Starting phenix.real_space_refine on Sat Aug 23 05:52:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7s_28909/08_2025/8f7s_28909.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 84 5.16 5 C 6523 2.51 5 N 1617 2.21 5 O 1751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9975 Number of models: 1 Model: "" Number of chains: 14 Chain: "R" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2268 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276} Chain: "P" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "P" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 43 Classifications: {'peptide': 6} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 5} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1783 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 218} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "D" Number of atoms: 2268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2268 Classifications: {'peptide': 289} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 276} Chain: "Q" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 43 Classifications: {'peptide': 6} Modifications used: {'PEPT-D': 1} Link IDs: {'TRANS': 5} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 149 Classifications: {'peptide': 19} Modifications used: {'COO': 1} Link IDs: {'TRANS': 18} Chain: "R" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Unusual residues: {'CLR': 2, 'PLM': 7} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 174 Unusual residues: {'CLR': 3, 'PLM': 5} Classifications: {'undetermined': 8} Link IDs: {None: 7} Time building chain proxies: 2.23, per 1000 atoms: 0.22 Number of scatterers: 9975 At special positions: 0 Unit cell: (143.64, 118.44, 105, 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 84 16.00 O 1751 8.00 N 1617 7.00 C 6523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 121 " - pdb=" SG CYS R 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 121 " - pdb=" SG CYS D 198 " 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=2, symmetry=0 Links applied TRANS " DAL P 2 " - " TYR P 1 " " DAL Q 2 " - " TYR Q 1 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 363.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL P 2 " pdb=" CB DAL Q 2 " Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 59.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'R' and resid 45 through 77 Processing helix chain 'R' and resid 82 through 100 Processing helix chain 'R' and resid 101 through 112 removed outlier: 3.699A pdb=" N GLN R 105 " --> pdb=" O THR R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 152 Processing helix chain 'R' and resid 152 through 160 removed outlier: 3.564A pdb=" N LEU R 157 " --> pdb=" O PRO R 153 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP R 158 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 186 removed outlier: 3.750A pdb=" N SER R 177 " --> pdb=" O TRP R 173 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY R 178 " --> pdb=" O VAL R 174 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL R 179 " --> pdb=" O LEU R 175 " (cutoff:3.500A) Proline residue: R 182 - end of helix Processing helix chain 'R' and resid 205 through 241 removed outlier: 4.943A pdb=" N VAL R 224 " --> pdb=" O PHE R 220 " (cutoff:3.500A) Proline residue: R 225 - end of helix removed outlier: 3.715A pdb=" N ARG R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 247 removed outlier: 6.084A pdb=" N LEU R 245 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 287 removed outlier: 4.212A pdb=" N VAL R 266 " --> pdb=" O MET R 262 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL R 267 " --> pdb=" O VAL R 263 " (cutoff:3.500A) Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 293 through 322 removed outlier: 3.524A pdb=" N VAL R 297 " --> pdb=" O ASP R 293 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN R 314 " --> pdb=" O ASN R 310 " (cutoff:3.500A) Proline residue: R 315 - end of helix Processing helix chain 'R' and resid 322 through 333 Processing helix chain 'P' and resid 2 through 7 removed outlier: 3.755A pdb=" N VAL P 6 " --> pdb=" O DAL P 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.018A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.292A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 217 removed outlier: 4.384A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 3.628A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.840A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.525A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.555A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 9 through 31 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 40 through 42 No H-bonds generated for 'chain 'B' and resid 40 through 42' Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.528A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.540A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 77 Processing helix chain 'D' and resid 82 through 100 Processing helix chain 'D' and resid 101 through 112 removed outlier: 3.706A pdb=" N GLN D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 152 Processing helix chain 'D' and resid 152 through 160 removed outlier: 3.539A pdb=" N LEU D 157 " --> pdb=" O PRO D 153 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP D 158 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 186 removed outlier: 3.540A pdb=" N GLY D 178 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 179 " --> pdb=" O LEU D 175 " (cutoff:3.500A) Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 205 through 241 removed outlier: 4.893A pdb=" N VAL D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Proline residue: D 225 - end of helix removed outlier: 3.716A pdb=" N ARG D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 287 removed outlier: 4.257A pdb=" N VAL D 266 " --> pdb=" O MET D 262 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL D 267 " --> pdb=" O VAL D 263 " (cutoff:3.500A) Proline residue: D 276 - end of helix Processing helix chain 'D' and resid 293 through 322 removed outlier: 3.739A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN D 314 " --> pdb=" O ASN D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix Processing helix chain 'D' and resid 322 through 333 removed outlier: 3.617A pdb=" N PHE D 329 " --> pdb=" O PHE D 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 removed outlier: 3.727A pdb=" N VAL Q 6 " --> pdb=" O DAL Q 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 352 Processing sheet with id=AA1, first strand: chain 'R' and resid 187 through 192 removed outlier: 3.575A pdb=" N MET R 199 " --> pdb=" O VAL R 188 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG R 190 " --> pdb=" O VAL R 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.256A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 56 removed outlier: 5.172A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.624A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 110 removed outlier: 6.225A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.578A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.096A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.770A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.909A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 192 removed outlier: 3.534A pdb=" N MET D 199 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG D 190 " --> pdb=" O VAL D 197 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1806 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: 1.74 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3058 1.35 - 1.46: 2175 1.46 - 1.58: 4811 1.58 - 1.70: 0 1.70 - 1.82: 121 Bond restraints: 10165 Sorted by residual: bond pdb=" CA ALA R 275 " pdb=" C ALA R 275 " ideal model delta sigma weight residual 1.521 1.544 -0.023 1.14e-02 7.69e+03 4.01e+00 bond pdb=" C ALA D 275 " pdb=" N PRO D 276 " ideal model delta sigma weight residual 1.336 1.359 -0.023 1.20e-02 6.94e+03 3.82e+00 bond pdb=" C VAL R 224 " pdb=" N PRO R 225 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.59e+00 bond pdb=" C ALA R 275 " pdb=" N PRO R 276 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.36e-02 5.41e+03 3.55e+00 bond pdb=" N GLU D 112 " pdb=" CA GLU D 112 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.32e-02 5.74e+03 3.41e+00 ... (remaining 10160 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 12882 1.60 - 3.21: 696 3.21 - 4.81: 116 4.81 - 6.42: 36 6.42 - 8.02: 11 Bond angle restraints: 13741 Sorted by residual: angle pdb=" N LEU R 102 " pdb=" CA LEU R 102 " pdb=" C LEU R 102 " ideal model delta sigma weight residual 113.16 118.79 -5.63 1.42e+00 4.96e-01 1.57e+01 angle pdb=" N LEU D 102 " pdb=" CA LEU D 102 " pdb=" C LEU D 102 " ideal model delta sigma weight residual 113.16 118.74 -5.58 1.42e+00 4.96e-01 1.54e+01 angle pdb=" C ILE B 86 " pdb=" N TRP B 87 " pdb=" CA TRP B 87 " ideal model delta sigma weight residual 121.32 129.21 -7.89 2.10e+00 2.27e-01 1.41e+01 angle pdb=" N GLU R 112 " pdb=" CA GLU R 112 " pdb=" C GLU R 112 " ideal model delta sigma weight residual 113.56 108.52 5.04 1.39e+00 5.18e-01 1.32e+01 angle pdb=" N GLU D 112 " pdb=" CA GLU D 112 " pdb=" C GLU D 112 " ideal model delta sigma weight residual 113.56 108.58 4.98 1.39e+00 5.18e-01 1.29e+01 ... (remaining 13736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.84: 5888 11.84 - 23.68: 368 23.68 - 35.52: 68 35.52 - 47.36: 17 47.36 - 59.20: 11 Dihedral angle restraints: 6352 sinusoidal: 2764 harmonic: 3588 Sorted by residual: dihedral pdb=" CA THR B 254 " pdb=" C THR B 254 " pdb=" N CYS B 255 " pdb=" CA CYS B 255 " ideal model delta harmonic sigma weight residual 180.00 162.89 17.11 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA PHE B 156 " pdb=" C PHE B 156 " pdb=" N LEU B 157 " pdb=" CA LEU B 157 " ideal model delta harmonic sigma weight residual 180.00 164.95 15.05 0 5.00e+00 4.00e-02 9.06e+00 dihedral pdb=" CA TRP B 302 " pdb=" C TRP B 302 " pdb=" N ASP B 303 " pdb=" CA ASP B 303 " ideal model delta harmonic sigma weight residual 180.00 165.13 14.87 0 5.00e+00 4.00e-02 8.85e+00 ... (remaining 6349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1444 0.082 - 0.164: 142 0.164 - 0.246: 17 0.246 - 0.328: 7 0.328 - 0.410: 5 Chirality restraints: 1615 Sorted by residual: chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" C14 CLR D 403 " pdb=" C13 CLR D 403 " pdb=" C15 CLR D 403 " pdb=" C8 CLR D 403 " both_signs ideal model delta sigma weight residual False -2.32 -2.72 0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" C14 CLR D 404 " pdb=" C13 CLR D 404 " pdb=" C15 CLR D 404 " pdb=" C8 CLR D 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 1612 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 240 " 0.043 5.00e-02 4.00e+02 6.45e-02 6.66e+00 pdb=" N PRO B 241 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 241 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 241 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG R 190 " -0.037 5.00e-02 4.00e+02 5.63e-02 5.08e+00 pdb=" N PRO R 191 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 191 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 191 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG D 190 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO D 191 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 191 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 191 " 0.031 5.00e-02 4.00e+02 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2323 2.81 - 3.33: 9046 3.33 - 3.86: 15653 3.86 - 4.38: 17783 4.38 - 4.90: 32025 Nonbonded interactions: 76830 Sorted by model distance: nonbonded pdb=" OG1 THR R 99 " pdb=" OG SER R 312 " model vdw 2.290 3.040 nonbonded pdb=" OH TYR R 208 " pdb=" O LEU D 237 " model vdw 2.292 3.040 nonbonded pdb=" O LEU R 237 " pdb=" OH TYR D 208 " model vdw 2.305 3.040 nonbonded pdb=" OE2 GLU B 265 " pdb=" OG1 THR B 268 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.342 3.120 ... (remaining 76825 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 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 45 through 333 or resid 406 through 408)) selection = (chain 'R' and (resid 45 through 333 or resid 406 through 408)) } ncs_group { reference = chain 'P' selection = chain 'Q' } 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: 1.020 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 0.045 10171 Z= 0.245 Angle : 0.867 8.024 13751 Z= 0.473 Chirality : 0.059 0.410 1615 Planarity : 0.006 0.065 1656 Dihedral : 8.474 59.200 4008 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.22), residues: 1203 helix: 1.68 (0.16), residues: 677 sheet: 1.03 (0.42), residues: 158 loop : -0.75 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 160 TYR 0.027 0.002 TYR D 87 PHE 0.029 0.002 PHE R 325 TRP 0.017 0.002 TRP R 209 HIS 0.006 0.001 HIS C 44 Details of bonding type rmsd covalent geometry : bond 0.00412 (10165) covalent geometry : angle 0.86680 (13741) SS BOND : bond 0.00213 ( 2) SS BOND : angle 2.23709 ( 4) hydrogen bonds : bond 0.11512 ( 617) hydrogen bonds : angle 5.39072 ( 1806) Misc. bond : bond 0.04063 ( 2) link_TRANS : bond 0.00089 ( 2) link_TRANS : angle 0.20726 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.433 Fit side-chains REVERT: R 220 PHE cc_start: 0.8204 (m-80) cc_final: 0.8000 (m-80) REVERT: A 22 ASN cc_start: 0.7411 (m-40) cc_final: 0.7193 (m-40) REVERT: A 216 GLU cc_start: 0.7625 (tt0) cc_final: 0.7404 (tt0) REVERT: A 251 ASP cc_start: 0.7559 (t0) cc_final: 0.7308 (t70) REVERT: B 70 THR cc_start: 0.8076 (m) cc_final: 0.7732 (p) REVERT: B 175 ASP cc_start: 0.7289 (t0) cc_final: 0.7086 (t70) REVERT: B 217 ASP cc_start: 0.7542 (t0) cc_final: 0.7150 (t0) REVERT: D 184 MET cc_start: 0.7860 (ttm) cc_final: 0.7643 (ttp) outliers start: 0 outliers final: 1 residues processed: 258 average time/residue: 0.5188 time to fit residues: 143.4980 Evaluate side-chains 165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 170 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 105 GLN R 169 ASN R 201 GLN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 269 ASN A 306 GLN B 49 GLN B 181 GLN C 44 HIS D 67 ASN D 85 ASN D 169 ASN D 314 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.129915 restraints weight = 11032.623| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.87 r_work: 0.3218 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10171 Z= 0.165 Angle : 0.601 8.186 13751 Z= 0.318 Chirality : 0.042 0.151 1615 Planarity : 0.005 0.053 1656 Dihedral : 7.589 59.598 1817 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.41 % Allowed : 9.19 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.23), residues: 1203 helix: 2.58 (0.18), residues: 671 sheet: 1.21 (0.42), residues: 162 loop : -0.66 (0.29), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 47 TYR 0.017 0.002 TYR P 1 PHE 0.015 0.002 PHE A 189 TRP 0.019 0.002 TRP B 87 HIS 0.007 0.002 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00375 (10165) covalent geometry : angle 0.60094 (13741) SS BOND : bond 0.00042 ( 2) SS BOND : angle 1.47033 ( 4) hydrogen bonds : bond 0.05360 ( 617) hydrogen bonds : angle 4.27647 ( 1806) Misc. bond : bond 0.00069 ( 2) link_TRANS : bond 0.00156 ( 2) link_TRANS : angle 0.45502 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 152 time to evaluate : 0.319 Fit side-chains REVERT: R 111 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.6950 (mpt) REVERT: R 113 THR cc_start: 0.8752 (t) cc_final: 0.8511 (t) REVERT: R 325 PHE cc_start: 0.6393 (OUTLIER) cc_final: 0.6185 (m-80) REVERT: A 22 ASN cc_start: 0.7716 (m-40) cc_final: 0.7315 (m-40) REVERT: A 26 ASP cc_start: 0.7245 (m-30) cc_final: 0.7026 (m-30) REVERT: A 53 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6066 (mpt) REVERT: A 186 GLU cc_start: 0.8107 (tt0) cc_final: 0.7753 (tm-30) REVERT: A 216 GLU cc_start: 0.8433 (tt0) cc_final: 0.8232 (tt0) REVERT: A 240 MET cc_start: 0.3993 (ppp) cc_final: 0.3695 (pp-130) REVERT: B 47 ARG cc_start: 0.6676 (mmm-85) cc_final: 0.6177 (mmt90) REVERT: B 175 ASP cc_start: 0.7865 (t0) cc_final: 0.7559 (t70) REVERT: B 217 ASP cc_start: 0.8114 (t0) cc_final: 0.7752 (t0) REVERT: D 158 ASP cc_start: 0.6333 (m-30) cc_final: 0.6126 (m-30) REVERT: D 325 PHE cc_start: 0.6336 (t80) cc_final: 0.6122 (t80) outliers start: 36 outliers final: 15 residues processed: 173 average time/residue: 0.6113 time to fit residues: 112.9238 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 179 VAL Chi-restraints excluded: chain R residue 206 SER Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 325 PHE Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 112 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 83 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN R 201 GLN A 188 HIS A 306 GLN B 37 GLN B 345 ASN D 67 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.179660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.141092 restraints weight = 10880.926| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.98 r_work: 0.3238 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10171 Z= 0.107 Angle : 0.477 7.474 13751 Z= 0.255 Chirality : 0.038 0.143 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.876 58.090 1815 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.84 % Allowed : 11.36 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.24), residues: 1203 helix: 2.99 (0.19), residues: 671 sheet: 1.33 (0.42), residues: 157 loop : -0.65 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 51 TYR 0.012 0.001 TYR R 87 PHE 0.018 0.001 PHE A 354 TRP 0.019 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00213 (10165) covalent geometry : angle 0.47748 (13741) SS BOND : bond 0.00124 ( 2) SS BOND : angle 0.69774 ( 4) hydrogen bonds : bond 0.04251 ( 617) hydrogen bonds : angle 3.99017 ( 1806) Misc. bond : bond 0.00045 ( 2) link_TRANS : bond 0.00070 ( 2) link_TRANS : angle 0.21320 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.400 Fit side-chains REVERT: R 302 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8041 (mp) REVERT: A 22 ASN cc_start: 0.7509 (m-40) cc_final: 0.7100 (m-40) REVERT: A 26 ASP cc_start: 0.7333 (m-30) cc_final: 0.7130 (m-30) REVERT: A 53 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6073 (mpt) REVERT: A 216 GLU cc_start: 0.8518 (tt0) cc_final: 0.8282 (tt0) REVERT: A 275 GLU cc_start: 0.7153 (tp30) cc_final: 0.6510 (tp30) REVERT: A 306 GLN cc_start: 0.6685 (mm-40) cc_final: 0.6484 (mm110) REVERT: B 47 ARG cc_start: 0.6553 (mmm-85) cc_final: 0.6110 (mmt90) REVERT: B 175 ASP cc_start: 0.8035 (t0) cc_final: 0.7754 (t70) REVERT: B 203 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8061 (pp) REVERT: B 217 ASP cc_start: 0.8250 (t0) cc_final: 0.7874 (t0) REVERT: D 158 ASP cc_start: 0.6327 (m-30) cc_final: 0.6106 (m-30) REVERT: D 193 ASP cc_start: 0.6383 (t0) cc_final: 0.5891 (m-30) REVERT: D 325 PHE cc_start: 0.6185 (t80) cc_final: 0.5967 (t80) REVERT: F 349 LYS cc_start: 0.7276 (mmtt) cc_final: 0.6900 (mmmt) outliers start: 30 outliers final: 12 residues processed: 156 average time/residue: 0.6060 time to fit residues: 101.2790 Evaluate side-chains 144 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 113 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN R 201 GLN D 67 ASN D 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.172699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.133482 restraints weight = 10950.038| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.80 r_work: 0.3201 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10171 Z= 0.127 Angle : 0.508 8.193 13751 Z= 0.268 Chirality : 0.039 0.143 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.044 58.273 1815 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.60 % Allowed : 11.84 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.51 (0.24), residues: 1203 helix: 2.95 (0.19), residues: 672 sheet: 1.25 (0.42), residues: 157 loop : -0.67 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 51 TYR 0.014 0.001 TYR P 1 PHE 0.017 0.001 PHE A 354 TRP 0.018 0.001 TRP B 87 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00281 (10165) covalent geometry : angle 0.50790 (13741) SS BOND : bond 0.00138 ( 2) SS BOND : angle 0.76428 ( 4) hydrogen bonds : bond 0.04602 ( 617) hydrogen bonds : angle 4.03584 ( 1806) Misc. bond : bond 0.00053 ( 2) link_TRANS : bond 0.00203 ( 2) link_TRANS : angle 0.25624 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 0.448 Fit side-chains REVERT: R 111 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7150 (mpp) REVERT: R 302 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8157 (mp) REVERT: A 22 ASN cc_start: 0.7576 (m-40) cc_final: 0.7254 (m-40) REVERT: A 216 GLU cc_start: 0.8600 (tt0) cc_final: 0.8390 (tt0) REVERT: A 306 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6709 (mm110) REVERT: B 47 ARG cc_start: 0.6558 (mmm-85) cc_final: 0.6082 (mmt90) REVERT: B 134 ARG cc_start: 0.6187 (ptp-170) cc_final: 0.5265 (tpt170) REVERT: B 175 ASP cc_start: 0.8102 (t0) cc_final: 0.7725 (t70) REVERT: B 217 ASP cc_start: 0.8273 (t0) cc_final: 0.7884 (t0) REVERT: D 155 LYS cc_start: 0.6338 (mttm) cc_final: 0.6089 (mttp) REVERT: D 158 ASP cc_start: 0.6468 (m-30) cc_final: 0.6260 (m-30) REVERT: D 193 ASP cc_start: 0.6432 (t0) cc_final: 0.6037 (m-30) outliers start: 38 outliers final: 17 residues processed: 162 average time/residue: 0.6020 time to fit residues: 104.0684 Evaluate side-chains 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 102 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN A 331 ASN C 18 GLN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.129876 restraints weight = 10995.329| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 1.89 r_work: 0.3146 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10171 Z= 0.128 Angle : 0.513 8.473 13751 Z= 0.270 Chirality : 0.039 0.143 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.177 53.440 1815 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.94 % Allowed : 12.97 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.24), residues: 1203 helix: 2.89 (0.19), residues: 672 sheet: 1.14 (0.41), residues: 157 loop : -0.76 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 51 TYR 0.013 0.001 TYR P 1 PHE 0.014 0.001 PHE A 354 TRP 0.020 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00283 (10165) covalent geometry : angle 0.51274 (13741) SS BOND : bond 0.00110 ( 2) SS BOND : angle 0.67727 ( 4) hydrogen bonds : bond 0.04619 ( 617) hydrogen bonds : angle 4.04442 ( 1806) Misc. bond : bond 0.00055 ( 2) link_TRANS : bond 0.00194 ( 2) link_TRANS : angle 0.25249 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.490 Fit side-chains REVERT: R 189 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.8002 (t) REVERT: R 302 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8093 (mp) REVERT: R 323 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: A 22 ASN cc_start: 0.7494 (m-40) cc_final: 0.7210 (m-40) REVERT: A 216 GLU cc_start: 0.8391 (tt0) cc_final: 0.8172 (tt0) REVERT: A 306 GLN cc_start: 0.6879 (mm-40) cc_final: 0.6676 (mm110) REVERT: B 47 ARG cc_start: 0.6501 (mmm-85) cc_final: 0.5951 (mmt90) REVERT: B 134 ARG cc_start: 0.6242 (ptp-170) cc_final: 0.5363 (tpt170) REVERT: B 175 ASP cc_start: 0.8033 (t0) cc_final: 0.7609 (t70) REVERT: B 217 ASP cc_start: 0.8087 (t0) cc_final: 0.7690 (t0) REVERT: B 313 LEU cc_start: 0.7933 (mp) cc_final: 0.7694 (mt) REVERT: D 155 LYS cc_start: 0.6577 (mttm) cc_final: 0.6319 (mttp) REVERT: D 158 ASP cc_start: 0.6367 (m-30) cc_final: 0.6150 (m-30) REVERT: D 193 ASP cc_start: 0.6480 (t0) cc_final: 0.6211 (m-30) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 0.6208 time to fit residues: 103.7181 Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 35 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN A 204 GLN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.170631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.132467 restraints weight = 11092.660| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.85 r_work: 0.3234 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10171 Z= 0.121 Angle : 0.502 8.380 13751 Z= 0.264 Chirality : 0.039 0.145 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.178 57.441 1815 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.03 % Allowed : 13.26 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.40 (0.24), residues: 1203 helix: 2.93 (0.19), residues: 672 sheet: 1.11 (0.41), residues: 157 loop : -0.79 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.014 0.001 TYR P 1 PHE 0.012 0.001 PHE A 354 TRP 0.021 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00266 (10165) covalent geometry : angle 0.50192 (13741) SS BOND : bond 0.00113 ( 2) SS BOND : angle 0.64344 ( 4) hydrogen bonds : bond 0.04481 ( 617) hydrogen bonds : angle 4.01007 ( 1806) Misc. bond : bond 0.00044 ( 2) link_TRANS : bond 0.00188 ( 2) link_TRANS : angle 0.24176 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.381 Fit side-chains REVERT: R 111 MET cc_start: 0.8535 (mtm) cc_final: 0.8232 (mpp) REVERT: R 302 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8186 (mp) REVERT: R 323 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: A 22 ASN cc_start: 0.7623 (m-40) cc_final: 0.7379 (m-40) REVERT: A 216 GLU cc_start: 0.8563 (tt0) cc_final: 0.8344 (tt0) REVERT: B 47 ARG cc_start: 0.6546 (mmm-85) cc_final: 0.6223 (mmm-85) REVERT: B 134 ARG cc_start: 0.6441 (ptp-170) cc_final: 0.5492 (tpt170) REVERT: B 175 ASP cc_start: 0.8140 (t0) cc_final: 0.7749 (t70) REVERT: B 217 ASP cc_start: 0.8207 (t0) cc_final: 0.7829 (t0) REVERT: B 313 LEU cc_start: 0.8135 (mp) cc_final: 0.7817 (mt) REVERT: C 21 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5238 (ptm) REVERT: D 155 LYS cc_start: 0.6567 (mttm) cc_final: 0.6334 (mttp) REVERT: D 193 ASP cc_start: 0.6585 (t0) cc_final: 0.6330 (m-30) outliers start: 32 outliers final: 21 residues processed: 154 average time/residue: 0.6395 time to fit residues: 105.2622 Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 46 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN A 306 GLN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.170211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.131191 restraints weight = 11003.842| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.81 r_work: 0.3235 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10171 Z= 0.107 Angle : 0.482 8.107 13751 Z= 0.253 Chirality : 0.038 0.144 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.896 59.960 1815 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.46 % Allowed : 13.64 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.48 (0.24), residues: 1203 helix: 3.01 (0.19), residues: 672 sheet: 1.14 (0.41), residues: 157 loop : -0.80 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 51 TYR 0.016 0.001 TYR A 230 PHE 0.011 0.001 PHE A 354 TRP 0.020 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00224 (10165) covalent geometry : angle 0.48213 (13741) SS BOND : bond 0.00085 ( 2) SS BOND : angle 0.56431 ( 4) hydrogen bonds : bond 0.04114 ( 617) hydrogen bonds : angle 3.92782 ( 1806) Misc. bond : bond 0.00032 ( 2) link_TRANS : bond 0.00164 ( 2) link_TRANS : angle 0.21654 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.480 Fit side-chains REVERT: R 323 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5894 (mp0) REVERT: A 22 ASN cc_start: 0.7553 (m-40) cc_final: 0.7300 (m-40) REVERT: A 216 GLU cc_start: 0.8617 (tt0) cc_final: 0.8363 (tt0) REVERT: B 47 ARG cc_start: 0.6459 (mmm-85) cc_final: 0.6164 (mmm-85) REVERT: B 134 ARG cc_start: 0.6467 (ptp-170) cc_final: 0.5432 (tpt170) REVERT: B 175 ASP cc_start: 0.8183 (t0) cc_final: 0.7788 (t70) REVERT: B 217 ASP cc_start: 0.8188 (t0) cc_final: 0.7833 (t0) REVERT: B 239 PHE cc_start: 0.8948 (OUTLIER) cc_final: 0.8430 (m-80) REVERT: B 313 LEU cc_start: 0.8068 (mp) cc_final: 0.7803 (mt) REVERT: C 21 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5176 (ptm) REVERT: D 155 LYS cc_start: 0.6506 (mttm) cc_final: 0.6300 (mttp) REVERT: D 193 ASP cc_start: 0.6515 (t0) cc_final: 0.6254 (m-30) outliers start: 26 outliers final: 15 residues processed: 151 average time/residue: 0.6309 time to fit residues: 102.1178 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 93 optimal weight: 0.0470 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.165334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.126090 restraints weight = 10954.413| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.85 r_work: 0.3145 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10171 Z= 0.166 Angle : 0.578 9.253 13751 Z= 0.300 Chirality : 0.041 0.146 1615 Planarity : 0.005 0.049 1656 Dihedral : 7.807 56.536 1815 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.75 % Allowed : 13.45 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.24), residues: 1203 helix: 2.66 (0.19), residues: 673 sheet: 1.10 (0.41), residues: 157 loop : -1.00 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.018 0.002 TYR P 1 PHE 0.012 0.002 PHE B 156 TRP 0.020 0.002 TRP B 87 HIS 0.006 0.001 HIS B 67 Details of bonding type rmsd covalent geometry : bond 0.00388 (10165) covalent geometry : angle 0.57771 (13741) SS BOND : bond 0.00358 ( 2) SS BOND : angle 0.79836 ( 4) hydrogen bonds : bond 0.05312 ( 617) hydrogen bonds : angle 4.21736 ( 1806) Misc. bond : bond 0.00052 ( 2) link_TRANS : bond 0.00330 ( 2) link_TRANS : angle 0.42910 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.390 Fit side-chains REVERT: R 323 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5878 (mp0) REVERT: A 22 ASN cc_start: 0.7610 (m-40) cc_final: 0.7363 (m-40) REVERT: A 284 THR cc_start: 0.7516 (p) cc_final: 0.7282 (t) REVERT: B 134 ARG cc_start: 0.6736 (ptp-170) cc_final: 0.5549 (tpt170) REVERT: B 175 ASP cc_start: 0.8315 (t0) cc_final: 0.7864 (t70) REVERT: B 217 ASP cc_start: 0.8223 (t0) cc_final: 0.7868 (t0) REVERT: B 313 LEU cc_start: 0.8176 (mp) cc_final: 0.7859 (mt) REVERT: C 21 MET cc_start: 0.6066 (OUTLIER) cc_final: 0.5166 (ptm) REVERT: D 193 ASP cc_start: 0.6593 (t0) cc_final: 0.5855 (m-30) REVERT: D 199 MET cc_start: 0.7593 (ptp) cc_final: 0.7175 (ptt) outliers start: 29 outliers final: 20 residues processed: 148 average time/residue: 0.5894 time to fit residues: 93.9157 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 53 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 81 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 314 ASN A 306 GLN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127329 restraints weight = 10953.048| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.88 r_work: 0.3213 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10171 Z= 0.162 Angle : 0.577 9.170 13751 Z= 0.300 Chirality : 0.041 0.147 1615 Planarity : 0.005 0.051 1656 Dihedral : 8.069 58.580 1815 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.84 % Allowed : 13.45 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.24), residues: 1203 helix: 2.61 (0.19), residues: 671 sheet: 0.98 (0.39), residues: 162 loop : -0.96 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 51 TYR 0.017 0.002 TYR P 1 PHE 0.013 0.002 PHE R 72 TRP 0.019 0.002 TRP B 87 HIS 0.005 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00379 (10165) covalent geometry : angle 0.57680 (13741) SS BOND : bond 0.00351 ( 2) SS BOND : angle 1.02683 ( 4) hydrogen bonds : bond 0.05201 ( 617) hydrogen bonds : angle 4.21655 ( 1806) Misc. bond : bond 0.00049 ( 2) link_TRANS : bond 0.00338 ( 2) link_TRANS : angle 0.32446 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 128 time to evaluate : 0.460 Fit side-chains REVERT: R 190 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7839 (mtt-85) REVERT: R 321 LEU cc_start: 0.7262 (mp) cc_final: 0.7044 (mt) REVERT: R 323 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.5858 (mp0) REVERT: A 22 ASN cc_start: 0.7586 (m-40) cc_final: 0.7331 (m-40) REVERT: A 231 ASP cc_start: 0.6900 (m-30) cc_final: 0.5525 (p0) REVERT: A 284 THR cc_start: 0.7494 (p) cc_final: 0.7250 (t) REVERT: B 47 ARG cc_start: 0.6679 (mmm-85) cc_final: 0.6108 (mmt90) REVERT: B 134 ARG cc_start: 0.6823 (ptp-170) cc_final: 0.5711 (tpt170) REVERT: B 175 ASP cc_start: 0.8339 (t0) cc_final: 0.7882 (t70) REVERT: B 217 ASP cc_start: 0.8194 (t0) cc_final: 0.7834 (t0) REVERT: B 313 LEU cc_start: 0.8242 (mp) cc_final: 0.7915 (mt) REVERT: C 21 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5153 (ptm) REVERT: D 193 ASP cc_start: 0.6720 (t0) cc_final: 0.6163 (m-30) REVERT: D 199 MET cc_start: 0.7605 (ptp) cc_final: 0.7156 (ptt) outliers start: 30 outliers final: 20 residues processed: 145 average time/residue: 0.5604 time to fit residues: 87.5411 Evaluate side-chains 148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 190 ARG Chi-restraints excluded: chain R residue 197 VAL Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 143 CYS Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.0060 chunk 106 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 96 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 314 ASN A 306 GLN D 67 ASN D 278 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.172422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.134099 restraints weight = 10803.161| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.88 r_work: 0.3276 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10171 Z= 0.105 Angle : 0.493 8.260 13751 Z= 0.258 Chirality : 0.038 0.147 1615 Planarity : 0.004 0.047 1656 Dihedral : 7.332 53.964 1815 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.70 % Allowed : 14.68 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.37 (0.24), residues: 1203 helix: 2.94 (0.19), residues: 671 sheet: 1.06 (0.41), residues: 157 loop : -0.88 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.019 0.001 TYR A 230 PHE 0.011 0.001 PHE A 354 TRP 0.024 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00206 (10165) covalent geometry : angle 0.49300 (13741) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.84092 ( 4) hydrogen bonds : bond 0.04015 ( 617) hydrogen bonds : angle 3.95644 ( 1806) Misc. bond : bond 0.00020 ( 2) link_TRANS : bond 0.00162 ( 2) link_TRANS : angle 0.21394 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.359 Fit side-chains REVERT: R 321 LEU cc_start: 0.7171 (mp) cc_final: 0.6965 (mt) REVERT: R 323 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5749 (mp0) REVERT: A 22 ASN cc_start: 0.7502 (m-40) cc_final: 0.7275 (m-40) REVERT: A 216 GLU cc_start: 0.8589 (tt0) cc_final: 0.8310 (tt0) REVERT: A 231 ASP cc_start: 0.6921 (m-30) cc_final: 0.5463 (p0) REVERT: A 284 THR cc_start: 0.7537 (p) cc_final: 0.7301 (t) REVERT: A 305 CYS cc_start: 0.7816 (m) cc_final: 0.6726 (p) REVERT: A 306 GLN cc_start: 0.7007 (mm-40) cc_final: 0.6794 (mm110) REVERT: B 47 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.5922 (mmt90) REVERT: B 134 ARG cc_start: 0.6798 (ptp-170) cc_final: 0.5669 (tpt170) REVERT: B 175 ASP cc_start: 0.8220 (t0) cc_final: 0.7809 (t70) REVERT: B 217 ASP cc_start: 0.8152 (t0) cc_final: 0.7813 (t0) REVERT: B 313 LEU cc_start: 0.8110 (mp) cc_final: 0.7844 (mt) REVERT: C 21 MET cc_start: 0.6019 (OUTLIER) cc_final: 0.5097 (ptm) REVERT: D 193 ASP cc_start: 0.6693 (t0) cc_final: 0.6129 (m-30) REVERT: D 199 MET cc_start: 0.7513 (ptp) cc_final: 0.7006 (ptt) REVERT: F 349 LYS cc_start: 0.7346 (mmtt) cc_final: 0.7059 (mmmt) outliers start: 18 outliers final: 11 residues processed: 140 average time/residue: 0.5958 time to fit residues: 89.7781 Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain D residue 265 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 24 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.172587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.134956 restraints weight = 10894.818| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.72 r_work: 0.3177 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10171 Z= 0.119 Angle : 0.517 8.508 13751 Z= 0.269 Chirality : 0.039 0.149 1615 Planarity : 0.004 0.047 1656 Dihedral : 7.312 55.187 1815 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 15.15 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.34 (0.24), residues: 1203 helix: 2.90 (0.19), residues: 671 sheet: 1.12 (0.40), residues: 157 loop : -0.88 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.016 0.001 TYR A 230 PHE 0.010 0.001 PHE A 354 TRP 0.023 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00259 (10165) covalent geometry : angle 0.51719 (13741) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.91074 ( 4) hydrogen bonds : bond 0.04310 ( 617) hydrogen bonds : angle 3.97772 ( 1806) Misc. bond : bond 0.00033 ( 2) link_TRANS : bond 0.00208 ( 2) link_TRANS : angle 0.23347 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.29 seconds wall clock time: 66 minutes 30.36 seconds (3990.36 seconds total)