Starting phenix.real_space_refine on Sat Jun 7 04:21:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992.map" model { file = "/net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ego_47992/06_2025/9ego_47992_neut.cif" } resolution = 3.2 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= 0.081 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: 5 Type Number sf(0) Gaussians S 61 5.16 5 C 5416 2.51 5 N 1454 2.21 5 O 1535 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8469 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1659 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 63 Chain: "B" Number of atoms: 2573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2573 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 438 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2018 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 124 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "S" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1751 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'YVF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.63 Number of scatterers: 8469 At special positions: 0 Unit cell: (106.512, 120.998, 109.069, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 61 16.00 F 3 9.00 O 1535 8.00 N 1454 7.00 C 5416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 938.4 milliseconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 26.7% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 13 through 24 removed outlier: 3.706A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASN A 22 " --> pdb=" O MET A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.857A pdb=" N THR A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.669A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.541A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.660A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.623A pdb=" N LYS A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.672A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.784A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N CYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN A 306 " --> pdb=" O TYR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.918A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 4.183A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.841A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 35' Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.527A pdb=" N VAL C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.612A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA C 39 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 133 Processing helix chain 'R' and resid 136 through 140 Processing helix chain 'R' and resid 153 through 161 removed outlier: 4.286A pdb=" N LEU R 159 " --> pdb=" O PHE R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 removed outlier: 3.750A pdb=" N GLY R 166 " --> pdb=" O ALA R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 178 removed outlier: 3.876A pdb=" N HIS R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 189 through 194 Processing helix chain 'R' and resid 204 through 214 removed outlier: 3.588A pdb=" N THR R 210 " --> pdb=" O SER R 206 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA R 211 " --> pdb=" O LEU R 207 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG R 214 " --> pdb=" O THR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 233 Processing helix chain 'R' and resid 235 through 239 removed outlier: 3.764A pdb=" N LEU R 239 " --> pdb=" O ALA R 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 275 through 284 removed outlier: 3.873A pdb=" N GLY R 281 " --> pdb=" O MET R 277 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL R 282 " --> pdb=" O PHE R 278 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 311 removed outlier: 4.839A pdb=" N HIS R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ALA R 305 " --> pdb=" O ALA R 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL R 306 " --> pdb=" O HIS R 302 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG R 307 " --> pdb=" O SER R 303 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET R 308 " --> pdb=" O HIS R 304 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE R 309 " --> pdb=" O ALA R 305 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ARG R 311 " --> pdb=" O ARG R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 351 removed outlier: 3.725A pdb=" N VAL R 350 " --> pdb=" O LEU R 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 358 through 368 removed outlier: 3.858A pdb=" N MET R 363 " --> pdb=" O LEU R 359 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL R 364 " --> pdb=" O LEU R 360 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP R 366 " --> pdb=" O ILE R 362 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL R 367 " --> pdb=" O MET R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 383 Processing helix chain 'R' and resid 384 through 386 No H-bonds generated for 'chain 'R' and resid 384 through 386' Processing helix chain 'R' and resid 392 through 397 Processing helix chain 'R' and resid 402 through 407 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.629A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.915A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.083A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.561A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.160A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.801A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.949A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.943A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.542A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.581A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.919A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN S 39 " --> pdb=" O MET S 93 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 129 removed outlier: 3.578A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE S 200 " --> pdb=" O CYS S 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 135 through 136 removed outlier: 5.855A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR S 216 " --> pdb=" O PHE S 165 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU S 162 " --> pdb=" O ARG S 179 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG S 179 " --> pdb=" O LEU S 162 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG S 179 " --> pdb=" O ASN S 182 " (cutoff:3.500A) 231 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1338 1.31 - 1.44: 2421 1.44 - 1.57: 4794 1.57 - 1.69: 5 1.69 - 1.82: 87 Bond restraints: 8645 Sorted by residual: bond pdb=" C05 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.722 1.612 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C12 YVF R 501 " pdb=" N11 YVF R 501 " ideal model delta sigma weight residual 1.345 1.449 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C06 YVF R 501 " pdb=" C07 YVF R 501 " ideal model delta sigma weight residual 1.420 1.523 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C08 YVF R 501 " pdb=" S09 YVF R 501 " ideal model delta sigma weight residual 1.710 1.613 0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C03 YVF R 501 " pdb=" O02 YVF R 501 " ideal model delta sigma weight residual 1.318 1.399 -0.081 2.00e-02 2.50e+03 1.66e+01 ... (remaining 8640 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 11364 2.71 - 5.42: 311 5.42 - 8.13: 42 8.13 - 10.83: 14 10.83 - 13.54: 4 Bond angle restraints: 11735 Sorted by residual: angle pdb=" N ILE R 395 " pdb=" CA ILE R 395 " pdb=" C ILE R 395 " ideal model delta sigma weight residual 113.71 105.19 8.52 9.50e-01 1.11e+00 8.04e+01 angle pdb=" N VAL R 196 " pdb=" CA VAL R 196 " pdb=" C VAL R 196 " ideal model delta sigma weight residual 113.71 106.33 7.38 9.50e-01 1.11e+00 6.03e+01 angle pdb=" C SER A 293 " pdb=" N ASN A 294 " pdb=" CA ASN A 294 " ideal model delta sigma weight residual 123.93 134.84 -10.91 1.54e+00 4.22e-01 5.01e+01 angle pdb=" N VAL R 350 " pdb=" CA VAL R 350 " pdb=" C VAL R 350 " ideal model delta sigma weight residual 113.47 106.72 6.75 1.01e+00 9.80e-01 4.46e+01 angle pdb=" N VAL R 246 " pdb=" CA VAL R 246 " pdb=" C VAL R 246 " ideal model delta sigma weight residual 113.20 107.17 6.03 9.60e-01 1.09e+00 3.94e+01 ... (remaining 11730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 4832 16.81 - 33.62: 213 33.62 - 50.44: 42 50.44 - 67.25: 5 67.25 - 84.06: 8 Dihedral angle restraints: 5100 sinusoidal: 1884 harmonic: 3216 Sorted by residual: dihedral pdb=" CA VAL R 179 " pdb=" C VAL R 179 " pdb=" N PHE R 180 " pdb=" CA PHE R 180 " ideal model delta harmonic sigma weight residual 180.00 -139.56 -40.44 0 5.00e+00 4.00e-02 6.54e+01 dihedral pdb=" CA ARG R 311 " pdb=" C ARG R 311 " pdb=" N GLY R 312 " pdb=" CA GLY R 312 " ideal model delta harmonic sigma weight residual -180.00 -144.25 -35.75 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA GLY S 26 " pdb=" C GLY S 26 " pdb=" N PHE S 27 " pdb=" CA PHE S 27 " ideal model delta harmonic sigma weight residual 180.00 145.25 34.75 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 5097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1261 0.107 - 0.214: 90 0.214 - 0.321: 8 0.321 - 0.428: 0 0.428 - 0.535: 1 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB ILE S 100 " pdb=" CA ILE S 100 " pdb=" CG1 ILE S 100 " pdb=" CG2 ILE S 100 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.54 2.00e-01 2.50e+01 7.17e+00 chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB ILE R 354 " pdb=" CA ILE R 354 " pdb=" CG1 ILE R 354 " pdb=" CG2 ILE R 354 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1357 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 357 " 0.049 5.00e-02 4.00e+02 7.36e-02 8.66e+00 pdb=" N PRO R 358 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO R 358 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 358 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 223 " -0.036 2.00e-02 2.50e+03 2.03e-02 8.21e+00 pdb=" CG TYR S 223 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR S 223 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR S 223 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR S 223 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 223 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR S 223 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR S 223 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 393 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO R 394 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO R 394 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 394 " 0.039 5.00e-02 4.00e+02 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 19 2.45 - 3.06: 4574 3.06 - 3.67: 11534 3.67 - 4.29: 16395 4.29 - 4.90: 28575 Nonbonded interactions: 61097 Sorted by model distance: nonbonded pdb=" OD2 ASP A 337 " pdb=" NH2 ARG R 311 " model vdw 1.837 3.120 nonbonded pdb=" O LEU A 39 " pdb=" NZ LYS A 46 " model vdw 2.122 3.120 nonbonded pdb=" ND1 HIS R 302 " pdb=" OD2 ASP R 338 " model vdw 2.129 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP B 254 " pdb=" N ALA B 257 " model vdw 2.272 3.120 ... (remaining 61092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 67.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.190 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 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 : 0.008 0.123 8646 Z= 0.337 Angle : 1.127 13.543 11737 Z= 0.627 Chirality : 0.063 0.535 1360 Planarity : 0.008 0.074 1471 Dihedral : 11.249 84.059 3019 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.93 % Rotamer: Outliers : 0.34 % Allowed : 2.97 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -4.60 (0.21), residues: 1088 helix: -5.18 (0.07), residues: 323 sheet: -1.02 (0.32), residues: 259 loop : -2.58 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP B 339 HIS 0.014 0.003 HIS B 183 PHE 0.031 0.003 PHE S 165 TYR 0.042 0.004 TYR S 163 ARG 0.023 0.002 ARG R 226 Details of bonding type rmsd hydrogen bonds : bond 0.33732 ( 231) hydrogen bonds : angle 9.88197 ( 627) SS BOND : bond 0.01454 ( 1) SS BOND : angle 0.74676 ( 2) covalent geometry : bond 0.00767 ( 8645) covalent geometry : angle 1.12691 (11735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 175 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: B 44 GLN cc_start: 0.8003 (tt0) cc_final: 0.7735 (tt0) REVERT: R 300 LYS cc_start: 0.7820 (tppt) cc_final: 0.7445 (mmmt) REVERT: S 190 ARG cc_start: 0.7133 (ptt-90) cc_final: 0.6914 (ptt90) REVERT: S 194 SER cc_start: 0.8200 (t) cc_final: 0.7998 (p) outliers start: 3 outliers final: 0 residues processed: 178 average time/residue: 0.3269 time to fit residues: 72.6132 Evaluate side-chains 113 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.0970 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 88 ASN B 175 GLN R 154 HIS R 389 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.137126 restraints weight = 10157.497| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.85 r_work: 0.3211 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8646 Z= 0.119 Angle : 0.608 10.704 11737 Z= 0.329 Chirality : 0.043 0.208 1360 Planarity : 0.005 0.060 1471 Dihedral : 8.507 81.426 1226 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 1.71 % Allowed : 7.42 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.44 (0.22), residues: 1088 helix: -3.80 (0.19), residues: 318 sheet: -0.59 (0.31), residues: 285 loop : -2.15 (0.24), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS B 54 PHE 0.026 0.002 PHE A 336 TYR 0.032 0.002 TYR S 223 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 231) hydrogen bonds : angle 5.28404 ( 627) SS BOND : bond 0.01013 ( 1) SS BOND : angle 0.62738 ( 2) covalent geometry : bond 0.00264 ( 8645) covalent geometry : angle 0.60812 (11735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.898 Fit side-chains REVERT: B 42 ARG cc_start: 0.7568 (ttt-90) cc_final: 0.6881 (ttt-90) REVERT: B 214 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7498 (mtm-85) REVERT: C 62 ARG cc_start: 0.7288 (ptt-90) cc_final: 0.7053 (ptt-90) REVERT: R 182 ARG cc_start: 0.6275 (mtp85) cc_final: 0.6055 (mtp85) REVERT: R 230 ARG cc_start: 0.5131 (tpp80) cc_final: 0.4915 (tpp80) REVERT: R 404 LEU cc_start: 0.7738 (mp) cc_final: 0.6545 (tt) REVERT: S 194 SER cc_start: 0.8143 (t) cc_final: 0.7597 (p) REVERT: S 207 LEU cc_start: 0.7792 (tt) cc_final: 0.7555 (tt) outliers start: 15 outliers final: 11 residues processed: 132 average time/residue: 0.2869 time to fit residues: 48.4640 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 280 ILE Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 226 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 98 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 66 optimal weight: 0.0970 chunk 31 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS A 256 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.125926 restraints weight = 10255.808| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.35 r_work: 0.3230 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8646 Z= 0.104 Angle : 0.554 7.612 11737 Z= 0.296 Chirality : 0.042 0.198 1360 Planarity : 0.004 0.053 1471 Dihedral : 7.830 76.760 1226 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.05 % Allowed : 8.79 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.24), residues: 1088 helix: -2.88 (0.25), residues: 324 sheet: -0.25 (0.30), residues: 283 loop : -1.81 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.015 0.001 PHE R 408 TYR 0.033 0.001 TYR S 223 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.03688 ( 231) hydrogen bonds : angle 4.59096 ( 627) SS BOND : bond 0.00977 ( 1) SS BOND : angle 0.41012 ( 2) covalent geometry : bond 0.00233 ( 8645) covalent geometry : angle 0.55372 (11735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.885 Fit side-chains REVERT: B 214 ARG cc_start: 0.7729 (mtm-85) cc_final: 0.7513 (mtm-85) REVERT: B 234 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.8326 (t80) REVERT: C 59 ASN cc_start: 0.7458 (t0) cc_final: 0.6916 (t0) REVERT: C 62 ARG cc_start: 0.7339 (ptt-90) cc_final: 0.7049 (ptt-90) REVERT: R 307 ARG cc_start: 0.6438 (mtp85) cc_final: 0.6196 (mtm180) REVERT: R 404 LEU cc_start: 0.7663 (mp) cc_final: 0.6506 (tt) REVERT: S 194 SER cc_start: 0.7998 (t) cc_final: 0.7528 (p) REVERT: S 207 LEU cc_start: 0.7857 (tt) cc_final: 0.7625 (tt) outliers start: 18 outliers final: 10 residues processed: 123 average time/residue: 0.2571 time to fit residues: 43.1308 Evaluate side-chains 112 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 183 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.0970 chunk 75 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS B 54 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.177618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.136338 restraints weight = 10174.496| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 3.29 r_work: 0.2998 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8646 Z= 0.106 Angle : 0.532 6.689 11737 Z= 0.285 Chirality : 0.042 0.200 1360 Planarity : 0.004 0.052 1471 Dihedral : 7.147 65.314 1226 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.51 % Allowed : 10.05 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.24), residues: 1088 helix: -2.43 (0.27), residues: 320 sheet: -0.06 (0.31), residues: 282 loop : -1.66 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE B 151 TYR 0.032 0.001 TYR S 223 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 231) hydrogen bonds : angle 4.44583 ( 627) SS BOND : bond 0.00996 ( 1) SS BOND : angle 0.42920 ( 2) covalent geometry : bond 0.00242 ( 8645) covalent geometry : angle 0.53211 (11735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.867 Fit side-chains REVERT: B 214 ARG cc_start: 0.7738 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: B 234 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8314 (t80) REVERT: C 59 ASN cc_start: 0.7494 (t0) cc_final: 0.7073 (t0) REVERT: C 62 ARG cc_start: 0.7377 (ptt-90) cc_final: 0.7089 (ptt-90) REVERT: R 153 TYR cc_start: 0.7294 (m-80) cc_final: 0.7080 (m-80) REVERT: R 404 LEU cc_start: 0.7466 (mp) cc_final: 0.6603 (tt) REVERT: S 194 SER cc_start: 0.7994 (t) cc_final: 0.7524 (p) REVERT: S 207 LEU cc_start: 0.7838 (tt) cc_final: 0.7606 (tt) outliers start: 22 outliers final: 17 residues processed: 112 average time/residue: 0.2063 time to fit residues: 32.1106 Evaluate side-chains 114 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 378 VAL Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 92 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 0.1980 chunk 63 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.141258 restraints weight = 10156.543| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.23 r_work: 0.3013 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8646 Z= 0.091 Angle : 0.495 6.625 11737 Z= 0.266 Chirality : 0.042 0.181 1360 Planarity : 0.004 0.052 1471 Dihedral : 5.641 39.818 1226 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.51 % Allowed : 10.62 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.97 (0.25), residues: 1088 helix: -2.10 (0.28), residues: 328 sheet: 0.12 (0.31), residues: 287 loop : -1.52 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.015 0.001 PHE S 27 TYR 0.031 0.001 TYR S 223 ARG 0.002 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02996 ( 231) hydrogen bonds : angle 4.16636 ( 627) SS BOND : bond 0.00837 ( 1) SS BOND : angle 0.32246 ( 2) covalent geometry : bond 0.00200 ( 8645) covalent geometry : angle 0.49515 (11735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 1.058 Fit side-chains REVERT: B 43 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8511 (mp) REVERT: B 214 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7540 (mtm-85) REVERT: B 219 ARG cc_start: 0.8148 (ttm110) cc_final: 0.7789 (mtt-85) REVERT: B 234 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.8382 (t80) REVERT: C 59 ASN cc_start: 0.7480 (t0) cc_final: 0.7241 (t0) REVERT: R 404 LEU cc_start: 0.7407 (mp) cc_final: 0.6668 (tt) REVERT: S 194 SER cc_start: 0.7984 (t) cc_final: 0.7514 (p) REVERT: S 207 LEU cc_start: 0.7824 (tt) cc_final: 0.7617 (tt) outliers start: 22 outliers final: 19 residues processed: 118 average time/residue: 0.2836 time to fit residues: 45.6390 Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 80 optimal weight: 0.0970 chunk 19 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.173462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.115479 restraints weight = 10143.626| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.21 r_work: 0.2997 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8646 Z= 0.133 Angle : 0.560 6.882 11737 Z= 0.299 Chirality : 0.043 0.214 1360 Planarity : 0.004 0.050 1471 Dihedral : 5.474 36.743 1226 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.08 % Allowed : 10.84 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.90 (0.25), residues: 1088 helix: -1.96 (0.28), residues: 325 sheet: 0.12 (0.31), residues: 287 loop : -1.52 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 213 PHE 0.019 0.002 PHE B 151 TYR 0.035 0.002 TYR S 223 ARG 0.002 0.000 ARG S 98 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 231) hydrogen bonds : angle 4.46761 ( 627) SS BOND : bond 0.01198 ( 1) SS BOND : angle 0.56421 ( 2) covalent geometry : bond 0.00315 ( 8645) covalent geometry : angle 0.55968 (11735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.899 Fit side-chains REVERT: A 8 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8462 (mm-30) REVERT: B 43 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8490 (mp) REVERT: B 234 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.8389 (t80) REVERT: C 59 ASN cc_start: 0.7312 (t0) cc_final: 0.7070 (t0) REVERT: R 345 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6871 (tt) REVERT: R 356 TRP cc_start: 0.8164 (m100) cc_final: 0.7942 (m100) REVERT: S 194 SER cc_start: 0.8017 (t) cc_final: 0.7448 (p) REVERT: S 207 LEU cc_start: 0.7855 (tt) cc_final: 0.7620 (tt) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.2331 time to fit residues: 40.4396 Evaluate side-chains 128 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 350 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 4 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 67 optimal weight: 0.0670 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 84 optimal weight: 0.9980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.174466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.133511 restraints weight = 10121.273| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.39 r_work: 0.3012 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8646 Z= 0.086 Angle : 0.488 6.549 11737 Z= 0.263 Chirality : 0.041 0.176 1360 Planarity : 0.003 0.041 1471 Dihedral : 5.081 40.557 1226 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.28 % Allowed : 11.64 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.25), residues: 1088 helix: -1.68 (0.28), residues: 333 sheet: 0.28 (0.31), residues: 282 loop : -1.48 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.001 PHE S 27 TYR 0.031 0.001 TYR S 223 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.02852 ( 231) hydrogen bonds : angle 4.08448 ( 627) SS BOND : bond 0.00780 ( 1) SS BOND : angle 0.33252 ( 2) covalent geometry : bond 0.00188 ( 8645) covalent geometry : angle 0.48809 (11735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.983 Fit side-chains REVERT: B 219 ARG cc_start: 0.8082 (ttm110) cc_final: 0.7739 (mtt-85) REVERT: B 234 PHE cc_start: 0.8660 (OUTLIER) cc_final: 0.8361 (t80) REVERT: R 345 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6904 (tt) REVERT: R 356 TRP cc_start: 0.8045 (m100) cc_final: 0.7838 (m100) REVERT: S 194 SER cc_start: 0.7953 (t) cc_final: 0.7460 (p) REVERT: S 207 LEU cc_start: 0.7855 (tt) cc_final: 0.7629 (tt) outliers start: 20 outliers final: 17 residues processed: 111 average time/residue: 0.2730 time to fit residues: 40.8382 Evaluate side-chains 117 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.175150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.117466 restraints weight = 10239.620| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.37 r_work: 0.3037 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8646 Z= 0.097 Angle : 0.499 6.382 11737 Z= 0.268 Chirality : 0.042 0.183 1360 Planarity : 0.003 0.044 1471 Dihedral : 5.075 40.354 1226 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.40 % Allowed : 11.76 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.25), residues: 1088 helix: -1.48 (0.29), residues: 333 sheet: 0.38 (0.31), residues: 281 loop : -1.41 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE S 27 TYR 0.030 0.001 TYR S 223 ARG 0.004 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 231) hydrogen bonds : angle 4.09754 ( 627) SS BOND : bond 0.00919 ( 1) SS BOND : angle 0.36898 ( 2) covalent geometry : bond 0.00219 ( 8645) covalent geometry : angle 0.49907 (11735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.908 Fit side-chains REVERT: B 219 ARG cc_start: 0.8229 (ttm110) cc_final: 0.7829 (mtt-85) REVERT: B 234 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8382 (t80) REVERT: C 62 ARG cc_start: 0.7214 (ptp90) cc_final: 0.6987 (ptt-90) REVERT: R 345 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7005 (tt) REVERT: S 194 SER cc_start: 0.7927 (t) cc_final: 0.7374 (p) REVERT: S 207 LEU cc_start: 0.7804 (tt) cc_final: 0.7550 (tt) outliers start: 21 outliers final: 18 residues processed: 111 average time/residue: 0.2505 time to fit residues: 37.5827 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 95 optimal weight: 0.4980 chunk 4 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 103 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.175016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.118650 restraints weight = 10242.121| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.35 r_work: 0.3022 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8646 Z= 0.096 Angle : 0.496 6.235 11737 Z= 0.265 Chirality : 0.042 0.178 1360 Planarity : 0.003 0.043 1471 Dihedral : 5.024 40.432 1226 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.40 % Allowed : 11.99 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1088 helix: -1.25 (0.29), residues: 333 sheet: 0.38 (0.31), residues: 282 loop : -1.32 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 213 PHE 0.016 0.001 PHE S 27 TYR 0.030 0.001 TYR S 223 ARG 0.004 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.02988 ( 231) hydrogen bonds : angle 4.07538 ( 627) SS BOND : bond 0.00904 ( 1) SS BOND : angle 0.36439 ( 2) covalent geometry : bond 0.00218 ( 8645) covalent geometry : angle 0.49560 (11735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.837 Fit side-chains REVERT: B 44 GLN cc_start: 0.8638 (mt0) cc_final: 0.8430 (mm-40) REVERT: B 219 ARG cc_start: 0.8251 (ttm110) cc_final: 0.7865 (mtt-85) REVERT: B 234 PHE cc_start: 0.8734 (OUTLIER) cc_final: 0.8402 (t80) REVERT: C 62 ARG cc_start: 0.7195 (ptp90) cc_final: 0.6976 (ptt-90) REVERT: R 345 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7062 (tt) REVERT: S 194 SER cc_start: 0.7927 (t) cc_final: 0.7361 (p) REVERT: S 207 LEU cc_start: 0.7817 (tt) cc_final: 0.7561 (tt) outliers start: 21 outliers final: 19 residues processed: 111 average time/residue: 0.2473 time to fit residues: 36.9728 Evaluate side-chains 118 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 26 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 0.0170 chunk 2 optimal weight: 0.5980 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.168586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.112897 restraints weight = 10162.935| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.30 r_work: 0.2929 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8646 Z= 0.207 Angle : 0.656 8.185 11737 Z= 0.348 Chirality : 0.047 0.248 1360 Planarity : 0.004 0.045 1471 Dihedral : 5.826 33.019 1226 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.74 % Allowed : 12.10 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.61 (0.25), residues: 1088 helix: -1.49 (0.29), residues: 331 sheet: 0.27 (0.32), residues: 280 loop : -1.49 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.006 0.002 HIS A 213 PHE 0.026 0.002 PHE B 151 TYR 0.039 0.002 TYR S 223 ARG 0.004 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.04702 ( 231) hydrogen bonds : angle 4.83865 ( 627) SS BOND : bond 0.01602 ( 1) SS BOND : angle 0.83337 ( 2) covalent geometry : bond 0.00506 ( 8645) covalent geometry : angle 0.65626 (11735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.908 Fit side-chains REVERT: A 8 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.6979 (mp0) REVERT: B 234 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.8355 (t80) REVERT: R 296 TYR cc_start: 0.7294 (t80) cc_final: 0.6846 (t80) REVERT: R 300 LYS cc_start: 0.6843 (tppt) cc_final: 0.6300 (mmmt) REVERT: R 345 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7154 (tt) REVERT: S 194 SER cc_start: 0.8073 (t) cc_final: 0.7445 (p) REVERT: S 207 LEU cc_start: 0.7838 (tt) cc_final: 0.7593 (tt) outliers start: 24 outliers final: 20 residues processed: 122 average time/residue: 0.3507 time to fit residues: 58.3902 Evaluate side-chains 124 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain R residue 109 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 345 LEU Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 351 VAL Chi-restraints excluded: chain R residue 384 MET Chi-restraints excluded: chain S residue 6 GLU Chi-restraints excluded: chain S residue 17 SER Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 156 SER Chi-restraints excluded: chain S residue 183 LEU Chi-restraints excluded: chain S residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 74 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 60 optimal weight: 0.0980 chunk 2 optimal weight: 0.0470 chunk 58 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 88 optimal weight: 0.7980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140573 restraints weight = 10256.883| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 3.08 r_work: 0.3093 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8646 Z= 0.087 Angle : 0.494 6.181 11737 Z= 0.266 Chirality : 0.042 0.174 1360 Planarity : 0.003 0.041 1471 Dihedral : 5.074 40.243 1226 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.94 % Allowed : 13.01 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.25), residues: 1088 helix: -1.10 (0.29), residues: 336 sheet: 0.37 (0.31), residues: 287 loop : -1.35 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 213 PHE 0.016 0.001 PHE S 27 TYR 0.031 0.001 TYR S 223 ARG 0.003 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.02726 ( 231) hydrogen bonds : angle 4.06207 ( 627) SS BOND : bond 0.00697 ( 1) SS BOND : angle 0.33176 ( 2) covalent geometry : bond 0.00183 ( 8645) covalent geometry : angle 0.49391 (11735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6227.26 seconds wall clock time: 111 minutes 45.19 seconds (6705.19 seconds total)