Starting phenix.real_space_refine on Mon Dec 30 05:30:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.map" model { file = "/net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y5h_38935/12_2024/8y5h_38935.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 69 5.16 5 C 8025 2.51 5 N 2057 2.21 5 O 2254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12405 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2876 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain: "B" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "C" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1936 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain: "D" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2862 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 13, 'TRANS': 344} Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2548 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 21, 'TRANS': 300} Chain: "E" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'SPD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 7.59, per 1000 atoms: 0.61 Number of scatterers: 12405 At special positions: 0 Unit cell: (98.496, 89.984, 165.376, 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 69 16.00 O 2254 8.00 N 2057 7.00 C 8025 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2934 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 49.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 105 through 116 removed outlier: 4.847A pdb=" N GLY A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 123 through 134 removed outlier: 3.926A pdb=" N ARG A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 163 Processing helix chain 'A' and resid 179 through 198 removed outlier: 4.011A pdb=" N ASN A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.785A pdb=" N MET A 214 " --> pdb=" O GLU A 210 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.656A pdb=" N ILE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 23 Processing helix chain 'B' and resid 23 through 34 removed outlier: 3.666A pdb=" N ASN B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 removed outlier: 3.850A pdb=" N LEU B 56 " --> pdb=" O ASN B 52 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 57 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 91 removed outlier: 4.567A pdb=" N VAL B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LEU B 65 " --> pdb=" O TYR B 61 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA B 72 " --> pdb=" O SER B 68 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 75 " --> pdb=" O MET B 71 " (cutoff:3.500A) Proline residue: B 85 - end of helix Processing helix chain 'B' and resid 97 through 104 Processing helix chain 'B' and resid 105 through 111 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.746A pdb=" N TYR B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 3.724A pdb=" N LEU B 137 " --> pdb=" O PHE B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 162 removed outlier: 3.886A pdb=" N VAL B 153 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 175 removed outlier: 3.538A pdb=" N MET B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) Proline residue: B 168 - end of helix removed outlier: 3.568A pdb=" N SER B 172 " --> pdb=" O PRO B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 188 removed outlier: 3.873A pdb=" N LEU B 181 " --> pdb=" O ASP B 177 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 185 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 198 removed outlier: 3.607A pdb=" N PHE B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 203 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.800A pdb=" N LEU B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 221 through 229 removed outlier: 4.385A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 3.799A pdb=" N VAL B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 277 removed outlier: 3.543A pdb=" N SER B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR B 259 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LEU B 260 " --> pdb=" O THR B 256 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 263 " --> pdb=" O THR B 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 28 Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 44 through 53 removed outlier: 3.966A pdb=" N SER C 48 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 52 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 88 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 107 through 123 Processing helix chain 'C' and resid 127 through 152 removed outlier: 3.620A pdb=" N LEU C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Proline residue: C 141 - end of helix Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 165 removed outlier: 4.234A pdb=" N GLU C 160 " --> pdb=" O VAL C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 176 Processing helix chain 'C' and resid 176 through 198 removed outlier: 3.522A pdb=" N LEU C 180 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Proline residue: C 183 - end of helix removed outlier: 3.931A pdb=" N ALA C 187 " --> pdb=" O PRO C 183 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 removed outlier: 3.772A pdb=" N PHE C 205 " --> pdb=" O VAL C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 removed outlier: 3.648A pdb=" N LYS C 217 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER C 220 " --> pdb=" O LEU C 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 253 removed outlier: 3.521A pdb=" N ALA C 232 " --> pdb=" O PRO C 228 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET C 244 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 105 through 117 removed outlier: 4.986A pdb=" N GLY D 113 " --> pdb=" O ASN D 109 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 135 removed outlier: 3.921A pdb=" N VAL D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 163 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.869A pdb=" N ASN D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 215 removed outlier: 3.603A pdb=" N ALA D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 238 Processing helix chain 'D' and resid 295 through 297 No H-bonds generated for 'chain 'D' and resid 295 through 297' Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.569A pdb=" N PHE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS E 48 " --> pdb=" O GLU E 44 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 Processing helix chain 'E' and resid 83 through 93 removed outlier: 4.221A pdb=" N ASP E 88 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N LYS E 89 " --> pdb=" O TYR E 85 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU E 93 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 110 removed outlier: 3.894A pdb=" N ASN E 109 " --> pdb=" O ASN E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 156 Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 191 through 200 removed outlier: 3.549A pdb=" N ASN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 206 Proline residue: E 204 - end of helix No H-bonds generated for 'chain 'E' and resid 201 through 206' Processing helix chain 'E' and resid 215 through 220 Processing helix chain 'E' and resid 230 through 238 Processing helix chain 'E' and resid 267 through 279 removed outlier: 3.558A pdb=" N LEU E 272 " --> pdb=" O LYS E 268 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 292 removed outlier: 3.621A pdb=" N THR E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 303 removed outlier: 3.797A pdb=" N LYS E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 346 removed outlier: 3.622A pdb=" N TYR E 337 " --> pdb=" O ALA E 333 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA E 346 " --> pdb=" O GLN E 342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 41 removed outlier: 6.470A pdb=" N VAL A 32 " --> pdb=" O CYS A 26 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N CYS A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ARG A 24 " --> pdb=" O PRO A 34 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU A 36 " --> pdb=" O GLY A 22 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 73 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE A 23 " --> pdb=" O SER A 71 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER A 71 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.551A pdb=" N ASN A 92 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N ASP A 172 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N VAL A 94 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 45 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL A 219 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N THR A 47 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET A 221 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 49 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE A 218 " --> pdb=" O ASP A 229 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP A 229 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL A 220 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 274 through 275 removed outlier: 7.745A pdb=" N ARG A 266 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ARG A 261 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARG A 268 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 259 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 303 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 33 removed outlier: 3.578A pdb=" N VAL D 32 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 30 through 33 removed outlier: 3.578A pdb=" N VAL D 32 " --> pdb=" O LYS D 25 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS D 25 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 23 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER D 71 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 92 through 94 removed outlier: 3.513A pdb=" N ASN D 92 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP D 172 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE D 45 " --> pdb=" O ARG D 217 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N VAL D 219 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR D 47 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N MET D 221 " --> pdb=" O THR D 47 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU D 49 " --> pdb=" O MET D 221 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE D 218 " --> pdb=" O ASP D 229 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP D 229 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL D 220 " --> pdb=" O GLU D 227 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 274 through 279 removed outlier: 3.758A pdb=" N GLU D 260 " --> pdb=" O ARG D 268 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN D 270 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL D 258 " --> pdb=" O ASN D 270 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB2, first strand: chain 'D' and resid 319 through 322 removed outlier: 3.550A pdb=" N GLU D 319 " --> pdb=" O VAL D 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 28 through 33 Processing sheet with id=AB4, first strand: chain 'E' and resid 225 through 229 Processing sheet with id=AB5, first strand: chain 'E' and resid 225 through 229 removed outlier: 6.873A pdb=" N ASP E 257 " --> pdb=" O TYR E 129 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TRP E 131 " --> pdb=" O TRP E 255 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N TRP E 255 " --> pdb=" O TRP E 131 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA E 133 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ILE E 253 " --> pdb=" O ALA E 133 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 164 through 165 563 hydrogen bonds defined for protein. 1617 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: 3.59 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2045 1.29 - 1.42: 3118 1.42 - 1.55: 7368 1.55 - 1.68: 4 1.68 - 1.81: 129 Bond restraints: 12664 Sorted by residual: bond pdb=" C ARG D 320 " pdb=" O ARG D 320 " ideal model delta sigma weight residual 1.234 1.161 0.073 1.22e-02 6.72e+03 3.55e+01 bond pdb=" CA ARG D 320 " pdb=" CB ARG D 320 " ideal model delta sigma weight residual 1.535 1.476 0.060 2.09e-02 2.29e+03 8.13e+00 bond pdb=" CA ASP D 353 " pdb=" C ASP D 353 " ideal model delta sigma weight residual 1.522 1.555 -0.033 1.24e-02 6.50e+03 7.22e+00 bond pdb=" CD ARG D 320 " pdb=" NE ARG D 320 " ideal model delta sigma weight residual 1.458 1.422 0.036 1.40e-02 5.10e+03 6.46e+00 bond pdb=" CA ASP D 351 " pdb=" C ASP D 351 " ideal model delta sigma weight residual 1.523 1.557 -0.033 1.34e-02 5.57e+03 6.20e+00 ... (remaining 12659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 16630 2.08 - 4.15: 467 4.15 - 6.23: 63 6.23 - 8.30: 18 8.30 - 10.38: 4 Bond angle restraints: 17182 Sorted by residual: angle pdb=" C ASP D 348 " pdb=" N ASP D 349 " pdb=" CA ASP D 349 " ideal model delta sigma weight residual 122.85 117.70 5.15 1.10e+00 8.26e-01 2.19e+01 angle pdb=" C SER A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 129.73 -8.19 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C ILE C 213 " pdb=" N LEU C 214 " pdb=" CA LEU C 214 " ideal model delta sigma weight residual 120.09 125.41 -5.32 1.25e+00 6.40e-01 1.81e+01 angle pdb=" C GLY C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 119.05 123.66 -4.61 1.11e+00 8.12e-01 1.72e+01 angle pdb=" N ASP D 351 " pdb=" CA ASP D 351 " pdb=" C ASP D 351 " ideal model delta sigma weight residual 110.80 119.30 -8.50 2.13e+00 2.20e-01 1.59e+01 ... (remaining 17177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 6860 18.01 - 36.03: 630 36.03 - 54.04: 103 54.04 - 72.05: 20 72.05 - 90.06: 11 Dihedral angle restraints: 7624 sinusoidal: 3080 harmonic: 4544 Sorted by residual: dihedral pdb=" CA GLU A 297 " pdb=" C GLU A 297 " pdb=" N ASP A 298 " pdb=" CA ASP A 298 " ideal model delta harmonic sigma weight residual -180.00 -151.87 -28.13 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA TYR E 59 " pdb=" C TYR E 59 " pdb=" N GLU E 60 " pdb=" CA GLU E 60 " ideal model delta harmonic sigma weight residual 180.00 152.31 27.69 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA TRP D 364 " pdb=" C TRP D 364 " pdb=" N VAL D 365 " pdb=" CA VAL D 365 " ideal model delta harmonic sigma weight residual -180.00 -155.99 -24.01 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 7621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1758 0.080 - 0.161: 214 0.161 - 0.241: 3 0.241 - 0.321: 2 0.321 - 0.402: 1 Chirality restraints: 1978 Sorted by residual: chirality pdb=" CA ASP D 351 " pdb=" N ASP D 351 " pdb=" C ASP D 351 " pdb=" CB ASP D 351 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA ASP D 349 " pdb=" N ASP D 349 " pdb=" C ASP D 349 " pdb=" CB ASP D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASP D 353 " pdb=" N ASP D 353 " pdb=" C ASP D 353 " pdb=" CB ASP D 353 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1975 not shown) Planarity restraints: 2183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 319 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLU D 319 " 0.063 2.00e-02 2.50e+03 pdb=" O GLU D 319 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG D 320 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 285 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 286 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 285 " 0.048 5.00e-02 4.00e+02 7.32e-02 8.58e+00 pdb=" N PRO D 286 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 286 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO D 286 " 0.040 5.00e-02 4.00e+02 ... (remaining 2180 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1599 2.74 - 3.28: 11551 3.28 - 3.82: 18763 3.82 - 4.36: 22101 4.36 - 4.90: 39253 Nonbonded interactions: 93267 Sorted by model distance: nonbonded pdb=" NH1 ARG A 261 " pdb=" O ASP A 263 " model vdw 2.206 3.120 nonbonded pdb=" OD2 ASP B 226 " pdb=" OH TYR C 219 " model vdw 2.215 3.040 nonbonded pdb=" O GLY E 240 " pdb=" OG1 THR E 241 " model vdw 2.226 3.040 nonbonded pdb=" O PRO A 145 " pdb=" ND1 HIS A 146 " model vdw 2.241 3.120 nonbonded pdb=" O SER E 183 " pdb=" OG1 THR E 186 " model vdw 2.252 3.040 ... (remaining 93262 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 'A' and resid 16 through 373) selection = chain 'D' } 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.580 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.430 Find NCS groups from input model: 0.310 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.007 0.073 12664 Z= 0.482 Angle : 0.851 10.378 17182 Z= 0.482 Chirality : 0.053 0.402 1978 Planarity : 0.006 0.078 2183 Dihedral : 14.337 90.065 4690 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.52 % Allowed : 0.74 % Favored : 98.75 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.20), residues: 1552 helix: -0.44 (0.20), residues: 685 sheet: -0.74 (0.34), residues: 239 loop : -2.26 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 364 HIS 0.012 0.002 HIS C 62 PHE 0.029 0.002 PHE B 48 TYR 0.036 0.003 TYR B 129 ARG 0.012 0.001 ARG D 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 372 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8267 (mmtt) cc_final: 0.8026 (mmtt) REVERT: A 210 GLU cc_start: 0.7397 (tt0) cc_final: 0.7101 (tt0) REVERT: A 237 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6832 (mt-10) REVERT: A 265 GLN cc_start: 0.6409 (pt0) cc_final: 0.6114 (pt0) REVERT: A 303 GLU cc_start: 0.6815 (pp20) cc_final: 0.6481 (pp20) REVERT: A 343 GLU cc_start: 0.7950 (pt0) cc_final: 0.7442 (pt0) REVERT: D 79 GLU cc_start: 0.6787 (mp0) cc_final: 0.6033 (mp0) REVERT: D 129 MET cc_start: 0.7563 (mmm) cc_final: 0.7234 (mmm) REVERT: D 164 ASN cc_start: 0.8405 (m110) cc_final: 0.8111 (m110) REVERT: D 298 ASP cc_start: 0.7954 (m-30) cc_final: 0.7721 (m-30) REVERT: D 325 MET cc_start: 0.7631 (ttt) cc_final: 0.7315 (ttt) REVERT: D 359 LYS cc_start: 0.8075 (tttp) cc_final: 0.7829 (mtpp) REVERT: E 70 LYS cc_start: 0.7910 (mtpt) cc_final: 0.7646 (mtpt) REVERT: E 72 TYR cc_start: 0.7899 (m-80) cc_final: 0.7635 (m-80) REVERT: E 109 ASN cc_start: 0.7921 (m-40) cc_final: 0.7672 (m110) REVERT: E 198 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6924 (tm-30) REVERT: E 322 LYS cc_start: 0.7220 (mtpt) cc_final: 0.7005 (mtpt) REVERT: E 328 ASN cc_start: 0.7976 (m-40) cc_final: 0.7751 (m-40) REVERT: E 339 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6889 (tm-30) outliers start: 7 outliers final: 3 residues processed: 378 average time/residue: 0.2791 time to fit residues: 144.9934 Evaluate side-chains 336 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain D residue 320 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 139 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 208 GLN D 147 GLN D 291 HIS D 335 ASN E 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12664 Z= 0.215 Angle : 0.643 8.553 17182 Z= 0.336 Chirality : 0.045 0.155 1978 Planarity : 0.006 0.065 2183 Dihedral : 5.533 52.271 1700 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.55 % Allowed : 10.54 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.21), residues: 1552 helix: 0.73 (0.21), residues: 694 sheet: -0.66 (0.35), residues: 243 loop : -2.07 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 151 HIS 0.007 0.001 HIS C 62 PHE 0.024 0.001 PHE C 138 TYR 0.016 0.002 TYR B 223 ARG 0.004 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 373 time to evaluate : 1.392 Fit side-chains revert: symmetry clash REVERT: A 61 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7343 (mtt-85) REVERT: A 118 LYS cc_start: 0.8255 (mmtt) cc_final: 0.8025 (mmtt) REVERT: A 210 GLU cc_start: 0.7363 (tt0) cc_final: 0.7088 (tt0) REVERT: A 234 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7388 (mt-10) REVERT: A 303 GLU cc_start: 0.6841 (pp20) cc_final: 0.6493 (pp20) REVERT: B 241 LYS cc_start: 0.8451 (tttt) cc_final: 0.8250 (tttm) REVERT: C 170 PHE cc_start: 0.7723 (t80) cc_final: 0.7266 (t80) REVERT: D 76 LEU cc_start: 0.7733 (tt) cc_final: 0.6979 (tt) REVERT: D 77 ASP cc_start: 0.6872 (m-30) cc_final: 0.6400 (m-30) REVERT: D 79 GLU cc_start: 0.6817 (mp0) cc_final: 0.6114 (mp0) REVERT: D 164 ASN cc_start: 0.8256 (m110) cc_final: 0.7921 (m110) REVERT: D 173 GLN cc_start: 0.7938 (mp10) cc_final: 0.7482 (mp10) REVERT: D 207 ASP cc_start: 0.7950 (t0) cc_final: 0.7698 (t0) REVERT: D 298 ASP cc_start: 0.7919 (m-30) cc_final: 0.7698 (m-30) REVERT: D 358 GLN cc_start: 0.7993 (tp40) cc_final: 0.7511 (tp-100) REVERT: D 359 LYS cc_start: 0.7882 (tttp) cc_final: 0.7437 (mtpp) REVERT: E 70 LYS cc_start: 0.7944 (mtpt) cc_final: 0.7684 (mtpt) REVERT: E 171 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7718 (mt-10) REVERT: E 193 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7087 (tm-30) REVERT: E 238 GLN cc_start: 0.8003 (tt0) cc_final: 0.7715 (tp40) REVERT: E 311 ASP cc_start: 0.7733 (t0) cc_final: 0.7477 (t0) REVERT: E 328 ASN cc_start: 0.7954 (m-40) cc_final: 0.7710 (m-40) REVERT: E 339 GLU cc_start: 0.7308 (tm-30) cc_final: 0.6928 (tm-30) outliers start: 21 outliers final: 14 residues processed: 382 average time/residue: 0.3026 time to fit residues: 158.3167 Evaluate side-chains 367 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 353 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 95 optimal weight: 0.0980 chunk 38 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 151 optimal weight: 0.0060 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 HIS A 363 ASN B 52 ASN E 342 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12664 Z= 0.162 Angle : 0.564 7.556 17182 Z= 0.293 Chirality : 0.043 0.153 1978 Planarity : 0.005 0.061 2183 Dihedral : 4.794 54.512 1694 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.87 % Allowed : 12.90 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.22), residues: 1552 helix: 1.18 (0.21), residues: 711 sheet: -0.57 (0.35), residues: 245 loop : -1.87 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.020 0.001 PHE C 138 TYR 0.012 0.001 TYR B 223 ARG 0.006 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 1.366 Fit side-chains REVERT: A 61 ARG cc_start: 0.7535 (mtt-85) cc_final: 0.7313 (mtt-85) REVERT: A 184 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7372 (ttpp) REVERT: A 210 GLU cc_start: 0.7377 (tt0) cc_final: 0.7106 (tt0) REVERT: A 238 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6744 (tm-30) REVERT: A 319 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6741 (mm-30) REVERT: A 320 ARG cc_start: 0.7911 (ptt90) cc_final: 0.7534 (ptt90) REVERT: C 170 PHE cc_start: 0.7691 (t80) cc_final: 0.7331 (t80) REVERT: D 76 LEU cc_start: 0.7629 (tt) cc_final: 0.6950 (tt) REVERT: D 77 ASP cc_start: 0.6702 (m-30) cc_final: 0.5680 (m-30) REVERT: D 79 GLU cc_start: 0.6813 (mp0) cc_final: 0.6355 (mp0) REVERT: D 116 MET cc_start: 0.7940 (mmm) cc_final: 0.7619 (mmm) REVERT: D 173 GLN cc_start: 0.7907 (mp10) cc_final: 0.7237 (mp10) REVERT: D 235 ILE cc_start: 0.8464 (mt) cc_final: 0.8219 (tt) REVERT: D 298 ASP cc_start: 0.7959 (m-30) cc_final: 0.7624 (m-30) REVERT: D 358 GLN cc_start: 0.7854 (tp40) cc_final: 0.7405 (tp-100) REVERT: D 359 LYS cc_start: 0.7762 (tttp) cc_final: 0.7238 (mtpp) REVERT: E 68 LYS cc_start: 0.7908 (tppp) cc_final: 0.7706 (ttmm) REVERT: E 72 TYR cc_start: 0.7150 (m-80) cc_final: 0.6911 (m-80) REVERT: E 171 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7772 (mt-10) REVERT: E 193 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7001 (tm-30) REVERT: E 311 ASP cc_start: 0.7746 (t0) cc_final: 0.7540 (t0) REVERT: E 328 ASN cc_start: 0.7950 (m-40) cc_final: 0.7706 (m-40) REVERT: E 339 GLU cc_start: 0.7296 (tm-30) cc_final: 0.6930 (tm-30) outliers start: 39 outliers final: 26 residues processed: 386 average time/residue: 0.2911 time to fit residues: 153.5368 Evaluate side-chains 380 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 353 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 240 LYS Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 314 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 73 optimal weight: 0.0980 chunk 133 optimal weight: 0.0970 chunk 40 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 252 ASN D 265 GLN E 97 GLN E 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12664 Z= 0.159 Angle : 0.552 6.898 17182 Z= 0.286 Chirality : 0.043 0.173 1978 Planarity : 0.005 0.056 2183 Dihedral : 4.646 54.110 1694 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.02 % Allowed : 15.62 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1552 helix: 1.39 (0.21), residues: 713 sheet: -0.47 (0.35), residues: 245 loop : -1.72 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 364 HIS 0.008 0.001 HIS A 146 PHE 0.022 0.001 PHE C 35 TYR 0.024 0.001 TYR E 196 ARG 0.006 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 356 time to evaluate : 1.478 Fit side-chains REVERT: A 61 ARG cc_start: 0.7550 (mtt-85) cc_final: 0.7315 (mtt-85) REVERT: A 210 GLU cc_start: 0.7374 (tt0) cc_final: 0.7075 (tt0) REVERT: A 238 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6730 (tm-30) REVERT: A 319 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6743 (mm-30) REVERT: A 338 MET cc_start: 0.7271 (mmt) cc_final: 0.6913 (mmt) REVERT: C 170 PHE cc_start: 0.7659 (t80) cc_final: 0.7293 (t80) REVERT: D 23 ILE cc_start: 0.8747 (mt) cc_final: 0.8521 (mm) REVERT: D 76 LEU cc_start: 0.7603 (tt) cc_final: 0.6797 (tt) REVERT: D 77 ASP cc_start: 0.6656 (m-30) cc_final: 0.5038 (m-30) REVERT: D 79 GLU cc_start: 0.6835 (mp0) cc_final: 0.6324 (mp0) REVERT: D 116 MET cc_start: 0.7956 (mmm) cc_final: 0.7609 (mmm) REVERT: D 173 GLN cc_start: 0.7878 (mp10) cc_final: 0.7149 (mp10) REVERT: D 248 ILE cc_start: 0.7354 (pt) cc_final: 0.7066 (pt) REVERT: D 358 GLN cc_start: 0.7814 (tp40) cc_final: 0.7371 (tp-100) REVERT: D 359 LYS cc_start: 0.7772 (tttp) cc_final: 0.7206 (mtpp) REVERT: E 68 LYS cc_start: 0.7892 (tppp) cc_final: 0.7669 (ttmm) REVERT: E 171 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7694 (mt-10) REVERT: E 193 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7100 (tm-30) REVERT: E 196 TYR cc_start: 0.8069 (t80) cc_final: 0.7775 (t80) REVERT: E 247 TRP cc_start: 0.7970 (m100) cc_final: 0.7650 (m100) REVERT: E 311 ASP cc_start: 0.7779 (t0) cc_final: 0.7511 (t0) REVERT: E 328 ASN cc_start: 0.7935 (m-40) cc_final: 0.7662 (m-40) REVERT: E 339 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6946 (tm-30) outliers start: 41 outliers final: 30 residues processed: 375 average time/residue: 0.2909 time to fit residues: 149.7292 Evaluate side-chains 386 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 356 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 123 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN A 354 HIS D 291 HIS E 106 ASN E 174 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 12664 Z= 0.529 Angle : 0.726 8.807 17182 Z= 0.376 Chirality : 0.052 0.310 1978 Planarity : 0.006 0.056 2183 Dihedral : 5.289 51.675 1694 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.98 % Allowed : 16.14 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.22), residues: 1552 helix: 0.97 (0.20), residues: 700 sheet: -0.52 (0.35), residues: 251 loop : -1.96 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 364 HIS 0.010 0.002 HIS A 354 PHE 0.024 0.003 PHE D 101 TYR 0.031 0.003 TYR B 223 ARG 0.006 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 365 time to evaluate : 1.428 Fit side-chains REVERT: A 118 LYS cc_start: 0.8293 (mmtt) cc_final: 0.8026 (mmtt) REVERT: A 210 GLU cc_start: 0.7342 (tt0) cc_final: 0.7044 (tt0) REVERT: A 238 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6803 (tm-30) REVERT: A 240 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7526 (ttpp) REVERT: A 320 ARG cc_start: 0.7857 (ptt90) cc_final: 0.7503 (ptt90) REVERT: C 197 MET cc_start: 0.8093 (tpp) cc_final: 0.7629 (mmt) REVERT: D 76 LEU cc_start: 0.7580 (tt) cc_final: 0.6719 (tt) REVERT: D 77 ASP cc_start: 0.6576 (m-30) cc_final: 0.5009 (m-30) REVERT: D 79 GLU cc_start: 0.6819 (mp0) cc_final: 0.6305 (mp0) REVERT: D 116 MET cc_start: 0.7969 (mmm) cc_final: 0.7653 (mmm) REVERT: D 173 GLN cc_start: 0.8063 (mp10) cc_final: 0.7819 (mt0) REVERT: D 242 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7410 (tt) REVERT: D 248 ILE cc_start: 0.7449 (pt) cc_final: 0.7223 (pt) REVERT: D 253 MET cc_start: 0.7812 (tmm) cc_final: 0.7257 (tmm) REVERT: D 298 ASP cc_start: 0.8016 (m-30) cc_final: 0.7624 (m-30) REVERT: D 358 GLN cc_start: 0.8116 (tp40) cc_final: 0.7616 (tp-100) REVERT: D 359 LYS cc_start: 0.7984 (tttp) cc_final: 0.7383 (mtpp) REVERT: E 59 TYR cc_start: 0.6799 (m-10) cc_final: 0.6359 (m-10) REVERT: E 98 LYS cc_start: 0.7406 (mmpt) cc_final: 0.7180 (mmtt) REVERT: E 171 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7739 (mt-10) REVERT: E 193 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7166 (tm-30) REVERT: E 247 TRP cc_start: 0.7735 (m100) cc_final: 0.7381 (m100) REVERT: E 311 ASP cc_start: 0.7937 (t0) cc_final: 0.7637 (t0) REVERT: E 328 ASN cc_start: 0.7914 (m-40) cc_final: 0.7681 (m-40) REVERT: E 339 GLU cc_start: 0.7307 (tm-30) cc_final: 0.6957 (tm-30) outliers start: 54 outliers final: 43 residues processed: 389 average time/residue: 0.2922 time to fit residues: 155.8765 Evaluate side-chains 392 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 348 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 40 ASP Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 48 SER Chi-restraints excluded: chain C residue 51 MET Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 147 GLN Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 241 ASN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 246 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 50 optimal weight: 0.0020 chunk 134 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 149 optimal weight: 0.8980 chunk 123 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 overall best weight: 0.2906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN E 106 ASN E 174 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12664 Z= 0.148 Angle : 0.553 7.268 17182 Z= 0.289 Chirality : 0.043 0.165 1978 Planarity : 0.005 0.053 2183 Dihedral : 4.755 54.265 1694 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.46 % Allowed : 17.91 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1552 helix: 1.40 (0.20), residues: 716 sheet: -0.53 (0.34), residues: 263 loop : -1.71 (0.24), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 364 HIS 0.005 0.001 HIS A 354 PHE 0.023 0.001 PHE C 35 TYR 0.012 0.001 TYR E 77 ARG 0.007 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 1.379 Fit side-chains REVERT: A 210 GLU cc_start: 0.7335 (tt0) cc_final: 0.7055 (tt0) REVERT: A 261 ARG cc_start: 0.7883 (mtp-110) cc_final: 0.7493 (ttt90) REVERT: A 338 MET cc_start: 0.7262 (mmt) cc_final: 0.6943 (mmt) REVERT: C 52 ASN cc_start: 0.7238 (t0) cc_final: 0.6996 (t0) REVERT: C 170 PHE cc_start: 0.7796 (t80) cc_final: 0.7478 (t80) REVERT: D 79 GLU cc_start: 0.6788 (mp0) cc_final: 0.6253 (mp0) REVERT: D 173 GLN cc_start: 0.7904 (mp10) cc_final: 0.7414 (mt0) REVERT: D 184 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7237 (mptt) REVERT: D 242 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7248 (tt) REVERT: D 248 ILE cc_start: 0.7343 (pt) cc_final: 0.5074 (mt) REVERT: D 253 MET cc_start: 0.7604 (tmm) cc_final: 0.7052 (tmt) REVERT: D 358 GLN cc_start: 0.7863 (tp40) cc_final: 0.7394 (tp-100) REVERT: D 359 LYS cc_start: 0.7769 (tttp) cc_final: 0.7205 (ttmm) REVERT: D 365 VAL cc_start: 0.8637 (p) cc_final: 0.8405 (t) REVERT: E 42 LEU cc_start: 0.8159 (tt) cc_final: 0.7941 (tt) REVERT: E 52 ILE cc_start: 0.7921 (mm) cc_final: 0.7716 (tt) REVERT: E 171 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7691 (mt-10) REVERT: E 193 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7179 (tm-30) REVERT: E 247 TRP cc_start: 0.8007 (m100) cc_final: 0.7651 (m100) REVERT: E 311 ASP cc_start: 0.7836 (t0) cc_final: 0.7565 (t0) REVERT: E 339 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6909 (tm-30) outliers start: 47 outliers final: 30 residues processed: 380 average time/residue: 0.2898 time to fit residues: 150.9363 Evaluate side-chains 397 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 366 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 118 LYS Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 0.0070 chunk 83 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 106 ASN E 174 GLN E 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12664 Z= 0.175 Angle : 0.559 6.864 17182 Z= 0.290 Chirality : 0.043 0.160 1978 Planarity : 0.005 0.051 2183 Dihedral : 4.603 54.524 1694 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.24 % Allowed : 18.94 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1552 helix: 1.51 (0.20), residues: 723 sheet: -0.46 (0.34), residues: 262 loop : -1.69 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 364 HIS 0.005 0.001 HIS A 354 PHE 0.026 0.001 PHE C 35 TYR 0.012 0.001 TYR D 98 ARG 0.006 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 371 time to evaluate : 1.430 Fit side-chains REVERT: A 186 MET cc_start: 0.8498 (mtp) cc_final: 0.7765 (mtp) REVERT: A 210 GLU cc_start: 0.7331 (tt0) cc_final: 0.7037 (tt0) REVERT: A 234 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7650 (mt-10) REVERT: A 338 MET cc_start: 0.7289 (mmt) cc_final: 0.6969 (mmt) REVERT: B 137 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 52 ASN cc_start: 0.7252 (t0) cc_final: 0.6997 (t0) REVERT: C 170 PHE cc_start: 0.7788 (t80) cc_final: 0.7482 (t80) REVERT: D 76 LEU cc_start: 0.7560 (tt) cc_final: 0.6629 (tt) REVERT: D 77 ASP cc_start: 0.6476 (m-30) cc_final: 0.4941 (m-30) REVERT: D 79 GLU cc_start: 0.6831 (mp0) cc_final: 0.6292 (mp0) REVERT: D 116 MET cc_start: 0.7912 (mmm) cc_final: 0.7611 (mmm) REVERT: D 173 GLN cc_start: 0.7888 (mp10) cc_final: 0.7362 (mt0) REVERT: D 184 LYS cc_start: 0.7405 (mmtm) cc_final: 0.7192 (mmtm) REVERT: D 242 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7248 (tt) REVERT: D 253 MET cc_start: 0.7610 (tmm) cc_final: 0.7035 (tmt) REVERT: D 358 GLN cc_start: 0.7822 (tp40) cc_final: 0.7382 (tp-100) REVERT: D 365 VAL cc_start: 0.8650 (p) cc_final: 0.8413 (t) REVERT: E 42 LEU cc_start: 0.8194 (tt) cc_final: 0.7978 (tt) REVERT: E 61 SER cc_start: 0.8132 (t) cc_final: 0.7687 (p) REVERT: E 193 GLU cc_start: 0.7665 (tm-30) cc_final: 0.7184 (tm-30) REVERT: E 311 ASP cc_start: 0.7843 (t0) cc_final: 0.7567 (t0) REVERT: E 339 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6919 (tm-30) outliers start: 44 outliers final: 36 residues processed: 388 average time/residue: 0.3073 time to fit residues: 165.9497 Evaluate side-chains 403 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 365 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 87 GLU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 60 GLU Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 106 ASN E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12664 Z= 0.192 Angle : 0.574 8.327 17182 Z= 0.296 Chirality : 0.044 0.154 1978 Planarity : 0.005 0.050 2183 Dihedral : 4.608 54.455 1694 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.39 % Allowed : 19.09 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1552 helix: 1.60 (0.20), residues: 718 sheet: -0.46 (0.34), residues: 264 loop : -1.65 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 364 HIS 0.004 0.001 HIS A 354 PHE 0.031 0.001 PHE C 35 TYR 0.016 0.001 TYR E 77 ARG 0.007 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 374 time to evaluate : 1.243 Fit side-chains REVERT: A 68 THR cc_start: 0.8088 (m) cc_final: 0.7824 (t) REVERT: A 210 GLU cc_start: 0.7334 (tt0) cc_final: 0.7037 (tt0) REVERT: A 234 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 261 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7474 (ttt90) REVERT: A 338 MET cc_start: 0.7308 (mmt) cc_final: 0.6995 (mmt) REVERT: C 52 ASN cc_start: 0.7243 (t0) cc_final: 0.6973 (t0) REVERT: C 170 PHE cc_start: 0.7788 (t80) cc_final: 0.7463 (t80) REVERT: C 197 MET cc_start: 0.7767 (tpp) cc_final: 0.7339 (mmt) REVERT: D 76 LEU cc_start: 0.7550 (tt) cc_final: 0.6628 (tt) REVERT: D 77 ASP cc_start: 0.6463 (m-30) cc_final: 0.4938 (m-30) REVERT: D 79 GLU cc_start: 0.6808 (mp0) cc_final: 0.6285 (mp0) REVERT: D 173 GLN cc_start: 0.7886 (mp10) cc_final: 0.7412 (mt0) REVERT: D 184 LYS cc_start: 0.7406 (mmtm) cc_final: 0.7151 (mmtm) REVERT: D 208 GLN cc_start: 0.7860 (mp10) cc_final: 0.7540 (mp10) REVERT: D 242 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7259 (tt) REVERT: D 253 MET cc_start: 0.7564 (tmm) cc_final: 0.6977 (tmt) REVERT: D 358 GLN cc_start: 0.7816 (tp40) cc_final: 0.7402 (tp-100) REVERT: D 365 VAL cc_start: 0.8656 (p) cc_final: 0.8427 (t) REVERT: E 42 LEU cc_start: 0.8232 (tt) cc_final: 0.7994 (tt) REVERT: E 63 GLU cc_start: 0.7514 (mp0) cc_final: 0.7178 (mp0) REVERT: E 193 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7186 (tm-30) REVERT: E 311 ASP cc_start: 0.7846 (t0) cc_final: 0.7568 (t0) REVERT: E 339 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6931 (tm-30) outliers start: 46 outliers final: 37 residues processed: 390 average time/residue: 0.2793 time to fit residues: 150.0340 Evaluate side-chains 408 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 370 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 106 ASN Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 142 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 0.0070 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12664 Z= 0.255 Angle : 0.604 8.105 17182 Z= 0.312 Chirality : 0.045 0.154 1978 Planarity : 0.005 0.050 2183 Dihedral : 4.713 53.688 1694 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.17 % Allowed : 19.38 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1552 helix: 1.57 (0.20), residues: 716 sheet: -0.44 (0.35), residues: 261 loop : -1.73 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 364 HIS 0.005 0.001 HIS A 354 PHE 0.020 0.001 PHE B 133 TYR 0.017 0.002 TYR E 77 ARG 0.006 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 376 time to evaluate : 1.414 Fit side-chains REVERT: A 68 THR cc_start: 0.8105 (m) cc_final: 0.7844 (t) REVERT: A 118 LYS cc_start: 0.8295 (mmtt) cc_final: 0.8038 (mmtt) REVERT: A 210 GLU cc_start: 0.7353 (tt0) cc_final: 0.7043 (tt0) REVERT: A 261 ARG cc_start: 0.7979 (mtp-110) cc_final: 0.7514 (ttt90) REVERT: A 320 ARG cc_start: 0.7755 (ptt90) cc_final: 0.7398 (ptt90) REVERT: A 338 MET cc_start: 0.7328 (mmt) cc_final: 0.7009 (mmt) REVERT: A 358 GLN cc_start: 0.8173 (tp-100) cc_final: 0.7707 (tp40) REVERT: C 170 PHE cc_start: 0.7781 (t80) cc_final: 0.7483 (t80) REVERT: C 197 MET cc_start: 0.7812 (tpp) cc_final: 0.7317 (mmt) REVERT: D 76 LEU cc_start: 0.7566 (tt) cc_final: 0.6639 (tt) REVERT: D 77 ASP cc_start: 0.6456 (m-30) cc_final: 0.4931 (m-30) REVERT: D 79 GLU cc_start: 0.6811 (mp0) cc_final: 0.6278 (mp0) REVERT: D 173 GLN cc_start: 0.7969 (mp10) cc_final: 0.7491 (mt0) REVERT: D 184 LYS cc_start: 0.7433 (mmtm) cc_final: 0.7178 (mmtm) REVERT: D 208 GLN cc_start: 0.7876 (mp10) cc_final: 0.7547 (mp10) REVERT: D 242 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7272 (tt) REVERT: D 253 MET cc_start: 0.7574 (tmm) cc_final: 0.7008 (tmt) REVERT: D 358 GLN cc_start: 0.7839 (tp40) cc_final: 0.7425 (tp-100) REVERT: D 365 VAL cc_start: 0.8669 (p) cc_final: 0.8432 (t) REVERT: E 42 LEU cc_start: 0.8279 (tt) cc_final: 0.8018 (tt) REVERT: E 98 LYS cc_start: 0.7410 (mmpt) cc_final: 0.7139 (mmtt) REVERT: E 193 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7221 (tm-30) REVERT: E 196 TYR cc_start: 0.8188 (t80) cc_final: 0.7898 (t80) REVERT: E 311 ASP cc_start: 0.7865 (t0) cc_final: 0.7579 (t0) REVERT: E 339 GLU cc_start: 0.7288 (tm-30) cc_final: 0.6943 (tm-30) outliers start: 43 outliers final: 38 residues processed: 391 average time/residue: 0.2853 time to fit residues: 152.5139 Evaluate side-chains 411 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 372 time to evaluate : 1.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 101 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 97 optimal weight: 0.0050 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN E 106 ASN E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12664 Z= 0.190 Angle : 0.579 8.202 17182 Z= 0.299 Chirality : 0.043 0.154 1978 Planarity : 0.005 0.051 2183 Dihedral : 4.628 53.879 1694 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.17 % Allowed : 19.97 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.22), residues: 1552 helix: 1.66 (0.20), residues: 719 sheet: -0.44 (0.35), residues: 261 loop : -1.66 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 364 HIS 0.005 0.001 HIS A 354 PHE 0.021 0.001 PHE B 133 TYR 0.017 0.001 TYR E 77 ARG 0.007 0.000 ARG A 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3104 Ramachandran restraints generated. 1552 Oldfield, 0 Emsley, 1552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 1.566 Fit side-chains REVERT: A 68 THR cc_start: 0.8072 (m) cc_final: 0.7819 (t) REVERT: A 186 MET cc_start: 0.8404 (mtp) cc_final: 0.7763 (mtp) REVERT: A 210 GLU cc_start: 0.7356 (tt0) cc_final: 0.7070 (tt0) REVERT: A 261 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7619 (ttt90) REVERT: A 338 MET cc_start: 0.7319 (mmt) cc_final: 0.7010 (mmt) REVERT: A 358 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7706 (tp40) REVERT: B 226 ASP cc_start: 0.7937 (t0) cc_final: 0.7732 (m-30) REVERT: C 170 PHE cc_start: 0.7774 (t80) cc_final: 0.7476 (t80) REVERT: D 76 LEU cc_start: 0.7562 (tt) cc_final: 0.6662 (tt) REVERT: D 77 ASP cc_start: 0.6462 (m-30) cc_final: 0.4918 (m-30) REVERT: D 79 GLU cc_start: 0.6834 (mp0) cc_final: 0.6244 (mp0) REVERT: D 173 GLN cc_start: 0.7916 (mp10) cc_final: 0.7667 (mt0) REVERT: D 184 LYS cc_start: 0.7391 (mmtm) cc_final: 0.7132 (mmtm) REVERT: D 208 GLN cc_start: 0.7861 (mp10) cc_final: 0.7542 (mp10) REVERT: D 242 LEU cc_start: 0.7564 (OUTLIER) cc_final: 0.7250 (tt) REVERT: D 253 MET cc_start: 0.7558 (tmm) cc_final: 0.6912 (tmt) REVERT: D 358 GLN cc_start: 0.7775 (tp40) cc_final: 0.7385 (tp-100) REVERT: D 365 VAL cc_start: 0.8644 (p) cc_final: 0.8426 (t) REVERT: E 42 LEU cc_start: 0.8246 (tt) cc_final: 0.7966 (tt) REVERT: E 193 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7193 (tm-30) REVERT: E 311 ASP cc_start: 0.7854 (t0) cc_final: 0.7572 (t0) REVERT: E 339 GLU cc_start: 0.7295 (tm-30) cc_final: 0.6946 (tm-30) outliers start: 43 outliers final: 40 residues processed: 394 average time/residue: 0.2828 time to fit residues: 152.8077 Evaluate side-chains 417 residues out of total 1357 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 376 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 302 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 168 SER Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 185 GLN Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 160 LYS Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 310 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 106 ASN E 174 GLN ** E 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.106786 restraints weight = 17908.655| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.06 r_work: 0.3252 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12664 Z= 0.250 Angle : 0.606 8.282 17182 Z= 0.313 Chirality : 0.045 0.153 1978 Planarity : 0.005 0.050 2183 Dihedral : 4.717 53.246 1694 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.17 % Allowed : 19.97 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.22), residues: 1552 helix: 1.64 (0.20), residues: 714 sheet: -0.42 (0.34), residues: 271 loop : -1.73 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 364 HIS 0.005 0.001 HIS A 354 PHE 0.026 0.002 PHE C 35 TYR 0.018 0.001 TYR B 223 ARG 0.007 0.000 ARG A 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.65 seconds wall clock time: 62 minutes 4.40 seconds (3724.40 seconds total)