (0.32), residues: 216 loop : -0.02 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 14 HIS 0.008 0.001 HIS A 357 PHE 0.030 0.002 PHE A 222 TYR 0.027 0.002 TYR R 191 ARG 0.003 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 489) hydrogen bonds : angle 4.59445 ( 1380) SS BOND : bond 0.00138 ( 6) SS BOND : angle 1.91090 ( 12) covalent geometry : bond 0.00347 ( 8920) covalent geometry : angle 0.55533 (12127) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.852 Fit side-chains REVERT: A 53 LYS cc_start: 0.6316 (ttpp) cc_final: 0.5650 (ttpt) REVERT: A 208 PHE cc_start: 0.7511 (m-80) cc_final: 0.7177 (m-10) REVERT: A 390 GLN cc_start: 0.6281 (mt0) cc_final: 0.6013 (pt0) REVERT: B 44 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.5749 (mp-120) REVERT: B 87 THR cc_start: 0.7664 (t) cc_final: 0.7383 (m) REVERT: B 170 ASP cc_start: 0.8017 (t70) cc_final: 0.7760 (p0) REVERT: B 175 GLN cc_start: 0.7240 (mm110) cc_final: 0.6315 (pt0) REVERT: B 219 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7182 (mmt-90) REVERT: B 280 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7655 (mtpt) REVERT: B 325 MET cc_start: 0.7457 (mmm) cc_final: 0.6977 (mmm) REVERT: G 50 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.5798 (mp) REVERT: N 83 MET cc_start: 0.6824 (mtm) cc_final: 0.6417 (mtm) REVERT: R 180 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: R 221 TYR cc_start: 0.7211 (t80) cc_final: 0.6808 (t80) REVERT: R 467 GLN cc_start: 0.7600 (tp40) cc_final: 0.7077 (tm-30) outliers start: 26 outliers final: 12 residues processed: 129 average time/residue: 1.2653 time to fit residues: 173.8194 Evaluate side-chains 123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 66 optimal weight: 0.0020 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 176 GLN N 77 ASN R 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.215190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173779 restraints weight = 10011.200| |-----------------------------------------------------------------------------| r_work (start): 0.4150 rms_B_bonded: 1.84 r_work: 0.4063 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8926 Z= 0.138 Angle : 0.549 8.965 12139 Z= 0.296 Chirality : 0.042 0.293 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.591 31.333 1231 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 15.95 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.15 (0.26), residues: 1119 helix: 2.42 (0.24), residues: 437 sheet: -0.73 (0.32), residues: 218 loop : -0.02 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 14 HIS 0.007 0.001 HIS A 357 PHE 0.034 0.002 PHE A 222 TYR 0.026 0.001 TYR R 191 ARG 0.005 0.000 ARG R 383 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 489) hydrogen bonds : angle 4.55411 ( 1380) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.73668 ( 12) covalent geometry : bond 0.00301 ( 8920) covalent geometry : angle 0.54664 (12127) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6976 (tp30) cc_final: 0.6541 (tp30) REVERT: A 53 LYS cc_start: 0.6302 (ttpp) cc_final: 0.5547 (ttpt) REVERT: A 208 PHE cc_start: 0.7517 (m-80) cc_final: 0.7181 (m-10) REVERT: A 390 GLN cc_start: 0.6269 (mt0) cc_final: 0.6036 (pt0) REVERT: B 44 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.5648 (mp10) REVERT: B 87 THR cc_start: 0.7660 (t) cc_final: 0.7404 (m) REVERT: B 170 ASP cc_start: 0.7978 (t70) cc_final: 0.7732 (p0) REVERT: B 175 GLN cc_start: 0.7234 (mm110) cc_final: 0.6307 (pt0) REVERT: B 219 ARG cc_start: 0.7720 (mtp-110) cc_final: 0.7163 (mmt-90) REVERT: B 280 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7685 (mtpt) REVERT: G 50 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.5738 (mp) REVERT: N 83 MET cc_start: 0.6743 (mtm) cc_final: 0.6344 (mtm) REVERT: R 180 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5541 (mp0) REVERT: R 221 TYR cc_start: 0.7227 (t80) cc_final: 0.6861 (t80) REVERT: R 467 GLN cc_start: 0.7574 (tp40) cc_final: 0.7096 (tm-30) outliers start: 22 outliers final: 9 residues processed: 125 average time/residue: 1.4235 time to fit residues: 190.2187 Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 38 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 106 optimal weight: 0.0370 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.215692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.174458 restraints weight = 10063.554| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 1.84 r_work: 0.4067 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8926 Z= 0.135 Angle : 0.542 9.803 12139 Z= 0.292 Chirality : 0.042 0.298 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.565 31.739 1231 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 15.95 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.18 (0.26), residues: 1119 helix: 2.41 (0.25), residues: 437 sheet: -0.68 (0.32), residues: 229 loop : 0.05 (0.32), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.038 0.002 PHE A 222 TYR 0.026 0.001 TYR R 191 ARG 0.003 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.03871 ( 489) hydrogen bonds : angle 4.52765 ( 1380) SS BOND : bond 0.00270 ( 6) SS BOND : angle 1.67935 ( 12) covalent geometry : bond 0.00294 ( 8920) covalent geometry : angle 0.53989 (12127) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6972 (tp30) cc_final: 0.6529 (tp30) REVERT: A 53 LYS cc_start: 0.6233 (ttpp) cc_final: 0.5611 (ttpt) REVERT: A 208 PHE cc_start: 0.7516 (m-80) cc_final: 0.7166 (m-10) REVERT: A 373 ARG cc_start: 0.7303 (tpp-160) cc_final: 0.6848 (mmm-85) REVERT: A 390 GLN cc_start: 0.6275 (mt0) cc_final: 0.6046 (pt0) REVERT: B 87 THR cc_start: 0.7635 (t) cc_final: 0.7402 (m) REVERT: B 170 ASP cc_start: 0.7954 (t70) cc_final: 0.7749 (p0) REVERT: B 219 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7159 (mmt-90) REVERT: B 280 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7642 (ttpt) REVERT: B 325 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6926 (mmt) REVERT: G 50 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.5765 (mp) REVERT: N 83 MET cc_start: 0.6728 (mtm) cc_final: 0.6280 (mtm) REVERT: R 178 THR cc_start: 0.6712 (t) cc_final: 0.6299 (p) REVERT: R 180 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5598 (mp0) REVERT: R 221 TYR cc_start: 0.7171 (t80) cc_final: 0.6819 (t80) REVERT: R 467 GLN cc_start: 0.7533 (tp40) cc_final: 0.7112 (tm-30) outliers start: 22 outliers final: 12 residues processed: 127 average time/residue: 1.2224 time to fit residues: 166.2315 Evaluate side-chains 122 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 311 TYR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 383 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 176 GLN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.207481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164933 restraints weight = 10001.486| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.83 r_work: 0.3993 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3881 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8926 Z= 0.245 Angle : 0.644 8.077 12139 Z= 0.346 Chirality : 0.046 0.289 1367 Planarity : 0.004 0.050 1544 Dihedral : 4.961 33.073 1231 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.20 % Allowed : 16.65 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.82 (0.26), residues: 1119 helix: 2.06 (0.24), residues: 438 sheet: -0.91 (0.32), residues: 223 loop : -0.07 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 297 HIS 0.011 0.002 HIS A 357 PHE 0.051 0.002 PHE A 222 TYR 0.031 0.002 TYR A 358 ARG 0.006 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 489) hydrogen bonds : angle 4.89196 ( 1380) SS BOND : bond 0.00449 ( 6) SS BOND : angle 2.39689 ( 12) covalent geometry : bond 0.00562 ( 8920) covalent geometry : angle 0.63972 (12127) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6423 (ttpp) cc_final: 0.5515 (ttpt) REVERT: A 216 LYS cc_start: 0.7389 (mttp) cc_final: 0.6991 (mmpt) REVERT: A 373 ARG cc_start: 0.7387 (tpp-160) cc_final: 0.6929 (mmm-85) REVERT: B 87 THR cc_start: 0.7724 (t) cc_final: 0.7452 (m) REVERT: B 170 ASP cc_start: 0.7979 (t70) cc_final: 0.7653 (p0) REVERT: B 219 ARG cc_start: 0.7803 (mtp-110) cc_final: 0.7190 (mmt-90) REVERT: B 325 MET cc_start: 0.7558 (OUTLIER) cc_final: 0.7059 (mmt) REVERT: G 50 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6139 (mp) REVERT: N 83 MET cc_start: 0.6763 (mtm) cc_final: 0.6382 (mtm) REVERT: R 180 GLU cc_start: 0.6530 (OUTLIER) cc_final: 0.5763 (mp0) REVERT: R 195 TYR cc_start: 0.8275 (m-80) cc_final: 0.7822 (m-80) REVERT: R 221 TYR cc_start: 0.7335 (t80) cc_final: 0.6904 (t80) REVERT: R 467 GLN cc_start: 0.7545 (tp40) cc_final: 0.7132 (tm-30) outliers start: 19 outliers final: 14 residues processed: 124 average time/residue: 1.5655 time to fit residues: 208.6882 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 383 ARG Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.2980 chunk 100 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 41 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN A 390 GLN B 44 GLN B 176 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.212736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.171469 restraints weight = 10007.498| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 1.81 r_work: 0.4059 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3947 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8926 Z= 0.137 Angle : 0.558 9.456 12139 Z= 0.301 Chirality : 0.043 0.296 1367 Planarity : 0.004 0.052 1544 Dihedral : 4.714 31.399 1231 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.97 % Allowed : 17.23 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.03 (0.26), residues: 1119 helix: 2.28 (0.25), residues: 438 sheet: -0.72 (0.32), residues: 218 loop : -0.08 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 352 HIS 0.007 0.001 HIS A 357 PHE 0.047 0.002 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.005 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 489) hydrogen bonds : angle 4.63128 ( 1380) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.61158 ( 12) covalent geometry : bond 0.00302 ( 8920) covalent geometry : angle 0.55561 (12127) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6907 (tp30) cc_final: 0.6453 (tp30) REVERT: A 53 LYS cc_start: 0.6230 (ttpp) cc_final: 0.5522 (ttpt) REVERT: A 373 ARG cc_start: 0.7336 (tpp-160) cc_final: 0.6884 (mmm-85) REVERT: A 390 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.6099 (pt0) REVERT: B 44 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6803 (mm110) REVERT: B 87 THR cc_start: 0.7638 (t) cc_final: 0.7414 (m) REVERT: B 170 ASP cc_start: 0.7926 (t70) cc_final: 0.7719 (p0) REVERT: B 219 ARG cc_start: 0.7788 (mtp-110) cc_final: 0.7223 (mmt-90) REVERT: B 280 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7697 (mtpt) REVERT: B 325 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6933 (mmt) REVERT: G 50 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5766 (mp) REVERT: N 83 MET cc_start: 0.6651 (mtm) cc_final: 0.5882 (mtm) REVERT: R 180 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5703 (mp0) REVERT: R 221 TYR cc_start: 0.7189 (t80) cc_final: 0.6810 (t80) outliers start: 17 outliers final: 9 residues processed: 124 average time/residue: 1.2714 time to fit residues: 169.0956 Evaluate side-chains 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU Chi-restraints excluded: chain R residue 370 SER Chi-restraints excluded: chain R residue 383 ARG Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 55 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN B 44 GLN B 155 ASN B 220 GLN N 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.212526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171009 restraints weight = 10004.762| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 1.84 r_work: 0.4051 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3940 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8926 Z= 0.141 Angle : 0.560 8.780 12139 Z= 0.303 Chirality : 0.043 0.299 1367 Planarity : 0.004 0.052 1544 Dihedral : 4.695 30.682 1231 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.85 % Allowed : 18.03 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.07 (0.26), residues: 1119 helix: 2.29 (0.25), residues: 438 sheet: -0.68 (0.32), residues: 223 loop : -0.04 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 352 HIS 0.007 0.001 HIS A 357 PHE 0.052 0.002 PHE R 335 TYR 0.025 0.002 TYR R 191 ARG 0.005 0.000 ARG R 181 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 489) hydrogen bonds : angle 4.60604 ( 1380) SS BOND : bond 0.00237 ( 6) SS BOND : angle 1.65952 ( 12) covalent geometry : bond 0.00312 ( 8920) covalent geometry : angle 0.55740 (12127) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7530.33 seconds wall clock time: 131 minutes 24.38 seconds (7884.38 seconds total)