Starting phenix.real_space_refine on Sun Dec 29 07:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7s_28909/12_2024/8f7s_28909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7s_28909/12_2024/8f7s_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_28909/12_2024/8f7s_28909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7s_28909/12_2024/8f7s_28909.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7s_28909/12_2024/8f7s_28909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7s_28909/12_2024/8f7s_28909.cif" } resolution = 3.0 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= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.20, per 1000 atoms: 0.62 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: 3.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 2.96 Time building geometry restraints manager: 3.15 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: 1.430 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: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 24.830 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- 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 10165 Z= 0.265 Angle : 0.867 8.024 13741 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 : 3.53 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 (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: 1.29 (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 TRP 0.017 0.002 TRP R 209 HIS 0.006 0.001 HIS C 44 PHE 0.029 0.002 PHE R 325 TYR 0.027 0.002 TYR D 87 ARG 0.008 0.001 ARG R 160 *********************** 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 : 1.015 Fit side-chains REVERT: R 190 ARG cc_start: 0.5956 (mtt180) cc_final: 0.5732 (mtt180) 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: 0.7192 (m-40) REVERT: A 216 GLU cc_start: 0.7625 (tt0) cc_final: 0.7406 (tt0) REVERT: A 251 ASP cc_start: 0.7559 (t0) cc_final: 0.7312 (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: 1.2126 time to fit residues: 335.1360 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 : 1.066 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 181 GLN C 44 HIS D 67 ASN D 85 ASN D 169 ASN D 314 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10165 Z= 0.210 Angle : 0.555 7.686 13741 Z= 0.295 Chirality : 0.040 0.146 1615 Planarity : 0.005 0.051 1656 Dihedral : 7.186 55.693 1817 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.75 % Allowed : 9.94 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.34 (0.23), residues: 1203 helix: 2.76 (0.18), residues: 671 sheet: 1.17 (0.42), residues: 164 loop : -0.64 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 87 HIS 0.005 0.001 HIS B 147 PHE 0.013 0.002 PHE A 189 TYR 0.015 0.002 TYR P 1 ARG 0.007 0.001 ARG B 47 *********************** 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 180 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 1.065 Fit side-chains REVERT: R 113 THR cc_start: 0.8605 (t) cc_final: 0.8297 (t) REVERT: R 145 ASP cc_start: 0.7979 (t70) cc_final: 0.7751 (t70) REVERT: A 22 ASN cc_start: 0.7647 (m-40) cc_final: 0.7244 (m-40) REVERT: A 26 ASP cc_start: 0.6765 (m-30) cc_final: 0.6542 (m-30) REVERT: A 53 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5855 (mpt) REVERT: A 240 MET cc_start: 0.4118 (ppp) cc_final: 0.3865 (pp-130) REVERT: A 275 GLU cc_start: 0.7446 (tp30) cc_final: 0.6779 (tp30) REVERT: B 47 ARG cc_start: 0.6455 (mmm-85) cc_final: 0.6035 (mmt90) REVERT: B 70 THR cc_start: 0.8172 (m) cc_final: 0.7913 (p) REVERT: B 217 ASP cc_start: 0.7703 (t0) cc_final: 0.7341 (t0) REVERT: D 142 MET cc_start: 0.7933 (ttt) cc_final: 0.7728 (ttp) REVERT: D 158 ASP cc_start: 0.5946 (m-30) cc_final: 0.5725 (m-30) outliers start: 29 outliers final: 11 residues processed: 167 average time/residue: 1.2260 time to fit residues: 219.8355 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 103 SER Chi-restraints excluded: chain B residue 151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 0.0070 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS A 306 GLN B 37 GLN B 345 ASN D 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10165 Z= 0.136 Angle : 0.468 7.363 13741 Z= 0.249 Chirality : 0.038 0.144 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.642 56.734 1815 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.94 % Allowed : 11.27 % 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 (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: 2.68 (0.24), residues: 1203 helix: 3.08 (0.19), residues: 671 sheet: 1.21 (0.42), residues: 165 loop : -0.53 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.017 0.001 PHE A 354 TYR 0.012 0.001 TYR R 87 ARG 0.006 0.000 ARG B 51 *********************** 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 174 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 1.152 Fit side-chains REVERT: R 111 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.6505 (mpt) REVERT: R 145 ASP cc_start: 0.7963 (t70) cc_final: 0.7702 (t70) REVERT: R 302 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 22 ASN cc_start: 0.7574 (m-40) cc_final: 0.7202 (m-40) REVERT: A 53 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6014 (mpt) REVERT: B 47 ARG cc_start: 0.6298 (mmm-85) cc_final: 0.5945 (mmt90) REVERT: B 83 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7978 (mttm) REVERT: B 203 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8026 (pp) REVERT: B 217 ASP cc_start: 0.7705 (t0) cc_final: 0.7356 (t0) REVERT: B 222 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6066 (ppp) REVERT: B 272 ASP cc_start: 0.5765 (m-30) cc_final: 0.5454 (m-30) REVERT: D 158 ASP cc_start: 0.5971 (m-30) cc_final: 0.5711 (m-30) outliers start: 31 outliers final: 14 residues processed: 159 average time/residue: 1.1855 time to fit residues: 203.2253 Evaluate side-chains 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 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 83 LYS 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 175 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 127 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- 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 ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN B 49 GLN B 264 GLN D 67 ASN D 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10165 Z= 0.144 Angle : 0.470 7.749 13741 Z= 0.249 Chirality : 0.038 0.142 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.446 58.089 1815 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.41 % Allowed : 11.74 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.77 (0.24), residues: 1203 helix: 3.19 (0.19), residues: 671 sheet: 1.34 (0.42), residues: 158 loop : -0.59 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.015 0.001 PHE A 354 TYR 0.011 0.001 TYR P 1 ARG 0.007 0.000 ARG D 192 *********************** 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 170 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.209 Fit side-chains REVERT: R 113 THR cc_start: 0.8675 (t) cc_final: 0.8360 (t) REVERT: R 145 ASP cc_start: 0.7989 (t70) cc_final: 0.7755 (t70) REVERT: R 302 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8061 (mp) REVERT: R 323 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: A 17 LYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6673 (mmtp) REVERT: A 22 ASN cc_start: 0.7463 (m-40) cc_final: 0.7202 (m-40) REVERT: A 53 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6242 (mpt) REVERT: B 47 ARG cc_start: 0.6299 (mmm-85) cc_final: 0.5815 (mmt90) REVERT: B 83 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7994 (mttm) REVERT: B 203 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7967 (pp) REVERT: B 217 ASP cc_start: 0.7676 (t0) cc_final: 0.7341 (t0) REVERT: D 158 ASP cc_start: 0.5971 (m-30) cc_final: 0.5719 (m-30) outliers start: 36 outliers final: 19 residues processed: 152 average time/residue: 1.1981 time to fit residues: 196.0743 Evaluate side-chains 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 26 ASP 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 A residue 341 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 83 LYS 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 64 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 201 GLN ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN C 18 GLN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10165 Z= 0.191 Angle : 0.520 8.373 13741 Z= 0.273 Chirality : 0.039 0.143 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.056 59.980 1815 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.98 % Allowed : 11.84 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.44 (0.24), residues: 1203 helix: 2.91 (0.19), residues: 672 sheet: 1.24 (0.42), residues: 157 loop : -0.74 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 87 HIS 0.005 0.001 HIS B 147 PHE 0.014 0.002 PHE A 354 TYR 0.015 0.001 TYR P 1 ARG 0.006 0.001 ARG B 51 *********************** 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 179 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 0.956 Fit side-chains REVERT: R 145 ASP cc_start: 0.7967 (t70) cc_final: 0.7715 (t70) REVERT: R 302 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8094 (mp) REVERT: A 17 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6744 (mmtp) REVERT: A 22 ASN cc_start: 0.7428 (m-40) cc_final: 0.7193 (m-40) REVERT: A 185 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8320 (t) REVERT: B 47 ARG cc_start: 0.6224 (mmm-85) cc_final: 0.5733 (mmt90) REVERT: B 83 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8013 (mttp) REVERT: B 217 ASP cc_start: 0.7653 (t0) cc_final: 0.7270 (t0) REVERT: B 222 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5632 (ppp) REVERT: C 21 MET cc_start: 0.5803 (mmm) cc_final: 0.5326 (ptm) REVERT: D 155 LYS cc_start: 0.6805 (mttm) cc_final: 0.6554 (mttp) REVERT: D 158 ASP cc_start: 0.5987 (m-30) cc_final: 0.5738 (m-30) outliers start: 42 outliers final: 20 residues processed: 159 average time/residue: 1.3418 time to fit residues: 228.5015 Evaluate side-chains 159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain A residue 17 LYS 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 341 ASP Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 83 LYS 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 222 MET 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 127 ILE 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 101 optimal weight: 0.0870 chunk 22 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 113 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 331 ASN D 67 ASN D 278 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10165 Z= 0.128 Angle : 0.461 7.779 13741 Z= 0.244 Chirality : 0.037 0.144 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.568 58.606 1815 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.75 % Allowed : 13.16 % 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 (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: 2.60 (0.24), residues: 1203 helix: 3.11 (0.19), residues: 674 sheet: 1.14 (0.40), residues: 162 loop : -0.78 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 87 HIS 0.003 0.000 HIS B 147 PHE 0.012 0.001 PHE A 354 TYR 0.011 0.001 TYR P 1 ARG 0.006 0.000 ARG B 51 *********************** 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 169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.098 Fit side-chains REVERT: R 145 ASP cc_start: 0.7904 (t70) cc_final: 0.7637 (t70) REVERT: R 199 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6917 (ptt) REVERT: R 323 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5840 (mp0) REVERT: A 17 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6661 (mmtp) REVERT: A 22 ASN cc_start: 0.7436 (m-40) cc_final: 0.7207 (m-40) REVERT: A 305 CYS cc_start: 0.7022 (m) cc_final: 0.6076 (p) REVERT: B 47 ARG cc_start: 0.6224 (mmm-85) cc_final: 0.5695 (mmt90) REVERT: B 83 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7979 (mttm) REVERT: B 217 ASP cc_start: 0.7634 (t0) cc_final: 0.7259 (t0) REVERT: C 21 MET cc_start: 0.5863 (mmm) cc_final: 0.5393 (ptm) REVERT: D 155 LYS cc_start: 0.6768 (mttm) cc_final: 0.6492 (mttp) REVERT: D 158 ASP cc_start: 0.5935 (m-30) cc_final: 0.5699 (m-30) outliers start: 29 outliers final: 15 residues processed: 155 average time/residue: 1.2727 time to fit residues: 211.5684 Evaluate side-chains 154 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 199 MET Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 17 LYS 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 B residue 83 LYS 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 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 263 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 69 optimal weight: 0.0970 chunk 45 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10165 Z= 0.177 Angle : 0.505 8.329 13741 Z= 0.265 Chirality : 0.039 0.146 1615 Planarity : 0.004 0.048 1656 Dihedral : 6.850 52.441 1815 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.37 % Allowed : 13.35 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.47 (0.24), residues: 1203 helix: 2.99 (0.19), residues: 674 sheet: 1.20 (0.41), residues: 157 loop : -0.84 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.001 PHE A 354 TYR 0.016 0.001 TYR P 1 ARG 0.009 0.001 ARG R 190 *********************** 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 163 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.125 Fit side-chains REVERT: R 145 ASP cc_start: 0.7967 (t70) cc_final: 0.7722 (t70) REVERT: R 323 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5891 (mp0) REVERT: A 17 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6766 (mmtp) REVERT: A 22 ASN cc_start: 0.7436 (m-40) cc_final: 0.7194 (m-40) REVERT: A 185 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8345 (t) REVERT: B 47 ARG cc_start: 0.6237 (mmm-85) cc_final: 0.5690 (mmt90) REVERT: B 83 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.8033 (mttm) REVERT: B 217 ASP cc_start: 0.7619 (t0) cc_final: 0.7256 (t0) REVERT: C 21 MET cc_start: 0.5880 (mmm) cc_final: 0.5404 (ptm) REVERT: D 155 LYS cc_start: 0.6802 (mttm) cc_final: 0.6530 (mttp) REVERT: D 158 ASP cc_start: 0.5993 (m-30) cc_final: 0.5765 (m-30) outliers start: 25 outliers final: 16 residues processed: 155 average time/residue: 1.2891 time to fit residues: 214.2050 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 323 GLU Chi-restraints excluded: chain A residue 17 LYS 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 B residue 83 LYS 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 284 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain D residue 127 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 B 225 GLN B 273 ASN D 67 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10165 Z= 0.259 Angle : 0.582 9.543 13741 Z= 0.304 Chirality : 0.041 0.145 1615 Planarity : 0.005 0.050 1656 Dihedral : 7.934 56.817 1815 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.84 % Allowed : 13.07 % 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 (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: 2.12 (0.24), residues: 1203 helix: 2.67 (0.19), residues: 673 sheet: 1.14 (0.41), residues: 157 loop : -0.93 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 87 HIS 0.005 0.001 HIS B 147 PHE 0.012 0.002 PHE B 156 TYR 0.019 0.002 TYR P 1 ARG 0.009 0.001 ARG R 190 *********************** 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 156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 1.150 Fit side-chains REVERT: R 145 ASP cc_start: 0.7986 (t70) cc_final: 0.7777 (t70) REVERT: R 323 GLU cc_start: 0.6559 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: A 22 ASN cc_start: 0.7502 (m-40) cc_final: 0.7248 (m-40) REVERT: B 217 ASP cc_start: 0.7635 (t0) cc_final: 0.7265 (t0) REVERT: C 21 MET cc_start: 0.5834 (mmm) cc_final: 0.5221 (ptm) REVERT: D 155 LYS cc_start: 0.6826 (mttm) cc_final: 0.6543 (mttp) REVERT: D 158 ASP cc_start: 0.5989 (m-30) cc_final: 0.5756 (m-30) REVERT: D 199 MET cc_start: 0.7034 (ptp) cc_final: 0.6621 (ptt) outliers start: 30 outliers final: 18 residues processed: 145 average time/residue: 1.2068 time to fit residues: 188.5704 Evaluate side-chains 142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 98 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 0.0670 chunk 63 optimal weight: 0.4980 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN B 49 GLN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10165 Z= 0.148 Angle : 0.499 8.353 13741 Z= 0.261 Chirality : 0.038 0.145 1615 Planarity : 0.004 0.048 1656 Dihedral : 7.244 54.099 1815 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.99 % Allowed : 14.58 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.37 (0.24), residues: 1203 helix: 2.89 (0.19), residues: 674 sheet: 1.19 (0.41), residues: 157 loop : -0.87 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.011 0.001 PHE A 354 TYR 0.014 0.001 TYR P 1 ARG 0.008 0.001 ARG R 190 *********************** 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 151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.087 Fit side-chains REVERT: R 81 LYS cc_start: 0.6502 (OUTLIER) cc_final: 0.6273 (ttpp) REVERT: R 145 ASP cc_start: 0.7926 (t70) cc_final: 0.7671 (t70) REVERT: R 323 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.5796 (mp0) REVERT: A 22 ASN cc_start: 0.7434 (m-40) cc_final: 0.7202 (m-40) REVERT: A 305 CYS cc_start: 0.7029 (m) cc_final: 0.6022 (p) REVERT: B 217 ASP cc_start: 0.7614 (t0) cc_final: 0.7254 (t0) REVERT: C 21 MET cc_start: 0.5789 (mmm) cc_final: 0.5245 (ptm) REVERT: D 155 LYS cc_start: 0.6806 (mttm) cc_final: 0.6534 (mttp) REVERT: D 158 ASP cc_start: 0.6016 (m-30) cc_final: 0.5788 (m-30) REVERT: D 199 MET cc_start: 0.6974 (ptp) cc_final: 0.6536 (ptt) outliers start: 21 outliers final: 13 residues processed: 143 average time/residue: 1.3185 time to fit residues: 202.0797 Evaluate side-chains 140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LYS 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 70 THR 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 284 SER Chi-restraints excluded: chain B residue 332 VAL 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 111 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 73 optimal weight: 0.0070 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10165 Z= 0.192 Angle : 0.534 8.974 13741 Z= 0.278 Chirality : 0.039 0.147 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.354 55.364 1815 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 1.61 % Allowed : 15.06 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.71 % 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: 2.27 (0.24), residues: 1203 helix: 2.81 (0.19), residues: 674 sheet: 1.20 (0.41), residues: 157 loop : -0.91 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.011 0.001 PHE B 156 TYR 0.016 0.001 TYR P 1 ARG 0.008 0.001 ARG R 190 ********************** 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 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.023 Fit side-chains REVERT: R 81 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.6198 (ttpp) REVERT: R 145 ASP cc_start: 0.7968 (t70) cc_final: 0.7740 (t70) REVERT: R 323 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: A 22 ASN cc_start: 0.7459 (m-40) cc_final: 0.7241 (m-40) REVERT: A 305 CYS cc_start: 0.6922 (m) cc_final: 0.6005 (p) REVERT: B 175 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7286 (t0) REVERT: B 217 ASP cc_start: 0.7609 (t0) cc_final: 0.7256 (t0) REVERT: C 21 MET cc_start: 0.5748 (mmm) cc_final: 0.5193 (ptm) REVERT: D 155 LYS cc_start: 0.6828 (mttm) cc_final: 0.6560 (mttp) REVERT: D 158 ASP cc_start: 0.5992 (m-30) cc_final: 0.5761 (m-30) REVERT: D 199 MET cc_start: 0.6990 (ptp) cc_final: 0.6528 (ptt) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 1.2333 time to fit residues: 178.4639 Evaluate side-chains 138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LYS 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 70 THR Chi-restraints excluded: chain B residue 119 CYS Chi-restraints excluded: chain B residue 175 ASP 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 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 98 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 overall best weight: 0.5350 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.164886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.131740 restraints weight = 11270.854| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.48 r_work: 0.3258 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10165 Z= 0.123 Angle : 0.472 8.297 13741 Z= 0.248 Chirality : 0.038 0.145 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.641 53.173 1815 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.42 % Allowed : 15.34 % 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 (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: 2.49 (0.24), residues: 1203 helix: 3.03 (0.19), residues: 673 sheet: 1.11 (0.41), residues: 158 loop : -0.82 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 87 HIS 0.002 0.001 HIS B 147 PHE 0.011 0.001 PHE A 354 TYR 0.010 0.001 TYR R 87 ARG 0.008 0.000 ARG R 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3791.12 seconds wall clock time: 69 minutes 5.19 seconds (4145.19 seconds total)