Starting phenix.real_space_refine on Sat Dec 28 15:12:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8flu_29287/12_2024/8flu_29287_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8flu_29287/12_2024/8flu_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_29287/12_2024/8flu_29287.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8flu_29287/12_2024/8flu_29287.map" model { file = "/net/cci-nas-00/data/ceres_data/8flu_29287/12_2024/8flu_29287_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8flu_29287/12_2024/8flu_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.53, per 1000 atoms: 0.63 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: 2.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.15 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: 5.40 Time building geometry restraints manager: 2.63 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.250 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.210 ------------------------------------------------------------------------------- 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 8920 Z= 0.269 Angle : 0.696 6.957 12127 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 *********************** 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 : 0.914 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: 1.4881 time to fit residues: 272.7995 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 : 1.008 ------------------------------------------------------------------------------- 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: 0.5980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 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: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8920 Z= 0.218 Angle : 0.606 10.867 12127 Z= 0.327 Chirality : 0.043 0.223 1367 Planarity : 0.004 0.056 1544 Dihedral : 5.672 85.154 1236 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.54 % Allowed : 9.71 % Favored : 87.75 % 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 (0.25), residues: 1119 helix: 2.22 (0.25), residues: 432 sheet: -0.80 (0.31), residues: 212 loop : -0.06 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.011 0.001 HIS A 357 PHE 0.017 0.002 PHE R 212 TYR 0.033 0.002 TYR R 191 ARG 0.005 0.000 ARG A 373 *********************** 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 154 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 1.003 Fit side-chains REVERT: A 53 LYS cc_start: 0.6299 (ttpp) cc_final: 0.5691 (ttpt) REVERT: A 208 PHE cc_start: 0.7358 (m-80) cc_final: 0.7137 (m-10) REVERT: A 373 ARG cc_start: 0.6988 (OUTLIER) cc_final: 0.6759 (mmm-85) REVERT: B 44 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.5659 (mp-120) REVERT: B 175 GLN cc_start: 0.6907 (mm110) cc_final: 0.6608 (pt0) REVERT: G 50 LEU cc_start: 0.6468 (OUTLIER) cc_final: 0.5827 (mp) REVERT: N 83 MET cc_start: 0.6444 (mtm) cc_final: 0.5544 (mtm) REVERT: R 36 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: R 180 GLU cc_start: 0.6138 (tp30) cc_final: 0.5483 (mp0) REVERT: R 221 TYR cc_start: 0.7217 (t80) cc_final: 0.6950 (t80) REVERT: R 438 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6954 (mm-40) outliers start: 22 outliers final: 5 residues processed: 143 average time/residue: 1.3339 time to fit residues: 203.0755 Evaluate side-chains 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 36 GLU 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 56 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN G 18 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8920 Z= 0.302 Angle : 0.617 9.782 12127 Z= 0.331 Chirality : 0.044 0.251 1367 Planarity : 0.004 0.048 1544 Dihedral : 5.586 87.347 1234 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.77 % Allowed : 12.83 % Favored : 84.39 % 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: 0.83 (0.25), residues: 1119 helix: 2.12 (0.24), residues: 436 sheet: -0.99 (0.31), residues: 217 loop : -0.09 (0.31), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP P 14 HIS 0.011 0.001 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.031 0.002 TYR R 191 ARG 0.005 0.000 ARG A 373 *********************** 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: 24 poor density : 128 time to evaluate : 1.375 Fit side-chains REVERT: A 53 LYS cc_start: 0.6346 (ttpp) cc_final: 0.5712 (ttpt) REVERT: B 87 THR cc_start: 0.7591 (t) cc_final: 0.7223 (m) REVERT: G 50 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.5967 (mp) REVERT: N 83 MET cc_start: 0.6551 (mtm) cc_final: 0.5953 (mtm) REVERT: R 180 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5672 (mp0) REVERT: R 221 TYR cc_start: 0.7231 (t80) cc_final: 0.6975 (t80) REVERT: R 438 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.7069 (mm-40) outliers start: 24 outliers final: 11 residues processed: 137 average time/residue: 1.3687 time to fit residues: 199.4266 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN 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 243 THR 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 Chi-restraints excluded: chain R residue 463 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 8.9990 chunk 52 optimal weight: 0.3980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 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 390 GLN B 44 GLN B 176 GLN B 220 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8920 Z= 0.228 Angle : 0.563 9.162 12127 Z= 0.305 Chirality : 0.042 0.248 1367 Planarity : 0.004 0.044 1544 Dihedral : 4.842 34.094 1231 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.66 % Allowed : 15.03 % Favored : 82.31 % 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: 0.89 (0.26), residues: 1119 helix: 2.23 (0.25), residues: 436 sheet: -0.95 (0.31), residues: 222 loop : -0.11 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 14 HIS 0.008 0.001 HIS A 357 PHE 0.016 0.002 PHE A 212 TYR 0.028 0.002 TYR R 191 ARG 0.004 0.000 ARG R 282 *********************** 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 148 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6734 (tp30) cc_final: 0.6475 (tp30) REVERT: A 53 LYS cc_start: 0.6338 (ttpp) cc_final: 0.5834 (ttpt) REVERT: A 208 PHE cc_start: 0.7317 (m-80) cc_final: 0.7077 (m-10) REVERT: B 87 THR cc_start: 0.7497 (t) cc_final: 0.7223 (m) REVERT: G 50 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5809 (mp) REVERT: N 83 MET cc_start: 0.6454 (mtm) cc_final: 0.5847 (mtm) REVERT: R 180 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5701 (mp0) REVERT: R 221 TYR cc_start: 0.7192 (t80) cc_final: 0.6942 (t80) REVERT: R 231 MET cc_start: 0.6211 (mmt) cc_final: 0.5888 (mmm) REVERT: R 438 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7054 (mm-40) outliers start: 23 outliers final: 7 residues processed: 132 average time/residue: 1.3029 time to fit residues: 183.5361 Evaluate side-chains 121 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 258 ASP 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 1 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 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 A 390 GLN B 44 GLN B 176 GLN B 220 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8920 Z= 0.249 Angle : 0.572 9.029 12127 Z= 0.309 Chirality : 0.043 0.266 1367 Planarity : 0.004 0.046 1544 Dihedral : 4.850 33.667 1231 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.24 % Allowed : 14.91 % 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: 0.88 (0.26), residues: 1119 helix: 2.20 (0.24), residues: 437 sheet: -0.98 (0.31), residues: 221 loop : -0.08 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP P 14 HIS 0.008 0.001 HIS A 357 PHE 0.022 0.002 PHE A 222 TYR 0.027 0.002 TYR R 191 ARG 0.004 0.000 ARG R 181 *********************** 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 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6688 (tp30) cc_final: 0.6445 (tp30) REVERT: A 53 LYS cc_start: 0.6356 (ttpp) cc_final: 0.5630 (ttpt) REVERT: B 87 THR cc_start: 0.7401 (t) cc_final: 0.7181 (m) REVERT: G 50 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.5797 (mp) REVERT: N 83 MET cc_start: 0.6409 (mtm) cc_final: 0.5834 (mtm) REVERT: R 180 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5793 (mp0) REVERT: R 221 TYR cc_start: 0.7177 (t80) cc_final: 0.6927 (t80) outliers start: 28 outliers final: 11 residues processed: 125 average time/residue: 1.2699 time to fit residues: 169.4865 Evaluate side-chains 117 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain B residue 243 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 176 GLN B 220 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8920 Z= 0.230 Angle : 0.553 8.454 12127 Z= 0.300 Chirality : 0.043 0.276 1367 Planarity : 0.004 0.048 1544 Dihedral : 4.790 31.789 1231 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.89 % Allowed : 15.95 % 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: 0.97 (0.26), residues: 1119 helix: 2.26 (0.24), residues: 438 sheet: -0.92 (0.31), residues: 226 loop : -0.03 (0.31), residues: 455 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 0.028 0.002 PHE A 222 TYR 0.027 0.002 TYR R 191 ARG 0.004 0.000 ARG R 181 *********************** 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 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 27 GLU cc_start: 0.6679 (tp30) cc_final: 0.6474 (tp30) REVERT: A 53 LYS cc_start: 0.6239 (ttpp) cc_final: 0.5639 (ttpt) REVERT: A 208 PHE cc_start: 0.7321 (m-80) cc_final: 0.7109 (m-10) REVERT: B 87 THR cc_start: 0.7340 (t) cc_final: 0.7137 (m) REVERT: G 50 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.5749 (mp) REVERT: N 83 MET cc_start: 0.6393 (mtm) cc_final: 0.5847 (mtm) REVERT: R 180 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5928 (mp0) REVERT: R 221 TYR cc_start: 0.7132 (t80) cc_final: 0.6900 (t80) outliers start: 25 outliers final: 11 residues processed: 129 average time/residue: 1.3071 time to fit residues: 180.6309 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain B residue 243 THR 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 384 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 49 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 32 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 B 44 GLN B 156 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8920 Z= 0.191 Angle : 0.547 8.923 12127 Z= 0.297 Chirality : 0.042 0.289 1367 Planarity : 0.004 0.048 1544 Dihedral : 4.677 30.423 1231 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.54 % Allowed : 16.76 % Favored : 80.69 % 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: 1.04 (0.26), residues: 1119 helix: 2.32 (0.25), residues: 437 sheet: -0.77 (0.32), residues: 221 loop : -0.07 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP P 14 HIS 0.006 0.001 HIS A 357 PHE 0.033 0.002 PHE A 222 TYR 0.026 0.001 TYR R 191 ARG 0.004 0.000 ARG R 383 *********************** 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 140 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6216 (ttpp) cc_final: 0.5617 (ttpt) REVERT: A 208 PHE cc_start: 0.7277 (m-80) cc_final: 0.7072 (m-10) REVERT: B 325 MET cc_start: 0.6683 (OUTLIER) cc_final: 0.6461 (mmt) REVERT: G 50 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.5715 (mp) REVERT: N 83 MET cc_start: 0.6321 (mtm) cc_final: 0.5750 (mtm) REVERT: R 180 GLU cc_start: 0.6448 (tp30) cc_final: 0.5776 (mp0) REVERT: R 221 TYR cc_start: 0.7153 (t80) cc_final: 0.6921 (t80) outliers start: 22 outliers final: 10 residues processed: 129 average time/residue: 1.2639 time to fit residues: 174.2135 Evaluate side-chains 120 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 173 THR Chi-restraints excluded: chain B residue 243 THR 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 206 VAL Chi-restraints excluded: chain R residue 370 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.4980 chunk 99 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 N 77 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8920 Z= 0.229 Angle : 0.567 8.949 12127 Z= 0.307 Chirality : 0.043 0.294 1367 Planarity : 0.004 0.048 1544 Dihedral : 4.708 31.797 1231 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.20 % Allowed : 17.11 % Favored : 80.69 % 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: 1.05 (0.26), residues: 1119 helix: 2.29 (0.25), residues: 438 sheet: -0.77 (0.32), residues: 221 loop : -0.01 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 298 HIS 0.009 0.001 HIS A 362 PHE 0.037 0.002 PHE A 222 TYR 0.025 0.002 TYR R 191 ARG 0.005 0.000 ARG R 181 *********************** 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 129 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6236 (ttpp) cc_final: 0.5657 (ttpt) REVERT: B 325 MET cc_start: 0.6742 (OUTLIER) cc_final: 0.6503 (mmt) REVERT: G 50 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5765 (mp) REVERT: N 83 MET cc_start: 0.6363 (mtm) cc_final: 0.5881 (mtm) REVERT: R 180 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5820 (mp0) REVERT: R 231 MET cc_start: 0.6627 (mmm) cc_final: 0.6285 (mtt) outliers start: 19 outliers final: 12 residues processed: 120 average time/residue: 1.2340 time to fit residues: 158.4305 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 : 0.955 ------------------------------------------------------------------------------- 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 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP 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 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 102 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 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 R 374 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8920 Z= 0.249 Angle : 0.580 8.184 12127 Z= 0.314 Chirality : 0.043 0.298 1367 Planarity : 0.004 0.049 1544 Dihedral : 4.758 31.251 1231 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.08 % Allowed : 17.69 % Favored : 80.23 % 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: 1.01 (0.26), residues: 1119 helix: 2.22 (0.25), residues: 438 sheet: -0.77 (0.32), residues: 221 loop : -0.01 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.008 0.001 HIS A 362 PHE 0.044 0.002 PHE A 222 TYR 0.025 0.002 TYR R 191 ARG 0.005 0.000 ARG R 181 *********************** 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 126 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6222 (ttpp) cc_final: 0.5665 (ttpt) REVERT: B 325 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6255 (mmm) REVERT: G 50 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.5769 (mp) REVERT: N 83 MET cc_start: 0.6383 (mtm) cc_final: 0.5902 (mtm) REVERT: R 180 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5851 (mp0) outliers start: 18 outliers final: 12 residues processed: 119 average time/residue: 1.2557 time to fit residues: 159.8001 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 : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP 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 370 SER Chi-restraints excluded: chain R residue 383 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 26 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: A 31 GLN A 390 GLN B 155 ASN N 77 ASN ** R 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8920 Z= 0.204 Angle : 0.559 8.333 12127 Z= 0.303 Chirality : 0.043 0.305 1367 Planarity : 0.004 0.049 1544 Dihedral : 4.673 30.323 1231 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.08 % Allowed : 17.57 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z (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: 1.06 (0.26), residues: 1119 helix: 2.29 (0.25), residues: 438 sheet: -0.75 (0.32), residues: 223 loop : 0.01 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 352 HIS 0.008 0.001 HIS A 362 PHE 0.041 0.002 PHE A 222 TYR 0.025 0.002 TYR R 191 ARG 0.003 0.000 ARG B 219 ********************** 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 133 residues out of total 976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.6237 (ttpp) cc_final: 0.5664 (ttpt) REVERT: B 325 MET cc_start: 0.6736 (OUTLIER) cc_final: 0.6211 (mmm) REVERT: G 50 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5667 (mp) REVERT: N 83 MET cc_start: 0.6302 (mtm) cc_final: 0.5757 (mtm) REVERT: R 178 THR cc_start: 0.6829 (t) cc_final: 0.6452 (p) REVERT: R 180 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5826 (mp0) outliers start: 18 outliers final: 13 residues processed: 123 average time/residue: 1.1561 time to fit residues: 153.1708 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 : 1.013 ------------------------------------------------------------------------------- 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 173 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP 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 370 SER Chi-restraints excluded: chain R residue 383 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 40.0000 chunk 5 optimal weight: 0.0370 chunk 63 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 156 GLN ** R 420 HIS ** 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 = 0.4483 r_free = 0.4483 target = 0.208336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166067 restraints weight = 9850.863| |-----------------------------------------------------------------------------| r_work (start): 0.4095 rms_B_bonded: 1.83 r_work: 0.4013 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3902 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8920 Z= 0.298 Angle : 0.613 8.038 12127 Z= 0.331 Chirality : 0.044 0.296 1367 Planarity : 0.004 0.049 1544 Dihedral : 4.868 31.092 1231 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.08 % Allowed : 18.38 % Favored : 79.54 % 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: 2.14 (0.25), residues: 438 sheet: -0.77 (0.32), residues: 221 loop : 0.02 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 14 HIS 0.009 0.002 HIS A 220 PHE 0.053 0.002 PHE A 222 TYR 0.028 0.002 TYR A 358 ARG 0.004 0.000 ARG R 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.17 seconds wall clock time: 66 minutes 1.92 seconds (3961.92 seconds total)