Starting phenix.real_space_refine on Sat Aug 23 00:07:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flu_29287/08_2025/8flu_29287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flu_29287/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8flu_29287/08_2025/8flu_29287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flu_29287/08_2025/8flu_29287_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8flu_29287/08_2025/8flu_29287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flu_29287/08_2025/8flu_29287.map" } resolution = 2.76 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= -0.002 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'GLN:plan1': 2, 'ASP:plan': 3, 'ARG:plan': 2} 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, 'ARG:plan': 4, 'ASP:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 1} 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, 'ASP:plan': 1, 'ARG: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: {'GLU:plan': 7, 'ARG:plan': 11, 'GLN:plan1': 1, 'ASP:plan': 2, 'ASN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1} 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: 2.22, per 1000 atoms: 0.25 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: 0.47 Conformation dependent library (CDL) restraints added in 331.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.31 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: 1.53 Time building geometry restraints manager: 0.65 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: 3.200 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.040 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:6.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 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: 0.56 (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 ARG 0.003 0.000 ARG B 197 TYR 0.014 0.001 TYR R 459 PHE 0.014 0.002 PHE R 314 TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS B 266 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8920) covalent geometry : angle 0.69624 (12127) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.13029 ( 12) hydrogen bonds : bond 0.14074 ( 489) hydrogen bonds : angle 6.51501 ( 1380) *********************** 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 : 0.343 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: 0.5301 (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: 0.6912 (t80) outliers start: 3 outliers final: 1 residues processed: 173 average time/residue: 0.5919 time to fit residues: 108.2711 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 : 0.402 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 = 0.4548 r_free = 0.4548 target = 0.215070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.173788 restraints weight = 10012.877| |-----------------------------------------------------------------------------| r_work (start): 0.4155 rms_B_bonded: 1.85 r_work: 0.4069 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3958 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7425 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8926 Z= 0.151 Angle : 0.606 9.875 12139 Z= 0.326 Chirality : 0.043 0.215 1367 Planarity : 0.004 0.056 1544 Dihedral : 5.677 86.515 1236 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.43 % Allowed : 9.48 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.96 (0.26), residues: 1119 helix: 2.16 (0.25), residues: 438 sheet: -0.77 (0.31), residues: 212 loop : -0.05 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 373 TYR 0.035 0.002 TYR R 191 PHE 0.017 0.002 PHE R 212 TRP 0.014 0.001 TRP B 211 HIS 0.010 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8920) covalent geometry : angle 0.60188 (12127) SS BOND : bond 0.00225 ( 6) SS BOND : angle 2.41228 ( 12) hydrogen bonds : bond 0.04426 ( 489) hydrogen bonds : angle 4.83505 ( 1380) *********************** 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 150 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.287 Fit side-chains REVERT: A 53 LYS cc_start: 0.6329 (ttpp) cc_final: 0.5591 (ttpt) REVERT: A 208 PHE cc_start: 0.7623 (m-80) cc_final: 0.7313 (m-10) REVERT: A 373 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7063 (mmm-85) REVERT: A 390 GLN cc_start: 0.6246 (mt0) cc_final: 0.5955 (pt0) REVERT: A 392 GLU cc_start: 0.7908 (mm-30) cc_final: 0.7563 (mt-10) REVERT: B 44 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5814 (mp-120) REVERT: B 170 ASP cc_start: 0.7947 (t70) cc_final: 0.7700 (p0) REVERT: B 219 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7352 (mmt-90) REVERT: G 50 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.5825 (mp) REVERT: N 83 MET cc_start: 0.6831 (mtm) cc_final: 0.6001 (mtm) REVERT: R 180 GLU cc_start: 0.6144 (tp30) cc_final: 0.5330 (mp0) REVERT: R 221 TYR cc_start: 0.7322 (t80) cc_final: 0.6848 (t80) REVERT: R 438 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7171 (mm-40) outliers start: 21 outliers final: 5 residues processed: 140 average time/residue: 0.5405 time to fit residues: 80.4147 Evaluate side-chains 123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 33 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.213414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171632 restraints weight = 9957.271| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.84 r_work: 0.4045 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8926 Z= 0.163 Angle : 0.577 9.804 12139 Z= 0.309 Chirality : 0.042 0.242 1367 Planarity : 0.004 0.047 1544 Dihedral : 4.814 35.318 1231 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.43 % Allowed : 12.95 % 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 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: 0.97 (0.26), residues: 1119 helix: 2.23 (0.24), residues: 437 sheet: -0.89 (0.31), residues: 217 loop : -0.02 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 373 TYR 0.030 0.002 TYR R 191 PHE 0.015 0.002 PHE B 199 TRP 0.015 0.001 TRP P 14 HIS 0.009 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8920) covalent geometry : angle 0.57417 (12127) SS BOND : bond 0.00415 ( 6) SS BOND : angle 1.96583 ( 12) hydrogen bonds : bond 0.04225 ( 489) hydrogen bonds : angle 4.73122 ( 1380) *********************** 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 152 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7121 (tp30) cc_final: 0.6698 (tp30) REVERT: A 53 LYS cc_start: 0.6361 (ttpp) cc_final: 0.5659 (ttpt) REVERT: A 373 ARG cc_start: 0.7398 (mmt-90) cc_final: 0.7121 (mmm-85) REVERT: A 390 GLN cc_start: 0.6274 (mt0) cc_final: 0.5996 (pt0) REVERT: A 392 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7541 (mt-10) REVERT: B 87 THR cc_start: 0.7849 (t) cc_final: 0.7470 (m) REVERT: B 105 TYR cc_start: 0.7600 (t80) cc_final: 0.7314 (t80) REVERT: B 170 ASP cc_start: 0.8011 (t70) cc_final: 0.7741 (p0) REVERT: B 175 GLN cc_start: 0.7296 (mm110) cc_final: 0.6361 (pt0) REVERT: B 197 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6704 (mpp80) REVERT: B 219 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7223 (mmt-90) REVERT: B 280 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7723 (mtpt) REVERT: G 50 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.5877 (mp) REVERT: N 83 MET cc_start: 0.6846 (mtm) cc_final: 0.6260 (mtm) REVERT: R 180 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5444 (mp0) REVERT: R 182 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7329 (tm-30) REVERT: R 221 TYR cc_start: 0.7292 (t80) cc_final: 0.6857 (t80) REVERT: R 438 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7201 (mm-40) REVERT: R 467 GLN cc_start: 0.7673 (tp40) cc_final: 0.6988 (tm-30) outliers start: 21 outliers final: 8 residues processed: 136 average time/residue: 0.5485 time to fit residues: 79.2164 Evaluate side-chains 131 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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 65 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 69 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 180 GLU 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 85 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN B 176 GLN B 220 GLN G 18 GLN N 77 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.212514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.171014 restraints weight = 10111.191| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.80 r_work: 0.4039 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3925 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8926 Z= 0.163 Angle : 0.563 8.708 12139 Z= 0.303 Chirality : 0.042 0.254 1367 Planarity : 0.004 0.043 1544 Dihedral : 4.784 33.347 1231 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.89 % Allowed : 13.76 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.98 (0.26), residues: 1119 helix: 2.27 (0.24), residues: 437 sheet: -0.85 (0.31), residues: 222 loop : -0.06 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.029 0.002 TYR R 191 PHE 0.015 0.002 PHE B 199 TRP 0.015 0.002 TRP P 14 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8920) covalent geometry : angle 0.56062 (12127) SS BOND : bond 0.00057 ( 6) SS BOND : angle 1.87311 ( 12) hydrogen bonds : bond 0.04135 ( 489) hydrogen bonds : angle 4.72247 ( 1380) *********************** 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 151 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 0.298 Fit side-chains REVERT: A 53 LYS cc_start: 0.6404 (ttpp) cc_final: 0.5515 (ttpt) REVERT: A 208 PHE cc_start: 0.7574 (m-80) cc_final: 0.7214 (m-10) REVERT: A 390 GLN cc_start: 0.6242 (mt0) cc_final: 0.5952 (pt0) REVERT: A 392 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7441 (mt-10) REVERT: B 87 THR cc_start: 0.7821 (t) cc_final: 0.7510 (m) REVERT: B 170 ASP cc_start: 0.8004 (t70) cc_final: 0.7717 (p0) REVERT: B 175 GLN cc_start: 0.7196 (mm110) cc_final: 0.6351 (pt0) REVERT: B 219 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7145 (mmt-90) REVERT: B 280 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7715 (mtpt) REVERT: G 50 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.5782 (mp) REVERT: N 53 GLN cc_start: 0.7898 (mp10) cc_final: 0.7653 (mp10) REVERT: N 83 MET cc_start: 0.6822 (mtm) cc_final: 0.6328 (mtm) REVERT: R 180 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5558 (mp0) REVERT: R 221 TYR cc_start: 0.7239 (t80) cc_final: 0.6789 (t80) REVERT: R 438 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7174 (mm-40) REVERT: R 467 GLN cc_start: 0.7622 (tp40) cc_final: 0.7125 (tm-30) outliers start: 25 outliers final: 11 residues processed: 136 average time/residue: 0.4836 time to fit residues: 69.8298 Evaluate side-chains 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 110 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 372 ILE 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 258 ASP 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 438 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 15 optimal weight: 0.0020 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 70 optimal weight: 0.0570 chunk 80 optimal weight: 0.0770 chunk 39 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 overall best weight: 0.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.217028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.176457 restraints weight = 10056.461| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 1.84 r_work: 0.4092 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8926 Z= 0.114 Angle : 0.522 10.212 12139 Z= 0.282 Chirality : 0.041 0.268 1367 Planarity : 0.003 0.045 1544 Dihedral : 4.579 31.848 1231 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.31 % Allowed : 15.03 % 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 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: 1.17 (0.26), residues: 1119 helix: 2.44 (0.24), residues: 438 sheet: -0.70 (0.31), residues: 221 loop : -0.02 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.027 0.001 TYR R 191 PHE 0.020 0.001 PHE A 222 TRP 0.014 0.001 TRP P 14 HIS 0.005 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8920) covalent geometry : angle 0.52057 (12127) SS BOND : bond 0.00169 ( 6) SS BOND : angle 1.30244 ( 12) hydrogen bonds : bond 0.03807 ( 489) hydrogen bonds : angle 4.53808 ( 1380) *********************** 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 141 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6937 (tp30) cc_final: 0.6565 (tp30) REVERT: A 53 LYS cc_start: 0.6213 (ttpp) cc_final: 0.5430 (ttpt) REVERT: A 208 PHE cc_start: 0.7540 (m-80) cc_final: 0.7237 (m-10) REVERT: A 344 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6491 (mm-30) REVERT: A 390 GLN cc_start: 0.6145 (mt0) cc_final: 0.5926 (pt0) REVERT: B 87 THR cc_start: 0.7645 (t) cc_final: 0.7348 (m) REVERT: B 170 ASP cc_start: 0.7960 (t70) cc_final: 0.7682 (p0) REVERT: B 219 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7204 (mmt-90) REVERT: B 280 LYS cc_start: 0.7952 (OUTLIER) cc_final: 0.7682 (ttpt) REVERT: B 325 MET cc_start: 0.7221 (mmm) cc_final: 0.6795 (mmm) REVERT: G 50 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.5737 (mp) REVERT: N 83 MET cc_start: 0.6700 (mtm) cc_final: 0.5997 (mtm) REVERT: R 180 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5518 (mp0) REVERT: R 221 TYR cc_start: 0.7166 (t80) cc_final: 0.6752 (t80) REVERT: R 360 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7496 (ptpp) outliers start: 20 outliers final: 4 residues processed: 130 average time/residue: 0.4949 time to fit residues: 68.6308 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 114 CYS 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 R residue 180 GLU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 81 optimal weight: 30.0000 chunk 97 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 N 77 ASN ** R 374 ASN ** 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 = 0.4512 r_free = 0.4512 target = 0.211667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.169406 restraints weight = 9970.008| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.84 r_work: 0.4014 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8926 Z= 0.197 Angle : 0.600 7.588 12139 Z= 0.322 Chirality : 0.044 0.285 1367 Planarity : 0.004 0.048 1544 Dihedral : 4.789 31.416 1231 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.01 % Allowed : 15.84 % 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 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: 1.02 (0.26), residues: 1119 helix: 2.26 (0.24), residues: 437 sheet: -0.82 (0.32), residues: 218 loop : -0.01 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.027 0.002 TYR R 191 PHE 0.032 0.002 PHE A 222 TRP 0.013 0.002 TRP P 14 HIS 0.010 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 8920) covalent geometry : angle 0.59654 (12127) SS BOND : bond 0.00405 ( 6) SS BOND : angle 2.15930 ( 12) hydrogen bonds : bond 0.04200 ( 489) hydrogen bonds : angle 4.76185 ( 1380) *********************** 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 136 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7032 (tp30) cc_final: 0.6610 (tp30) REVERT: A 53 LYS cc_start: 0.6322 (ttpp) cc_final: 0.5538 (ttpt) REVERT: A 373 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.6875 (mmm-85) REVERT: A 390 GLN cc_start: 0.6234 (mt0) cc_final: 0.6032 (pt0) REVERT: A 392 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7461 (mt-10) REVERT: B 44 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.5817 (mp-120) REVERT: B 87 THR cc_start: 0.7753 (t) cc_final: 0.7489 (m) REVERT: B 170 ASP cc_start: 0.8027 (t70) cc_final: 0.7729 (p0) REVERT: B 219 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7213 (mmt-90) REVERT: B 280 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7716 (mtpt) REVERT: B 325 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7031 (mmt) REVERT: G 50 LEU cc_start: 0.6689 (OUTLIER) cc_final: 0.5818 (mp) REVERT: N 83 MET cc_start: 0.6827 (mtm) cc_final: 0.6362 (mtm) REVERT: R 180 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5626 (mp0) REVERT: R 203 THR cc_start: 0.7529 (m) cc_final: 0.7289 (p) REVERT: R 221 TYR cc_start: 0.7298 (t80) cc_final: 0.6861 (t80) REVERT: R 467 GLN cc_start: 0.7641 (tp40) cc_final: 0.7013 (tm-30) outliers start: 26 outliers final: 10 residues processed: 119 average time/residue: 0.5244 time to fit residues: 66.1353 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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 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 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 12 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.210536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.168680 restraints weight = 10116.737| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.84 r_work: 0.4030 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3917 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8926 Z= 0.169 Angle : 0.570 7.930 12139 Z= 0.308 Chirality : 0.043 0.282 1367 Planarity : 0.004 0.050 1544 Dihedral : 4.759 30.888 1231 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.66 % Allowed : 16.76 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.98 (0.26), residues: 1119 helix: 2.25 (0.24), residues: 437 sheet: -0.85 (0.32), residues: 218 loop : -0.05 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 383 TYR 0.025 0.002 TYR R 191 PHE 0.034 0.002 PHE A 222 TRP 0.014 0.002 TRP P 14 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 8920) covalent geometry : angle 0.56693 (12127) SS BOND : bond 0.00308 ( 6) SS BOND : angle 1.91885 ( 12) hydrogen bonds : bond 0.04072 ( 489) hydrogen bonds : angle 4.71736 ( 1380) *********************** 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 134 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7004 (tp30) cc_final: 0.6611 (tp30) REVERT: A 53 LYS cc_start: 0.6336 (ttpp) cc_final: 0.5547 (ttpt) REVERT: A 373 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6850 (mmm-85) REVERT: A 392 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7424 (mt-10) REVERT: B 87 THR cc_start: 0.7682 (t) cc_final: 0.7455 (m) REVERT: B 170 ASP cc_start: 0.7981 (t70) cc_final: 0.7683 (p0) REVERT: B 219 ARG cc_start: 0.7781 (mtp-110) cc_final: 0.7288 (mmt-90) REVERT: B 280 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7669 (mtpt) REVERT: B 325 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.6973 (mmt) REVERT: G 50 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5744 (mp) REVERT: N 83 MET cc_start: 0.6797 (mtm) cc_final: 0.6258 (mtm) REVERT: R 180 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5675 (mp0) REVERT: R 221 TYR cc_start: 0.7205 (t80) cc_final: 0.6799 (t80) outliers start: 23 outliers final: 11 residues processed: 119 average time/residue: 0.4819 time to fit residues: 61.3104 Evaluate side-chains 119 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 114 CYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP 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 38 MET 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 370 SER 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 45 optimal weight: 0.0170 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.6620 ------------------------------------------------------------------------------- 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 N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.211802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170184 restraints weight = 9993.808| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 1.85 r_work: 0.4040 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3926 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2755 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= 0.150 Angle : 0.562 8.778 12139 Z= 0.303 Chirality : 0.043 0.298 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.703 31.399 1231 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 16.65 % 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 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: 1.03 (0.26), residues: 1119 helix: 2.27 (0.24), residues: 436 sheet: -0.77 (0.32), residues: 223 loop : -0.00 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.025 0.001 TYR R 191 PHE 0.037 0.002 PHE A 222 TRP 0.013 0.001 TRP P 14 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8920) covalent geometry : angle 0.55993 (12127) SS BOND : bond 0.00265 ( 6) SS BOND : angle 1.79868 ( 12) hydrogen bonds : bond 0.03983 ( 489) hydrogen bonds : angle 4.64752 ( 1380) *********************** 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 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6944 (tp30) cc_final: 0.6551 (tp30) REVERT: A 53 LYS cc_start: 0.6345 (ttpp) cc_final: 0.5569 (ttpt) REVERT: A 208 PHE cc_start: 0.7600 (m-80) cc_final: 0.7251 (m-10) REVERT: A 373 ARG cc_start: 0.7282 (tpp-160) cc_final: 0.6879 (mmm-85) REVERT: A 392 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7439 (mt-10) REVERT: B 87 THR cc_start: 0.7676 (t) cc_final: 0.7460 (m) REVERT: B 170 ASP cc_start: 0.7968 (t70) cc_final: 0.7710 (p0) REVERT: B 219 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7394 (mmt-90) REVERT: B 280 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7711 (mtpt) REVERT: B 325 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6930 (mmt) REVERT: G 50 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.5707 (mp) REVERT: N 83 MET cc_start: 0.6731 (mtm) cc_final: 0.6232 (mtm) REVERT: R 180 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5647 (mp0) REVERT: R 221 TYR cc_start: 0.7215 (t80) cc_final: 0.6832 (t80) outliers start: 22 outliers final: 12 residues processed: 120 average time/residue: 0.4805 time to fit residues: 61.6327 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 : 0.300 ------------------------------------------------------------------------------- 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 336 LEU Chi-restraints excluded: chain G residue 38 MET 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 383 ARG Chi-restraints excluded: chain R residue 384 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 50.0000 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 85 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 80 optimal weight: 0.0570 chunk 91 optimal weight: 0.6980 overall best weight: 0.4876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 374 ASN R 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.213836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.172762 restraints weight = 9981.072| |-----------------------------------------------------------------------------| r_work (start): 0.4162 rms_B_bonded: 1.83 r_work: 0.4080 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8926 Z= 0.130 Angle : 0.536 8.644 12139 Z= 0.290 Chirality : 0.042 0.297 1367 Planarity : 0.004 0.052 1544 Dihedral : 4.576 29.791 1231 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.97 % Allowed : 17.46 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.14 (0.26), residues: 1119 helix: 2.36 (0.25), residues: 437 sheet: -0.72 (0.32), residues: 218 loop : 0.03 (0.31), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.025 0.001 TYR R 191 PHE 0.037 0.001 PHE A 222 TRP 0.012 0.001 TRP A 234 HIS 0.007 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8920) covalent geometry : angle 0.53365 (12127) SS BOND : bond 0.00187 ( 6) SS BOND : angle 1.51648 ( 12) hydrogen bonds : bond 0.03841 ( 489) hydrogen bonds : angle 4.53441 ( 1380) *********************** 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 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6878 (tp30) cc_final: 0.6474 (tp30) REVERT: A 53 LYS cc_start: 0.6248 (ttpp) cc_final: 0.5516 (ttpt) REVERT: A 208 PHE cc_start: 0.7537 (m-80) cc_final: 0.7192 (m-10) REVERT: A 373 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.6840 (mmm-85) REVERT: A 392 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7369 (mt-10) REVERT: B 87 THR cc_start: 0.7623 (t) cc_final: 0.7418 (m) REVERT: B 219 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7362 (mmt-90) REVERT: B 280 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7652 (ttpt) REVERT: B 325 MET cc_start: 0.7294 (OUTLIER) cc_final: 0.6827 (mmt) REVERT: G 50 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5689 (mp) REVERT: N 83 MET cc_start: 0.6698 (mtm) cc_final: 0.6091 (mtm) REVERT: R 178 THR cc_start: 0.6797 (t) cc_final: 0.6355 (p) REVERT: R 180 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5659 (mp0) REVERT: R 221 TYR cc_start: 0.7171 (t80) cc_final: 0.6821 (t80) outliers start: 17 outliers final: 9 residues processed: 130 average time/residue: 0.4783 time to fit residues: 66.2554 Evaluate side-chains 123 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 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 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 110 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- 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 155 ASN N 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.208551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.166679 restraints weight = 9989.669| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.81 r_work: 0.4012 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8926 Z= 0.208 Angle : 0.617 8.096 12139 Z= 0.332 Chirality : 0.045 0.300 1367 Planarity : 0.004 0.050 1544 Dihedral : 4.842 31.103 1231 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.85 % Allowed : 18.15 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.00 (0.26), residues: 1119 helix: 2.19 (0.25), residues: 437 sheet: -0.78 (0.32), residues: 223 loop : 0.03 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 181 TYR 0.027 0.002 TYR A 358 PHE 0.050 0.002 PHE A 222 TRP 0.013 0.002 TRP P 14 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8920) covalent geometry : angle 0.61412 (12127) SS BOND : bond 0.00350 ( 6) SS BOND : angle 2.13070 ( 12) hydrogen bonds : bond 0.04183 ( 489) hydrogen bonds : angle 4.76930 ( 1380) ********************** 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 125 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6983 (tp30) cc_final: 0.6558 (tp30) REVERT: A 53 LYS cc_start: 0.6331 (ttpp) cc_final: 0.5627 (ttpt) REVERT: A 392 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7425 (mt-10) REVERT: B 87 THR cc_start: 0.7704 (t) cc_final: 0.7466 (m) REVERT: B 219 ARG cc_start: 0.7808 (mtp-110) cc_final: 0.7379 (mmt-90) REVERT: B 280 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7751 (mtpt) REVERT: B 325 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: G 50 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.5890 (mp) REVERT: N 83 MET cc_start: 0.6758 (mtm) cc_final: 0.6325 (mtm) REVERT: R 178 THR cc_start: 0.6834 (t) cc_final: 0.6435 (p) REVERT: R 180 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.5783 (mp0) REVERT: R 221 TYR cc_start: 0.7320 (t80) cc_final: 0.6927 (t80) outliers start: 16 outliers final: 11 residues processed: 116 average time/residue: 0.4782 time to fit residues: 59.5354 Evaluate side-chains 115 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 258 ASP 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 384 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 66 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 94 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 1 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 R 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.212974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.172285 restraints weight = 10100.522| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.78 r_work: 0.4032 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3921 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8926 Z= 0.170 Angle : 0.578 7.692 12139 Z= 0.313 Chirality : 0.043 0.297 1367 Planarity : 0.004 0.051 1544 Dihedral : 4.794 30.462 1231 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.85 % Allowed : 18.50 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 1.01 (0.26), residues: 1119 helix: 2.20 (0.25), residues: 437 sheet: -0.74 (0.32), residues: 221 loop : 0.01 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.025 0.002 TYR R 191 PHE 0.050 0.002 PHE R 335 TRP 0.014 0.002 TRP P 14 HIS 0.008 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 8920) covalent geometry : angle 0.57576 (12127) SS BOND : bond 0.00268 ( 6) SS BOND : angle 1.82775 ( 12) hydrogen bonds : bond 0.04007 ( 489) hydrogen bonds : angle 4.70075 ( 1380) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.87 seconds wall clock time: 51 minutes 8.07 seconds (3068.07 seconds total)