Starting phenix.real_space_refine on Fri Feb 14 10:33:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7s_28909/02_2025/8f7s_28909.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7s_28909/02_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_28909/02_2025/8f7s_28909.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7s_28909/02_2025/8f7s_28909.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7s_28909/02_2025/8f7s_28909.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7s_28909/02_2025/8f7s_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-5592/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: 6.10, per 1000 atoms: 0.61 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: 2.47 Conformation dependent library (CDL) restraints added in 940.6 milliseconds 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: 0.81 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: 2.84 Time building geometry restraints manager: 2.86 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.060 Set scattering table: 0.090 Process input model: 24.060 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.090 ------------------------------------------------------------------------------- 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 : 0.948 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: 1.2280 time to fit residues: 339.4880 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 : 1.120 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.176128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.138037 restraints weight = 10957.214| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.85 r_work: 0.3324 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 : 1.162 Fit side-chains REVERT: R 113 THR cc_start: 0.8743 (t) cc_final: 0.8483 (t) REVERT: A 22 ASN cc_start: 0.7818 (m-40) cc_final: 0.7405 (m-40) REVERT: A 26 ASP cc_start: 0.7461 (m-30) cc_final: 0.7260 (m-30) REVERT: A 53 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6079 (mpt) REVERT: A 240 MET cc_start: 0.4089 (ppp) cc_final: 0.3809 (pp-130) REVERT: A 275 GLU cc_start: 0.7428 (tp30) cc_final: 0.6678 (tp30) REVERT: B 47 ARG cc_start: 0.6797 (mmm-85) cc_final: 0.6274 (mmt90) REVERT: B 70 THR cc_start: 0.8154 (m) cc_final: 0.7882 (p) REVERT: B 175 ASP cc_start: 0.7918 (t0) cc_final: 0.7654 (t70) REVERT: B 217 ASP cc_start: 0.8214 (t0) cc_final: 0.7865 (t0) REVERT: D 130 TYR cc_start: 0.8803 (t80) cc_final: 0.8593 (t80) outliers start: 29 outliers final: 11 residues processed: 167 average time/residue: 1.2513 time to fit residues: 224.3975 Evaluate side-chains 152 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 9 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 30 optimal weight: 0.1980 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 273 ASN B 345 ASN D 67 ASN D 105 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.172945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.133847 restraints weight = 11007.640| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.90 r_work: 0.3233 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3084 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= 0.222 Angle : 0.552 8.338 13741 Z= 0.292 Chirality : 0.040 0.145 1615 Planarity : 0.005 0.049 1656 Dihedral : 7.504 55.465 1815 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.69 % Allowed : 10.51 % 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: 2.34 (0.23), residues: 1203 helix: 2.76 (0.19), residues: 671 sheet: 1.27 (0.42), residues: 157 loop : -0.66 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 87 HIS 0.006 0.001 HIS B 147 PHE 0.017 0.002 PHE A 354 TYR 0.014 0.002 TYR P 1 ARG 0.006 0.001 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 183 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 1.016 Fit side-chains REVERT: R 111 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7127 (mpp) REVERT: R 201 GLN cc_start: 0.7609 (tt0) cc_final: 0.7364 (tt0) REVERT: R 302 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 22 ASN cc_start: 0.7684 (m-40) cc_final: 0.7322 (m-40) REVERT: A 53 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6363 (mpt) REVERT: A 275 GLU cc_start: 0.7294 (tp30) cc_final: 0.7082 (tp30) REVERT: B 175 ASP cc_start: 0.8170 (t0) cc_final: 0.7775 (t70) REVERT: B 217 ASP cc_start: 0.8214 (t0) cc_final: 0.7868 (t0) REVERT: D 193 ASP cc_start: 0.6373 (t0) cc_final: 0.5796 (m-30) outliers start: 39 outliers final: 20 residues processed: 166 average time/residue: 1.2567 time to fit residues: 223.6222 Evaluate side-chains 153 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 1.092 ------------------------------------------------------------------------------- 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 42 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 70 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 overall best weight: 0.4440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN A 306 GLN B 273 ASN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.177711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.139081 restraints weight = 10868.517| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.86 r_work: 0.3246 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3115 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= 0.119 Angle : 0.454 7.562 13741 Z= 0.242 Chirality : 0.037 0.143 1615 Planarity : 0.004 0.047 1656 Dihedral : 6.656 56.237 1815 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.56 % Allowed : 13.54 % 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 (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: 2.65 (0.24), residues: 1203 helix: 3.08 (0.19), residues: 672 sheet: 1.25 (0.42), residues: 161 loop : -0.62 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 87 HIS 0.002 0.001 HIS B 147 PHE 0.015 0.001 PHE A 354 TYR 0.012 0.001 TYR R 87 ARG 0.006 0.000 ARG B 51 *********************** 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 168 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.292 Fit side-chains REVERT: R 81 LYS cc_start: 0.6386 (ttpt) cc_final: 0.6180 (ttpp) REVERT: A 22 ASN cc_start: 0.7435 (m-40) cc_final: 0.7161 (m-40) REVERT: B 47 ARG cc_start: 0.6663 (mmm-85) cc_final: 0.6221 (mmt90) REVERT: B 175 ASP cc_start: 0.8070 (t0) cc_final: 0.7734 (t70) REVERT: B 217 ASP cc_start: 0.8191 (t0) cc_final: 0.7883 (t0) REVERT: D 193 ASP cc_start: 0.6387 (t0) cc_final: 0.6060 (m-30) outliers start: 27 outliers final: 13 residues processed: 154 average time/residue: 1.3258 time to fit residues: 220.0245 Evaluate side-chains 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 167 LEU 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 119 CYS Chi-restraints excluded: chain B residue 189 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 85 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 114 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 306 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 = 0.3883 r_free = 0.3883 target = 0.169201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130556 restraints weight = 10962.297| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.77 r_work: 0.3219 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10165 Z= 0.201 Angle : 0.534 8.555 13741 Z= 0.280 Chirality : 0.040 0.147 1615 Planarity : 0.004 0.050 1656 Dihedral : 7.234 53.106 1815 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.31 % Allowed : 12.97 % 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 (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: 2.40 (0.24), residues: 1203 helix: 2.89 (0.19), residues: 672 sheet: 1.16 (0.42), residues: 157 loop : -0.75 (0.30), residues: 374 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 0.014 0.002 PHE A 354 TYR 0.017 0.002 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 171 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 136 time to evaluate : 1.117 Fit side-chains REVERT: R 111 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8369 (mpp) REVERT: R 189 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.8086 (t) REVERT: A 22 ASN cc_start: 0.7656 (m-40) cc_final: 0.7392 (m-40) REVERT: B 47 ARG cc_start: 0.6682 (mmm-85) cc_final: 0.6188 (mmt90) REVERT: B 134 ARG cc_start: 0.6376 (ptp-170) cc_final: 0.5377 (tpt170) REVERT: B 175 ASP cc_start: 0.8185 (t0) cc_final: 0.7743 (t70) REVERT: B 217 ASP cc_start: 0.8222 (t0) cc_final: 0.7840 (t0) REVERT: B 313 LEU cc_start: 0.8145 (mp) cc_final: 0.7810 (mt) REVERT: C 21 MET cc_start: 0.5851 (mmm) cc_final: 0.5069 (ptm) REVERT: D 193 ASP cc_start: 0.6491 (t0) cc_final: 0.6230 (m-30) outliers start: 35 outliers final: 18 residues processed: 154 average time/residue: 1.2884 time to fit residues: 212.5053 Evaluate side-chains 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 MET 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 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 266 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 54 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 108 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 306 GLN A 331 ASN B 225 GLN D 67 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.171131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133023 restraints weight = 10827.178| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.74 r_work: 0.3253 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10165 Z= 0.211 Angle : 0.538 8.732 13741 Z= 0.282 Chirality : 0.040 0.144 1615 Planarity : 0.004 0.050 1656 Dihedral : 7.643 57.767 1815 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.65 % Allowed : 13.54 % 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 (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: 2.26 (0.24), residues: 1203 helix: 2.79 (0.19), residues: 672 sheet: 1.08 (0.41), residues: 157 loop : -0.84 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.012 0.002 PHE A 354 TYR 0.017 0.002 TYR P 1 ARG 0.008 0.001 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 157 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.047 Fit side-chains REVERT: R 111 MET cc_start: 0.8508 (mtm) cc_final: 0.8048 (mpp) REVERT: R 323 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5843 (mp0) REVERT: A 22 ASN cc_start: 0.7557 (m-40) cc_final: 0.7275 (m-40) REVERT: A 231 ASP cc_start: 0.6849 (m-30) cc_final: 0.5338 (p0) REVERT: B 47 ARG cc_start: 0.6614 (mmm-85) cc_final: 0.6079 (mmt90) REVERT: B 134 ARG cc_start: 0.6532 (ptp-170) cc_final: 0.5546 (tpt170) REVERT: B 175 ASP cc_start: 0.8265 (t0) cc_final: 0.7800 (t70) REVERT: B 217 ASP cc_start: 0.8158 (t0) cc_final: 0.7790 (t0) REVERT: B 313 LEU cc_start: 0.8100 (mp) cc_final: 0.7804 (mt) REVERT: C 21 MET cc_start: 0.5741 (mmm) cc_final: 0.4962 (ptm) REVERT: D 193 ASP cc_start: 0.6592 (t0) cc_final: 0.5838 (m-30) outliers start: 28 outliers final: 18 residues processed: 146 average time/residue: 1.2215 time to fit residues: 191.9150 Evaluate side-chains 146 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 1.022 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.166233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126278 restraints weight = 11061.929| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.88 r_work: 0.3201 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10165 Z= 0.173 Angle : 0.509 8.424 13741 Z= 0.267 Chirality : 0.039 0.150 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.405 58.527 1815 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.56 % Allowed : 13.83 % 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 (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: 2.28 (0.24), residues: 1203 helix: 2.84 (0.19), residues: 674 sheet: 1.06 (0.40), residues: 157 loop : -0.91 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.012 0.001 PHE A 354 TYR 0.016 0.001 TYR A 230 ARG 0.006 0.000 ARG B 51 *********************** 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 158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 1.045 Fit side-chains REVERT: R 111 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8095 (mpp) REVERT: R 323 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.5821 (mp0) REVERT: A 22 ASN cc_start: 0.7511 (m-40) cc_final: 0.7257 (m-40) REVERT: B 134 ARG cc_start: 0.6646 (ptp-170) cc_final: 0.5720 (tpt170) REVERT: B 175 ASP cc_start: 0.8091 (t0) cc_final: 0.7659 (t70) REVERT: B 217 ASP cc_start: 0.8025 (t0) cc_final: 0.7659 (t0) REVERT: B 313 LEU cc_start: 0.7997 (mp) cc_final: 0.7747 (mt) REVERT: C 21 MET cc_start: 0.5704 (mmm) cc_final: 0.4934 (ptm) REVERT: D 193 ASP cc_start: 0.6479 (t0) cc_final: 0.5796 (m-30) REVERT: D 199 MET cc_start: 0.7429 (ptp) cc_final: 0.6985 (ptt) outliers start: 27 outliers final: 17 residues processed: 144 average time/residue: 1.2076 time to fit residues: 187.2508 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 : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 MET Chi-restraints excluded: chain R residue 167 LEU 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 119 CYS Chi-restraints excluded: chain B residue 186 THR 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 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 16 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 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 = 0.3841 r_free = 0.3841 target = 0.165775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127325 restraints weight = 10985.750| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.86 r_work: 0.3196 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10165 Z= 0.216 Angle : 0.552 9.358 13741 Z= 0.288 Chirality : 0.040 0.143 1615 Planarity : 0.004 0.050 1656 Dihedral : 7.689 56.817 1815 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 2.46 % Allowed : 14.11 % 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: 2.17 (0.24), residues: 1203 helix: 2.73 (0.19), residues: 672 sheet: 1.02 (0.40), residues: 157 loop : -0.90 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 87 HIS 0.005 0.001 HIS B 67 PHE 0.012 0.002 PHE A 354 TYR 0.017 0.002 TYR P 1 ARG 0.007 0.001 ARG B 51 *********************** 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 150 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 124 time to evaluate : 1.043 Fit side-chains REVERT: R 111 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8034 (mpp) REVERT: R 323 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: A 22 ASN cc_start: 0.7577 (m-40) cc_final: 0.7308 (m-40) REVERT: A 231 ASP cc_start: 0.7004 (m-30) cc_final: 0.5464 (p0) REVERT: B 47 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.5952 (mmt90) REVERT: B 134 ARG cc_start: 0.6726 (ptp-170) cc_final: 0.5673 (tpt170) REVERT: B 175 ASP cc_start: 0.8302 (t0) cc_final: 0.7852 (t70) REVERT: B 217 ASP cc_start: 0.8162 (t0) cc_final: 0.7808 (t0) REVERT: B 313 LEU cc_start: 0.8126 (mp) cc_final: 0.7831 (mt) REVERT: C 21 MET cc_start: 0.5716 (mmm) cc_final: 0.4879 (ptm) REVERT: D 193 ASP cc_start: 0.6617 (t0) cc_final: 0.6062 (m-30) REVERT: D 199 MET cc_start: 0.7513 (ptp) cc_final: 0.7039 (ptt) outliers start: 26 outliers final: 19 residues processed: 138 average time/residue: 1.1773 time to fit residues: 175.2647 Evaluate side-chains 143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 111 MET 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 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 186 THR 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 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 45 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 0.0010 chunk 14 optimal weight: 1.9990 chunk 87 optimal weight: 0.0370 overall best weight: 0.7866 ------------------------------------------------------------------------------- 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 D 278 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.167857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128464 restraints weight = 11027.348| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.84 r_work: 0.3184 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10165 Z= 0.135 Angle : 0.483 8.106 13741 Z= 0.253 Chirality : 0.038 0.144 1615 Planarity : 0.004 0.048 1656 Dihedral : 7.058 58.318 1815 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.99 % Allowed : 14.87 % Favored : 83.14 % 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: 2.38 (0.24), residues: 1203 helix: 2.96 (0.19), residues: 673 sheet: 1.02 (0.40), residues: 159 loop : -0.88 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.010 0.001 PHE A 354 TYR 0.013 0.001 TYR A 230 ARG 0.006 0.000 ARG B 51 *********************** 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 145 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 1.084 Fit side-chains REVERT: R 81 LYS cc_start: 0.6472 (ttpt) cc_final: 0.6249 (ttpp) REVERT: R 323 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5739 (mp0) REVERT: A 22 ASN cc_start: 0.7513 (m-40) cc_final: 0.7282 (m-40) REVERT: A 231 ASP cc_start: 0.7038 (m-30) cc_final: 0.5530 (p0) REVERT: A 305 CYS cc_start: 0.7800 (m) cc_final: 0.6689 (p) REVERT: A 306 GLN cc_start: 0.7028 (mm-40) cc_final: 0.6782 (mm110) REVERT: B 47 ARG cc_start: 0.6406 (mmm-85) cc_final: 0.5857 (mmt90) REVERT: B 134 ARG cc_start: 0.6790 (ptp-170) cc_final: 0.5692 (tpt170) REVERT: B 175 ASP cc_start: 0.8188 (t0) cc_final: 0.7767 (t70) REVERT: B 217 ASP cc_start: 0.8159 (t0) cc_final: 0.7822 (t0) REVERT: B 313 LEU cc_start: 0.8085 (mp) cc_final: 0.7808 (mt) REVERT: C 21 MET cc_start: 0.5628 (mmm) cc_final: 0.4797 (ptm) REVERT: D 193 ASP cc_start: 0.6690 (t0) cc_final: 0.6151 (m-30) outliers start: 21 outliers final: 13 residues processed: 138 average time/residue: 1.1750 time to fit residues: 175.1688 Evaluate side-chains 135 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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 4 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 69 optimal weight: 0.0040 chunk 45 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 111 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127702 restraints weight = 11037.359| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.87 r_work: 0.3258 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10165 Z= 0.152 Angle : 0.493 8.524 13741 Z= 0.259 Chirality : 0.038 0.146 1615 Planarity : 0.004 0.048 1656 Dihedral : 7.026 57.090 1815 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % 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: 2.39 (0.24), residues: 1203 helix: 2.95 (0.19), residues: 673 sheet: 1.05 (0.41), residues: 160 loop : -0.88 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.011 0.001 PHE A 354 TYR 0.013 0.001 TYR P 1 ARG 0.007 0.000 ARG B 51 ********************** 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 141 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.042 Fit side-chains REVERT: R 323 GLU cc_start: 0.6635 (OUTLIER) cc_final: 0.5723 (mp0) REVERT: A 22 ASN cc_start: 0.7516 (m-40) cc_final: 0.7267 (m-40) REVERT: A 231 ASP cc_start: 0.6934 (m-30) cc_final: 0.5423 (p0) REVERT: A 305 CYS cc_start: 0.7493 (m) cc_final: 0.6512 (p) REVERT: B 47 ARG cc_start: 0.6335 (mmm-85) cc_final: 0.5780 (mmt90) REVERT: B 134 ARG cc_start: 0.6683 (ptp-170) cc_final: 0.5690 (tpt170) REVERT: B 175 ASP cc_start: 0.8068 (t0) cc_final: 0.7620 (t70) REVERT: B 217 ASP cc_start: 0.7999 (t0) cc_final: 0.7689 (t0) REVERT: B 313 LEU cc_start: 0.7991 (mp) cc_final: 0.7760 (mt) REVERT: C 21 MET cc_start: 0.5683 (mmm) cc_final: 0.4854 (ptm) REVERT: D 193 ASP cc_start: 0.6646 (t0) cc_final: 0.6123 (m-30) outliers start: 15 outliers final: 13 residues processed: 137 average time/residue: 1.1968 time to fit residues: 176.6271 Evaluate side-chains 137 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 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 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 14 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 169 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.167269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128399 restraints weight = 10870.606| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.93 r_work: 0.3241 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10165 Z= 0.186 Angle : 0.522 8.517 13741 Z= 0.273 Chirality : 0.039 0.148 1615 Planarity : 0.004 0.049 1656 Dihedral : 7.349 59.440 1815 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.52 % Allowed : 15.53 % Favored : 82.95 % 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: 2.29 (0.24), residues: 1203 helix: 2.85 (0.19), residues: 673 sheet: 1.13 (0.40), residues: 157 loop : -0.93 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.011 0.001 PHE A 354 TYR 0.017 0.001 TYR P 1 ARG 0.007 0.001 ARG B 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7485.23 seconds wall clock time: 133 minutes 1.58 seconds (7981.58 seconds total)