Starting phenix.real_space_refine on Tue Jan 14 15:47:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1d_61972/01_2025/9k1d_61972.cif" } resolution = 3.34 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= -0.005 sd= 0.088 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 48 5.16 5 C 4464 2.51 5 N 1151 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6892 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2130 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1756 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'BUA': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 4.36, per 1000 atoms: 0.63 Number of scatterers: 6892 At special positions: 0 Unit cell: (77.112, 99.603, 127.449, 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 48 16.00 O 1229 8.00 N 1151 7.00 C 4464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 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: 1.74 Conformation dependent library (CDL) restraints added in 900.4 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 46.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'R' and resid 4 through 38 removed outlier: 3.563A pdb=" N MET R 12 " --> pdb=" O SER R 8 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU R 22 " --> pdb=" O PHE R 18 " (cutoff:3.500A) Proline residue: R 23 - end of helix removed outlier: 3.862A pdb=" N ARG R 30 " --> pdb=" O LEU R 26 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.907A pdb=" N ILE R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 71 removed outlier: 3.632A pdb=" N LYS R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 113 removed outlier: 3.557A pdb=" N ILE R 105 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 119 Processing helix chain 'R' and resid 122 through 139 removed outlier: 3.975A pdb=" N GLY R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA R 129 " --> pdb=" O TYR R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 150 removed outlier: 3.595A pdb=" N GLN R 148 " --> pdb=" O VAL R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 187 Proline residue: R 178 - end of helix removed outlier: 3.745A pdb=" N LEU R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 removed outlier: 3.517A pdb=" N SER R 208 " --> pdb=" O TRP R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 235 removed outlier: 3.957A pdb=" N PHE R 235 " --> pdb=" O PHE R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 249 removed outlier: 3.625A pdb=" N ASN R 239 " --> pdb=" O PHE R 235 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS R 242 " --> pdb=" O TYR R 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU R 243 " --> pdb=" O ASN R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 275 removed outlier: 3.516A pdb=" N LEU R 264 " --> pdb=" O VAL R 260 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.987A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.578A pdb=" N LYS A 46 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.225A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.845A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.545A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.080A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.178A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.635A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.981A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.794A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.678A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.832A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.597A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.466A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 948 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: 1.95 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2196 1.36 - 1.48: 1744 1.48 - 1.61: 3006 1.61 - 1.74: 29 1.74 - 1.87: 76 Bond restraints: 7051 Sorted by residual: bond pdb=" C7 CLR R 403 " pdb=" C8 CLR R 403 " ideal model delta sigma weight residual 1.525 1.870 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C7 CLR R 405 " pdb=" C8 CLR R 405 " ideal model delta sigma weight residual 1.525 1.869 -0.344 2.00e-02 2.50e+03 2.96e+02 bond pdb=" C7 CLR R 402 " pdb=" C8 CLR R 402 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" C7 CLR R 404 " pdb=" C8 CLR R 404 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" C7 CLR R 406 " pdb=" C8 CLR R 406 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.93e+02 ... (remaining 7046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9399 2.30 - 4.60: 139 4.60 - 6.90: 46 6.90 - 9.20: 8 9.20 - 11.50: 1 Bond angle restraints: 9593 Sorted by residual: angle pdb=" CB MET A 53 " pdb=" CG MET A 53 " pdb=" SD MET A 53 " ideal model delta sigma weight residual 112.70 124.20 -11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C18 CLR R 402 " ideal model delta sigma weight residual 112.24 103.76 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C18 CLR R 403 " ideal model delta sigma weight residual 112.24 103.92 8.32 3.00e+00 1.11e-01 7.70e+00 angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 120.78 -6.38 2.30e+00 1.89e-01 7.69e+00 angle pdb=" C12 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C14 CLR R 405 " ideal model delta sigma weight residual 106.64 114.49 -7.85 3.00e+00 1.11e-01 6.84e+00 ... (remaining 9588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3754 17.93 - 35.87: 499 35.87 - 53.80: 130 53.80 - 71.74: 24 71.74 - 89.67: 7 Dihedral angle restraints: 4414 sinusoidal: 1911 harmonic: 2503 Sorted by residual: dihedral pdb=" CB CYS R 82 " pdb=" SG CYS R 82 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB GLU A 275 " pdb=" CG GLU A 275 " pdb=" CD GLU A 275 " pdb=" OE1 GLU A 275 " ideal model delta sinusoidal sigma weight residual 0.00 89.67 -89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 137 " pdb=" CD ARG B 137 " pdb=" NE ARG B 137 " pdb=" CZ ARG B 137 " ideal model delta sinusoidal sigma weight residual -180.00 -137.42 -42.58 2 1.50e+01 4.44e-03 9.77e+00 ... (remaining 4411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1095 0.163 - 0.325: 12 0.325 - 0.488: 4 0.488 - 0.650: 0 0.650 - 0.813: 5 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C13 CLR R 405 " pdb=" C12 CLR R 405 " pdb=" C14 CLR R 405 " pdb=" C17 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.12 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C13 CLR R 406 " pdb=" C12 CLR R 406 " pdb=" C14 CLR R 406 " pdb=" C17 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.93 -2.12 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.14 -0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 1113 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.50e+00 pdb=" C THR B 87 " 0.021 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 42 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO R 43 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 43 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 43 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C THR B 196 " -0.020 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.007 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 313 2.73 - 3.27: 6723 3.27 - 3.81: 11339 3.81 - 4.36: 13464 4.36 - 4.90: 23625 Nonbonded interactions: 55464 Sorted by model distance: nonbonded pdb=" OD1 ASP B 153 " pdb=" N ASP B 154 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR B 159 " pdb=" NE1 TRP B 169 " model vdw 2.259 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR B 102 " pdb=" O SER B 147 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.296 3.040 ... (remaining 55459 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.820 Find NCS groups from input model: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.020 0.345 7051 Z= 1.344 Angle : 0.718 11.504 9593 Z= 0.308 Chirality : 0.072 0.813 1116 Planarity : 0.003 0.030 1173 Dihedral : 16.966 89.670 2784 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.27 % Allowed : 29.20 % Favored : 70.53 % 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: 0.87 (0.30), residues: 844 helix: 1.50 (0.28), residues: 368 sheet: 0.96 (0.40), residues: 180 loop : -0.83 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.005 0.000 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.005 0.001 TYR R 14 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.773 Fit side-chains REVERT: R 73 PHE cc_start: 0.6920 (m-10) cc_final: 0.6553 (m-10) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2089 time to fit residues: 36.1128 Evaluate side-chains 119 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128601 restraints weight = 9180.737| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.87 r_work: 0.3321 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7051 Z= 0.209 Angle : 0.569 8.872 9593 Z= 0.282 Chirality : 0.043 0.279 1116 Planarity : 0.004 0.034 1173 Dihedral : 5.880 48.165 1254 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.68 % Allowed : 24.56 % Favored : 71.76 % 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: 0.98 (0.29), residues: 844 helix: 1.65 (0.28), residues: 367 sheet: 0.78 (0.39), residues: 186 loop : -0.70 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR A 302 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.770 Fit side-chains REVERT: R 73 PHE cc_start: 0.6937 (m-10) cc_final: 0.6537 (m-10) REVERT: A 20 ASP cc_start: 0.7758 (m-30) cc_final: 0.7553 (m-30) REVERT: B 61 MET cc_start: 0.8655 (ppp) cc_final: 0.8147 (ptm) REVERT: B 127 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8196 (mmtm) outliers start: 27 outliers final: 18 residues processed: 136 average time/residue: 0.1845 time to fit residues: 33.9869 Evaluate side-chains 131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 51 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127969 restraints weight = 9333.691| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.92 r_work: 0.3318 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7051 Z= 0.155 Angle : 0.505 7.310 9593 Z= 0.251 Chirality : 0.041 0.194 1116 Planarity : 0.003 0.030 1173 Dihedral : 5.383 43.860 1254 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.50 % Allowed : 25.38 % Favored : 70.12 % 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: 1.00 (0.30), residues: 844 helix: 1.70 (0.28), residues: 367 sheet: 0.82 (0.39), residues: 186 loop : -0.75 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR R 76 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.742 Fit side-chains REVERT: R 73 PHE cc_start: 0.6890 (m-10) cc_final: 0.6536 (m-10) REVERT: A 20 ASP cc_start: 0.8118 (m-30) cc_final: 0.7764 (m-30) REVERT: A 52 GLN cc_start: 0.6867 (pp30) cc_final: 0.6634 (pp30) REVERT: B 75 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8224 (mp10) REVERT: B 88 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: B 127 LYS cc_start: 0.8510 (mmtp) cc_final: 0.8272 (mmtm) REVERT: B 156 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7813 (mt0) outliers start: 33 outliers final: 18 residues processed: 135 average time/residue: 0.1840 time to fit residues: 33.6102 Evaluate side-chains 135 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 66 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 overall best weight: 1.0102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.123271 restraints weight = 9298.002| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.89 r_work: 0.3244 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7051 Z= 0.244 Angle : 0.558 10.640 9593 Z= 0.275 Chirality : 0.043 0.280 1116 Planarity : 0.003 0.032 1173 Dihedral : 5.435 47.327 1254 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.18 % Allowed : 25.51 % Favored : 69.30 % 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: 0.92 (0.30), residues: 844 helix: 1.68 (0.28), residues: 367 sheet: 0.57 (0.38), residues: 194 loop : -0.74 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 5 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.001 PHE B 199 TYR 0.011 0.001 TYR R 94 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 122 time to evaluate : 0.734 Fit side-chains REVERT: R 73 PHE cc_start: 0.6834 (m-10) cc_final: 0.6446 (m-10) REVERT: R 75 TRP cc_start: 0.7319 (m-90) cc_final: 0.6908 (m-10) REVERT: R 138 PHE cc_start: 0.6839 (m-10) cc_final: 0.6140 (m-10) REVERT: A 20 ASP cc_start: 0.8109 (m-30) cc_final: 0.7621 (m-30) REVERT: A 296 TYR cc_start: 0.6907 (t80) cc_final: 0.6666 (t80) REVERT: B 75 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8196 (mp10) REVERT: B 88 ASN cc_start: 0.8521 (OUTLIER) cc_final: 0.8140 (m-40) REVERT: B 127 LYS cc_start: 0.8496 (mmtp) cc_final: 0.8243 (mmtm) REVERT: B 156 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8024 (mt0) outliers start: 38 outliers final: 24 residues processed: 146 average time/residue: 0.1895 time to fit residues: 37.0465 Evaluate side-chains 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.158523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123385 restraints weight = 9211.568| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.91 r_work: 0.3250 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7051 Z= 0.188 Angle : 0.531 8.224 9593 Z= 0.265 Chirality : 0.042 0.190 1116 Planarity : 0.003 0.033 1173 Dihedral : 5.318 51.024 1254 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.77 % Allowed : 26.33 % Favored : 68.89 % 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: 0.94 (0.30), residues: 844 helix: 1.71 (0.28), residues: 367 sheet: 0.51 (0.38), residues: 194 loop : -0.69 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE B 199 TYR 0.009 0.001 TYR R 94 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.738 Fit side-chains REVERT: R 73 PHE cc_start: 0.6867 (m-10) cc_final: 0.6535 (m-10) REVERT: R 75 TRP cc_start: 0.7353 (m-90) cc_final: 0.7046 (m-10) REVERT: R 138 PHE cc_start: 0.6879 (m-10) cc_final: 0.6149 (m-10) REVERT: A 20 ASP cc_start: 0.8174 (m-30) cc_final: 0.7606 (m-30) REVERT: B 75 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8154 (mp10) REVERT: B 88 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8137 (m-40) REVERT: B 127 LYS cc_start: 0.8451 (mmtp) cc_final: 0.8151 (mmtm) REVERT: B 156 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7977 (mt0) outliers start: 35 outliers final: 23 residues processed: 140 average time/residue: 0.2010 time to fit residues: 37.8210 Evaluate side-chains 139 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 0.1980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.0050 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125008 restraints weight = 9103.475| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.83 r_work: 0.3294 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7051 Z= 0.145 Angle : 0.518 8.177 9593 Z= 0.255 Chirality : 0.041 0.187 1116 Planarity : 0.003 0.034 1173 Dihedral : 5.224 54.865 1254 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.23 % Allowed : 27.01 % Favored : 68.76 % 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: 0.99 (0.30), residues: 844 helix: 1.72 (0.28), residues: 367 sheet: 0.62 (0.38), residues: 191 loop : -0.67 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.017 0.001 TYR A 296 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 122 time to evaluate : 0.869 Fit side-chains REVERT: R 73 PHE cc_start: 0.6809 (m-10) cc_final: 0.6461 (m-10) REVERT: R 75 TRP cc_start: 0.7313 (m-90) cc_final: 0.7007 (m-10) REVERT: R 121 ARG cc_start: 0.7436 (OUTLIER) cc_final: 0.7169 (mtm110) REVERT: R 138 PHE cc_start: 0.6660 (m-10) cc_final: 0.5984 (m-10) REVERT: A 20 ASP cc_start: 0.8158 (m-30) cc_final: 0.7550 (m-30) REVERT: B 75 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8651 (mp10) REVERT: B 88 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: B 127 LYS cc_start: 0.8380 (mmtp) cc_final: 0.8160 (mmtp) REVERT: B 156 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7974 (mt0) outliers start: 31 outliers final: 21 residues processed: 145 average time/residue: 0.1949 time to fit residues: 38.0207 Evaluate side-chains 143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 189 PHE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 0.0870 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123598 restraints weight = 9083.434| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.83 r_work: 0.3274 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7051 Z= 0.189 Angle : 0.572 12.209 9593 Z= 0.280 Chirality : 0.043 0.241 1116 Planarity : 0.003 0.039 1173 Dihedral : 5.297 59.606 1254 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.05 % Allowed : 26.88 % Favored : 68.08 % 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: 0.93 (0.30), residues: 844 helix: 1.75 (0.28), residues: 367 sheet: 0.45 (0.38), residues: 194 loop : -0.71 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE B 199 TYR 0.016 0.001 TYR A 296 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.744 Fit side-chains REVERT: R 22 LEU cc_start: 0.9020 (mm) cc_final: 0.8799 (mm) REVERT: R 73 PHE cc_start: 0.6833 (m-10) cc_final: 0.6484 (m-10) REVERT: R 75 TRP cc_start: 0.7335 (m-90) cc_final: 0.7038 (m-10) REVERT: R 138 PHE cc_start: 0.6765 (m-10) cc_final: 0.6042 (m-10) REVERT: A 20 ASP cc_start: 0.8178 (m-30) cc_final: 0.7548 (m-30) REVERT: B 58 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8372 (pt) REVERT: B 75 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8149 (mp10) REVERT: B 88 ASN cc_start: 0.8444 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: B 127 LYS cc_start: 0.8394 (mmtp) cc_final: 0.8181 (mmtp) REVERT: B 156 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7989 (mt0) outliers start: 37 outliers final: 26 residues processed: 147 average time/residue: 0.1804 time to fit residues: 35.7979 Evaluate side-chains 145 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.155936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.122783 restraints weight = 9079.071| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.74 r_work: 0.3267 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7051 Z= 0.277 Angle : 0.623 9.907 9593 Z= 0.309 Chirality : 0.044 0.241 1116 Planarity : 0.004 0.043 1173 Dihedral : 5.301 51.324 1254 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.91 % Allowed : 27.29 % Favored : 67.80 % 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: 0.81 (0.30), residues: 844 helix: 1.68 (0.29), residues: 366 sheet: 0.27 (0.37), residues: 194 loop : -0.72 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.015 0.001 PHE B 199 TYR 0.016 0.001 TYR A 296 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.773 Fit side-chains REVERT: R 22 LEU cc_start: 0.9055 (mm) cc_final: 0.8762 (mm) REVERT: R 73 PHE cc_start: 0.6825 (m-10) cc_final: 0.6522 (m-10) REVERT: R 75 TRP cc_start: 0.7259 (m-90) cc_final: 0.7031 (m-10) REVERT: R 121 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7299 (mtm110) REVERT: R 138 PHE cc_start: 0.6682 (m-10) cc_final: 0.6396 (m-80) REVERT: A 20 ASP cc_start: 0.8152 (m-30) cc_final: 0.7513 (m-30) REVERT: B 58 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8598 (pt) REVERT: B 75 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: B 127 LYS cc_start: 0.8425 (mmtp) cc_final: 0.7893 (mmtt) REVERT: B 307 VAL cc_start: 0.8817 (t) cc_final: 0.8530 (p) outliers start: 36 outliers final: 29 residues processed: 142 average time/residue: 0.1997 time to fit residues: 37.6179 Evaluate side-chains 144 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 75 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.156815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.123735 restraints weight = 9081.746| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.76 r_work: 0.3264 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7051 Z= 0.224 Angle : 0.640 13.665 9593 Z= 0.307 Chirality : 0.044 0.316 1116 Planarity : 0.004 0.049 1173 Dihedral : 5.087 39.596 1254 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.32 % Allowed : 26.74 % Favored : 67.94 % 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: 0.73 (0.30), residues: 844 helix: 1.63 (0.28), residues: 366 sheet: 0.15 (0.37), residues: 194 loop : -0.72 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE B 199 TYR 0.026 0.001 TYR A 302 ARG 0.011 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.826 Fit side-chains REVERT: R 22 LEU cc_start: 0.9097 (mm) cc_final: 0.8803 (mm) REVERT: R 73 PHE cc_start: 0.6749 (m-10) cc_final: 0.6465 (m-10) REVERT: R 94 TYR cc_start: 0.8372 (m-80) cc_final: 0.6996 (m-80) REVERT: R 121 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7310 (mtm110) REVERT: R 138 PHE cc_start: 0.6578 (m-10) cc_final: 0.6183 (m-80) REVERT: R 238 TYR cc_start: 0.8599 (t80) cc_final: 0.7874 (t80) REVERT: A 20 ASP cc_start: 0.8156 (m-30) cc_final: 0.7489 (m-30) REVERT: A 273 LEU cc_start: 0.8900 (mt) cc_final: 0.8646 (tt) REVERT: B 58 ILE cc_start: 0.8878 (OUTLIER) cc_final: 0.8463 (pt) REVERT: B 127 LYS cc_start: 0.8413 (mmtp) cc_final: 0.7899 (mmtt) REVERT: B 156 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: B 307 VAL cc_start: 0.8837 (t) cc_final: 0.8536 (p) outliers start: 39 outliers final: 30 residues processed: 146 average time/residue: 0.2106 time to fit residues: 40.2104 Evaluate side-chains 148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.123803 restraints weight = 9194.790| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.78 r_work: 0.3280 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7051 Z= 0.211 Angle : 0.637 13.514 9593 Z= 0.308 Chirality : 0.044 0.306 1116 Planarity : 0.004 0.049 1173 Dihedral : 4.939 30.991 1254 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.50 % Allowed : 27.83 % Favored : 67.67 % 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: 0.70 (0.30), residues: 844 helix: 1.60 (0.28), residues: 366 sheet: 0.12 (0.37), residues: 194 loop : -0.71 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE B 199 TYR 0.029 0.001 TYR A 302 ARG 0.011 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 0.786 Fit side-chains REVERT: R 22 LEU cc_start: 0.9075 (mm) cc_final: 0.8786 (mm) REVERT: R 73 PHE cc_start: 0.6784 (m-10) cc_final: 0.6380 (m-10) REVERT: R 94 TYR cc_start: 0.8419 (m-80) cc_final: 0.7089 (m-80) REVERT: R 121 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7305 (mtm110) REVERT: R 138 PHE cc_start: 0.6575 (m-10) cc_final: 0.6187 (m-80) REVERT: R 238 TYR cc_start: 0.8609 (t80) cc_final: 0.7945 (t80) REVERT: A 20 ASP cc_start: 0.8183 (m-30) cc_final: 0.7506 (m-30) REVERT: A 273 LEU cc_start: 0.8906 (mt) cc_final: 0.8636 (tt) REVERT: B 58 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8449 (pt) REVERT: B 88 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8095 (m-40) REVERT: B 127 LYS cc_start: 0.8366 (mmtp) cc_final: 0.7890 (mmtt) REVERT: B 156 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: B 307 VAL cc_start: 0.8843 (t) cc_final: 0.8541 (p) outliers start: 33 outliers final: 29 residues processed: 144 average time/residue: 0.2095 time to fit residues: 39.9395 Evaluate side-chains 148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 97 THR Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.125217 restraints weight = 9066.945| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.72 r_work: 0.3273 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7051 Z= 0.216 Angle : 0.637 13.131 9593 Z= 0.309 Chirality : 0.044 0.299 1116 Planarity : 0.004 0.050 1173 Dihedral : 4.915 31.749 1254 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.23 % Allowed : 27.83 % Favored : 67.94 % 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: 0.65 (0.30), residues: 844 helix: 1.58 (0.28), residues: 366 sheet: 0.05 (0.37), residues: 194 loop : -0.72 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE A 189 TYR 0.033 0.001 TYR A 302 ARG 0.011 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3964.21 seconds wall clock time: 71 minutes 8.57 seconds (4268.57 seconds total)