Starting phenix.real_space_refine on Wed Nov 19 08:00:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024.map" model { file = "/net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ebk_9024/11_2025/6ebk_9024_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 12 5.49 5 S 120 5.16 5 C 14240 2.51 5 N 3728 2.21 5 O 4112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22212 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "B" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 7, 'ASP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 7, 'ASP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "F" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 7, 'ASP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "G" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "H" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2925 Classifications: {'peptide': 387} Incomplete info: {'backbone_only': 11, 'truncation_to_alanine': 53} Link IDs: {'PTRANS': 19, 'TRANS': 367} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4, 'ASN:plan1': 4, 'GLN:plan1': 7, 'ASP:plan': 3, 'HIS:plan': 2, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 159 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.46, per 1000 atoms: 0.25 Number of scatterers: 22212 At special positions: 0 Unit cell: (131.095, 131.095, 161.99, 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 120 16.00 P 12 15.00 O 4112 8.00 N 3728 7.00 C 14240 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: 1.81 Conformation dependent library (CDL) restraints added in 1.1 seconds 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5208 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 12 sheets defined 59.7% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.543A pdb=" N ALA A 92 " --> pdb=" O VAL A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.793A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.680A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.501A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 236 removed outlier: 4.140A pdb=" N GLU A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.723A pdb=" N ASP A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 257 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.513A pdb=" N LYS A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 299 removed outlier: 3.520A pdb=" N GLN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.674A pdb=" N VAL A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.973A pdb=" N ARG B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.845A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.644A pdb=" N GLU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.821A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.576A pdb=" N LEU B 152 " --> pdb=" O GLN B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA B 166 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 210 removed outlier: 4.159A pdb=" N GLN B 207 " --> pdb=" O HIS B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 removed outlier: 3.660A pdb=" N CYS B 229 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL B 239 " --> pdb=" O PHE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.713A pdb=" N PHE B 250 " --> pdb=" O LYS B 247 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE B 251 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 253 through 276 removed outlier: 3.536A pdb=" N ILE B 257 " --> pdb=" O ASN B 253 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP B 259 " --> pdb=" O MET B 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.713A pdb=" N ASN B 276 " --> pdb=" O LEU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.658A pdb=" N ILE B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.959A pdb=" N GLN B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 346 removed outlier: 3.683A pdb=" N LEU B 327 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 345 " --> pdb=" O ALA B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 369 removed outlier: 3.820A pdb=" N TRP B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 365 " --> pdb=" O PHE B 361 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 399 removed outlier: 3.514A pdb=" N ILE B 385 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 389 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 414 removed outlier: 3.502A pdb=" N ILE B 405 " --> pdb=" O PRO B 401 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 417 No H-bonds generated for 'chain 'B' and resid 415 through 417' Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.544A pdb=" N ALA C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.789A pdb=" N VAL C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.502A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 227 through 236 removed outlier: 4.009A pdb=" N GLU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.728A pdb=" N ASP C 256 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 258 " --> pdb=" O TYR C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 258' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.533A pdb=" N LYS C 274 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 299 removed outlier: 3.560A pdb=" N GLN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.661A pdb=" N VAL C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 64 through 67 removed outlier: 3.967A pdb=" N ARG D 67 " --> pdb=" O LYS D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.847A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.640A pdb=" N GLU D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.814A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 153 removed outlier: 3.559A pdb=" N LEU D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 184 removed outlier: 3.789A pdb=" N ALA D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N THR D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 210 removed outlier: 4.222A pdb=" N GLN D 207 " --> pdb=" O HIS D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 removed outlier: 3.644A pdb=" N CYS D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE D 230 " --> pdb=" O GLU D 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL D 239 " --> pdb=" O PHE D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 252 removed outlier: 3.668A pdb=" N PHE D 250 " --> pdb=" O LYS D 247 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 251 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 276 removed outlier: 3.588A pdb=" N ILE D 257 " --> pdb=" O ASN D 253 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP D 259 " --> pdb=" O MET D 255 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Proline residue: D 265 - end of helix removed outlier: 3.710A pdb=" N ASN D 276 " --> pdb=" O LEU D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.676A pdb=" N ILE D 294 " --> pdb=" O GLN D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.929A pdb=" N GLN D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 346 removed outlier: 3.703A pdb=" N LEU D 327 " --> pdb=" O GLU D 323 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 336 " --> pdb=" O PHE D 332 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA D 345 " --> pdb=" O ALA D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 369 removed outlier: 3.813A pdb=" N TRP D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL D 365 " --> pdb=" O PHE D 361 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR D 369 " --> pdb=" O VAL D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 399 removed outlier: 3.503A pdb=" N ILE D 385 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 389 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS D 390 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 391 " --> pdb=" O GLY D 387 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE D 392 " --> pdb=" O SER D 388 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 414 removed outlier: 3.506A pdb=" N ILE D 405 " --> pdb=" O PRO D 401 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.543A pdb=" N ALA E 92 " --> pdb=" O VAL E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.790A pdb=" N VAL E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG E 129 " --> pdb=" O GLU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 227 through 236 removed outlier: 4.054A pdb=" N GLU E 231 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.728A pdb=" N ASP E 256 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER E 257 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 258 " --> pdb=" O TYR E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 258' Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.532A pdb=" N LYS E 274 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 299 removed outlier: 3.561A pdb=" N GLN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 310 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.660A pdb=" N VAL E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 64 through 67 removed outlier: 3.969A pdb=" N ARG F 67 " --> pdb=" O LYS F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.844A pdb=" N TYR F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.637A pdb=" N GLU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.767A pdb=" N GLU F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 153 removed outlier: 3.532A pdb=" N TRP F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 184 removed outlier: 3.822A pdb=" N ALA F 166 " --> pdb=" O ALA F 162 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU F 174 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU F 183 " --> pdb=" O SER F 179 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR F 184 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 210 removed outlier: 4.082A pdb=" N GLN F 207 " --> pdb=" O HIS F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 243 removed outlier: 3.774A pdb=" N CYS F 229 " --> pdb=" O VAL F 225 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE F 230 " --> pdb=" O GLU F 226 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 239 " --> pdb=" O PHE F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 252 removed outlier: 3.651A pdb=" N PHE F 250 " --> pdb=" O LYS F 247 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE F 251 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 252 " --> pdb=" O GLY F 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 247 through 252' Processing helix chain 'F' and resid 253 through 275 removed outlier: 3.548A pdb=" N ILE F 257 " --> pdb=" O ASN F 253 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP F 259 " --> pdb=" O MET F 255 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) Proline residue: F 265 - end of helix Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.628A pdb=" N ILE F 294 " --> pdb=" O GLN F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 306 Processing helix chain 'F' and resid 307 through 319 removed outlier: 3.924A pdb=" N GLN F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 346 removed outlier: 3.640A pdb=" N LEU F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE F 336 " --> pdb=" O PHE F 332 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 345 " --> pdb=" O ALA F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 369 removed outlier: 3.817A pdb=" N TRP F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 365 " --> pdb=" O PHE F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 399 removed outlier: 3.566A pdb=" N LEU F 389 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS F 390 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 391 " --> pdb=" O GLY F 387 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 414 removed outlier: 3.515A pdb=" N ILE F 405 " --> pdb=" O PRO F 401 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.544A pdb=" N ALA G 92 " --> pdb=" O VAL G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 93 through 106 removed outlier: 3.791A pdb=" N VAL G 97 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 125 through 129 removed outlier: 3.865A pdb=" N ARG G 129 " --> pdb=" O GLU G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.500A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 227 through 236 removed outlier: 4.011A pdb=" N GLU G 231 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 removed outlier: 3.722A pdb=" N ASP G 256 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY G 258 " --> pdb=" O TYR G 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 258' Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.533A pdb=" N LYS G 274 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 299 removed outlier: 3.521A pdb=" N GLN G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.663A pdb=" N VAL G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.970A pdb=" N ARG H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.844A pdb=" N TYR H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 114 removed outlier: 3.638A pdb=" N GLU H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 131 removed outlier: 3.800A pdb=" N GLU H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 153 removed outlier: 3.513A pdb=" N TRP H 150 " --> pdb=" O GLN H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 184 removed outlier: 3.814A pdb=" N ALA H 166 " --> pdb=" O ALA H 162 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 174 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU H 183 " --> pdb=" O SER H 179 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR H 184 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 210 removed outlier: 3.987A pdb=" N GLN H 207 " --> pdb=" O HIS H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 243 removed outlier: 3.722A pdb=" N CYS H 229 " --> pdb=" O VAL H 225 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE H 230 " --> pdb=" O GLU H 226 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TRP H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 239 " --> pdb=" O PHE H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.613A pdb=" N PHE H 250 " --> pdb=" O LYS H 247 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE H 251 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR H 252 " --> pdb=" O GLY H 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 247 through 252' Processing helix chain 'H' and resid 253 through 276 removed outlier: 4.456A pdb=" N ASP H 259 " --> pdb=" O MET H 255 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE H 264 " --> pdb=" O ILE H 260 " (cutoff:3.500A) Proline residue: H 265 - end of helix removed outlier: 3.753A pdb=" N ASN H 276 " --> pdb=" O LEU H 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 296 removed outlier: 3.654A pdb=" N ILE H 294 " --> pdb=" O GLN H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 Processing helix chain 'H' and resid 307 through 319 removed outlier: 3.955A pdb=" N GLN H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 346 removed outlier: 3.699A pdb=" N LEU H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 336 " --> pdb=" O PHE H 332 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA H 345 " --> pdb=" O ALA H 341 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 369 removed outlier: 3.821A pdb=" N TRP H 363 " --> pdb=" O ASP H 359 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 365 " --> pdb=" O PHE H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 399 removed outlier: 3.576A pdb=" N LEU H 389 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS H 390 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O GLY H 387 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 414 removed outlier: 3.650A pdb=" N ASN H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS H 414 " --> pdb=" O ASN H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 417 No H-bonds generated for 'chain 'H' and resid 415 through 417' Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 214 removed outlier: 10.213A pdb=" N CYS A 212 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP A 185 " --> pdb=" O CYS A 212 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLN A 214 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR A 187 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP A 153 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY A 186 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 155 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER A 188 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA A 157 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 115 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE A 156 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 117 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU A 83 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA A 240 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL A 320 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 242 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 322 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 47 removed outlier: 3.505A pdb=" N ILE B 37 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 212 through 214 removed outlier: 10.209A pdb=" N CYS C 212 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP C 185 " --> pdb=" O CYS C 212 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLN C 214 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C 187 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASP C 153 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY C 186 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 155 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER C 188 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA C 157 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE C 115 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL C 155 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 117 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA C 157 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AA7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 214 removed outlier: 10.210A pdb=" N CYS E 212 " --> pdb=" O MET E 183 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP E 185 " --> pdb=" O CYS E 212 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLN E 214 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR E 187 " --> pdb=" O GLN E 214 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP E 153 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY E 186 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL E 155 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N SER E 188 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA E 157 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 115 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL E 155 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N THR E 117 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA E 157 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA E 240 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 320 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR E 242 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU E 322 " --> pdb=" O THR E 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 42 through 47 Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'G' and resid 212 through 214 removed outlier: 10.209A pdb=" N CYS G 212 " --> pdb=" O MET G 183 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP G 185 " --> pdb=" O CYS G 212 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N GLN G 214 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR G 187 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP G 153 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLY G 186 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL G 155 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER G 188 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA G 157 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE G 115 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL G 155 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR G 117 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA G 157 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU G 83 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 42 through 47 988 hydrogen bonds defined for protein. 2793 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: 4.33 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4463 1.32 - 1.45: 5520 1.45 - 1.57: 12389 1.57 - 1.69: 28 1.69 - 1.81: 200 Bond restraints: 22600 Sorted by residual: bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.612 0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O2B NAP G1001 " pdb=" P2B NAP G1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" O2B NAP E1001 " pdb=" P2B NAP E1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" O3 NAP A1001 " pdb=" PN NAP A1001 " ideal model delta sigma weight residual 1.643 1.745 -0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 22595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 30561 7.12 - 14.23: 85 14.23 - 21.35: 14 21.35 - 28.46: 4 28.46 - 35.58: 4 Bond angle restraints: 30668 Sorted by residual: angle pdb=" O1A NAP A1001 " pdb=" PA NAP A1001 " pdb=" O3 NAP A1001 " ideal model delta sigma weight residual 111.13 75.55 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP G1001 " pdb=" PA NAP G1001 " pdb=" O3 NAP G1001 " ideal model delta sigma weight residual 111.13 75.58 35.55 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP C1001 " pdb=" PA NAP C1001 " pdb=" O3 NAP C1001 " ideal model delta sigma weight residual 111.13 75.62 35.51 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP E1001 " pdb=" PA NAP E1001 " pdb=" O3 NAP E1001 " ideal model delta sigma weight residual 111.13 75.65 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C5D NAP E1001 " pdb=" O5D NAP E1001 " pdb=" PN NAP E1001 " ideal model delta sigma weight residual 121.57 100.15 21.42 3.00e+00 1.11e-01 5.10e+01 ... (remaining 30663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.89: 12562 14.89 - 29.78: 712 29.78 - 44.68: 150 44.68 - 59.57: 40 59.57 - 74.46: 16 Dihedral angle restraints: 13480 sinusoidal: 5336 harmonic: 8144 Sorted by residual: dihedral pdb=" CA PHE B 235 " pdb=" C PHE B 235 " pdb=" N GLU B 236 " pdb=" CA GLU B 236 " ideal model delta harmonic sigma weight residual 180.00 155.39 24.61 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA PHE D 235 " pdb=" C PHE D 235 " pdb=" N GLU D 236 " pdb=" CA GLU D 236 " ideal model delta harmonic sigma weight residual 180.00 155.50 24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO F 186 " pdb=" C PRO F 186 " pdb=" N ILE F 187 " pdb=" CA ILE F 187 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 13477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.153: 3332 0.153 - 0.306: 64 0.306 - 0.459: 16 0.459 - 0.612: 0 0.612 - 0.765: 4 Chirality restraints: 3416 Sorted by residual: chirality pdb=" C2B NAP E1001 " pdb=" C1B NAP E1001 " pdb=" C3B NAP E1001 " pdb=" O2B NAP E1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.46e+01 chirality pdb=" C2B NAP C1001 " pdb=" C1B NAP C1001 " pdb=" C3B NAP C1001 " pdb=" O2B NAP C1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 3413 not shown) Planarity restraints: 3892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 103 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.44e+01 pdb=" C ILE G 103 " 0.066 2.00e-02 2.50e+03 pdb=" O ILE G 103 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 104 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.87e+00 pdb=" C ILE C 136 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE C 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 294 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.51e+00 pdb=" C ILE D 294 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 294 " -0.018 2.00e-02 2.50e+03 pdb=" N MET D 295 " -0.016 2.00e-02 2.50e+03 ... (remaining 3889 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 284 2.62 - 3.19: 19614 3.19 - 3.76: 34401 3.76 - 4.33: 50790 4.33 - 4.90: 80049 Nonbonded interactions: 185138 Sorted by model distance: nonbonded pdb=" OD1 ASP B 375 " pdb=" N MET B 376 " model vdw 2.049 3.120 nonbonded pdb=" OD1 ASP D 375 " pdb=" N MET D 376 " model vdw 2.051 3.120 nonbonded pdb=" OD1 ASP F 375 " pdb=" N MET F 376 " model vdw 2.053 3.120 nonbonded pdb=" OD1 ASP H 375 " pdb=" N MET H 376 " model vdw 2.054 3.120 nonbonded pdb=" NH2 ARG B 34 " pdb=" OE1 GLU B 45 " model vdw 2.072 3.120 ... (remaining 185133 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 4.450 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.320 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 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 : 0.012 0.124 22600 Z= 0.516 Angle : 1.291 35.578 30668 Z= 0.656 Chirality : 0.070 0.765 3416 Planarity : 0.008 0.068 3892 Dihedral : 10.861 74.461 8272 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 0.13 % Allowed : 1.53 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.63 (0.12), residues: 2832 helix: -3.55 (0.08), residues: 1608 sheet: -0.54 (0.38), residues: 176 loop : -2.39 (0.16), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG D 80 TYR 0.045 0.004 TYR H 116 PHE 0.031 0.004 PHE E 84 TRP 0.036 0.003 TRP C 185 HIS 0.012 0.004 HIS F 306 Details of bonding type rmsd covalent geometry : bond 0.01152 (22600) covalent geometry : angle 1.29087 (30668) hydrogen bonds : bond 0.31839 ( 988) hydrogen bonds : angle 9.93298 ( 2793) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 723 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.9040 (tp) cc_final: 0.8614 (tt) REVERT: B 66 MET cc_start: 0.8046 (tpp) cc_final: 0.7433 (ttp) REVERT: C 75 LEU cc_start: 0.9058 (tp) cc_final: 0.8477 (tt) REVERT: C 277 ILE cc_start: 0.8304 (mt) cc_final: 0.8017 (mt) REVERT: D 113 ILE cc_start: 0.8941 (mt) cc_final: 0.8424 (tt) REVERT: E 75 LEU cc_start: 0.9083 (tp) cc_final: 0.8665 (tt) REVERT: F 113 ILE cc_start: 0.8925 (mt) cc_final: 0.8497 (tt) REVERT: F 124 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6721 (mt-10) outliers start: 3 outliers final: 2 residues processed: 726 average time/residue: 0.1725 time to fit residues: 187.7002 Evaluate side-chains 491 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 489 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain B residue 46 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 135 HIS A 175 HIS A 314 ASN A 333 ASN B 53 GLN B 353 GLN B 414 HIS C 135 HIS C 175 HIS C 204 GLN C 314 ASN D 53 GLN D 353 GLN D 414 HIS E 135 HIS E 175 HIS E 204 GLN E 314 ASN F 53 GLN F 353 GLN F 414 HIS G 135 HIS G 175 HIS G 204 GLN G 314 ASN H 53 GLN H 353 GLN H 414 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.199960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.116907 restraints weight = 29893.688| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.03 r_work: 0.2979 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22600 Z= 0.157 Angle : 0.726 11.915 30668 Z= 0.366 Chirality : 0.045 0.252 3416 Planarity : 0.005 0.045 3892 Dihedral : 9.327 64.894 3363 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.56 % Allowed : 9.44 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.14), residues: 2832 helix: -1.66 (0.11), residues: 1636 sheet: -0.46 (0.36), residues: 176 loop : -1.55 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 296 TYR 0.016 0.002 TYR H 90 PHE 0.027 0.002 PHE F 361 TRP 0.021 0.002 TRP H 232 HIS 0.004 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00327 (22600) covalent geometry : angle 0.72641 (30668) hydrogen bonds : bond 0.05679 ( 988) hydrogen bonds : angle 5.12585 ( 2793) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 544 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 ARG cc_start: 0.8334 (tpp-160) cc_final: 0.8051 (tpp-160) REVERT: B 66 MET cc_start: 0.8721 (tpp) cc_final: 0.8429 (ttp) REVERT: B 237 PHE cc_start: 0.9548 (t80) cc_final: 0.9018 (m-80) REVERT: B 311 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: B 331 LEU cc_start: 0.9403 (tp) cc_final: 0.9088 (pp) REVERT: B 362 TRP cc_start: 0.8796 (t-100) cc_final: 0.8568 (t-100) REVERT: B 366 VAL cc_start: 0.8926 (t) cc_final: 0.8597 (p) REVERT: B 413 TYR cc_start: 0.8142 (t80) cc_final: 0.7894 (t80) REVERT: C 277 ILE cc_start: 0.8416 (mt) cc_final: 0.8143 (mt) REVERT: C 283 ARG cc_start: 0.8272 (tpp-160) cc_final: 0.7913 (tpp-160) REVERT: D 237 PHE cc_start: 0.9630 (t80) cc_final: 0.9067 (m-80) REVERT: D 311 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: D 331 LEU cc_start: 0.9424 (tp) cc_final: 0.9123 (pp) REVERT: D 362 TRP cc_start: 0.8919 (t-100) cc_final: 0.8708 (t-100) REVERT: E 283 ARG cc_start: 0.8301 (tpp-160) cc_final: 0.7993 (tpp-160) REVERT: F 120 GLU cc_start: 0.7860 (tp30) cc_final: 0.7424 (tp30) REVERT: F 124 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8106 (mt-10) REVERT: F 237 PHE cc_start: 0.9570 (t80) cc_final: 0.9126 (m-80) REVERT: F 244 CYS cc_start: 0.7489 (p) cc_final: 0.6713 (p) REVERT: F 311 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8470 (pm20) REVERT: F 315 GLN cc_start: 0.9506 (mt0) cc_final: 0.9300 (pt0) REVERT: F 318 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9033 (mmmt) REVERT: F 326 LEU cc_start: 0.9697 (tp) cc_final: 0.9423 (tp) REVERT: F 330 PHE cc_start: 0.9408 (m-80) cc_final: 0.9191 (m-80) REVERT: H 111 GLU cc_start: 0.8450 (tp30) cc_final: 0.8164 (tt0) REVERT: H 182 LEU cc_start: 0.9038 (mm) cc_final: 0.8297 (pp) REVERT: H 237 PHE cc_start: 0.9536 (t80) cc_final: 0.9131 (m-80) REVERT: H 238 LEU cc_start: 0.9662 (mt) cc_final: 0.9419 (mp) REVERT: H 244 CYS cc_start: 0.7835 (p) cc_final: 0.7235 (p) REVERT: H 311 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8560 (pm20) REVERT: H 362 TRP cc_start: 0.8878 (t-100) cc_final: 0.8658 (t-100) outliers start: 57 outliers final: 30 residues processed: 568 average time/residue: 0.1698 time to fit residues: 145.3741 Evaluate side-chains 478 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 444 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 353 GLN Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 163 ASN Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 353 GLN Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain E residue 73 MET Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain F residue 53 GLN Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 353 GLN Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 408 ASN Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 338 GLN Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 353 GLN Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 267 optimal weight: 0.4980 chunk 240 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 120 optimal weight: 40.0000 chunk 17 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 315 GLN ** B 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 333 ASN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 GLN E 333 ASN ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 GLN F 353 GLN G 271 GLN G 333 ASN ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.163372 restraints weight = 29898.288| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.99 r_work: 0.3305 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22600 Z= 0.140 Angle : 0.690 12.899 30668 Z= 0.337 Chirality : 0.044 0.256 3416 Planarity : 0.005 0.042 3892 Dihedral : 8.498 59.336 3361 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.74 % Allowed : 11.96 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.15), residues: 2832 helix: -0.85 (0.12), residues: 1636 sheet: -0.43 (0.36), residues: 176 loop : -1.25 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 284 TYR 0.012 0.001 TYR H 343 PHE 0.053 0.002 PHE D 354 TRP 0.024 0.002 TRP F 150 HIS 0.005 0.001 HIS E 135 Details of bonding type rmsd covalent geometry : bond 0.00301 (22600) covalent geometry : angle 0.69011 (30668) hydrogen bonds : bond 0.04879 ( 988) hydrogen bonds : angle 4.73165 ( 2793) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 477 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 124 GLU cc_start: 0.7963 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 182 LEU cc_start: 0.8841 (mt) cc_final: 0.8508 (tt) REVERT: B 311 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8454 (pm20) REVERT: B 313 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.8967 (tp) REVERT: B 331 LEU cc_start: 0.9429 (tp) cc_final: 0.9005 (pp) REVERT: B 368 MET cc_start: 0.8561 (ttm) cc_final: 0.8261 (mmt) REVERT: C 75 LEU cc_start: 0.9149 (tp) cc_final: 0.8907 (tp) REVERT: C 283 ARG cc_start: 0.8086 (tpp-160) cc_final: 0.7859 (tpp-160) REVERT: D 311 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8526 (pm20) REVERT: D 368 MET cc_start: 0.8661 (ttm) cc_final: 0.8400 (ttp) REVERT: E 75 LEU cc_start: 0.9129 (tp) cc_final: 0.8881 (tp) REVERT: F 120 GLU cc_start: 0.7960 (tp30) cc_final: 0.7578 (tp30) REVERT: F 124 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8164 (mt-10) REVERT: F 175 ILE cc_start: 0.9355 (mt) cc_final: 0.9055 (tp) REVERT: F 182 LEU cc_start: 0.8713 (mt) cc_final: 0.8334 (tt) REVERT: F 244 CYS cc_start: 0.8496 (p) cc_final: 0.8087 (p) REVERT: F 290 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7703 (pm20) REVERT: F 311 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: F 326 LEU cc_start: 0.9700 (tp) cc_final: 0.9068 (tp) REVERT: F 330 PHE cc_start: 0.9313 (m-10) cc_final: 0.8682 (m-80) REVERT: F 375 ASP cc_start: 0.8433 (p0) cc_final: 0.8207 (p0) REVERT: H 182 LEU cc_start: 0.8747 (mm) cc_final: 0.8161 (tt) REVERT: H 244 CYS cc_start: 0.8565 (p) cc_final: 0.8338 (p) REVERT: H 297 ILE cc_start: 0.9461 (pt) cc_final: 0.9245 (mm) REVERT: H 311 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8483 (pm20) outliers start: 61 outliers final: 28 residues processed: 504 average time/residue: 0.1666 time to fit residues: 128.5850 Evaluate side-chains 467 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 433 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 254 ILE Chi-restraints excluded: chain F residue 290 GLN Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain G residue 338 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 88 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 264 optimal weight: 30.0000 chunk 218 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 272 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 259 optimal weight: 40.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 53 GLN B 290 GLN C 286 GLN D 53 GLN ** D 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 GLN F 53 GLN F 290 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 286 GLN G 314 ASN H 53 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.193787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.122503 restraints weight = 29464.287| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.43 r_work: 0.2928 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 22600 Z= 0.339 Angle : 0.785 13.594 30668 Z= 0.384 Chirality : 0.050 0.288 3416 Planarity : 0.005 0.050 3892 Dihedral : 9.274 64.031 3361 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.37 % Allowed : 13.08 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.15), residues: 2832 helix: -0.42 (0.13), residues: 1636 sheet: -0.41 (0.43), residues: 136 loop : -1.13 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 82 TYR 0.023 0.002 TYR B 116 PHE 0.042 0.003 PHE D 292 TRP 0.023 0.003 TRP F 232 HIS 0.012 0.002 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00795 (22600) covalent geometry : angle 0.78486 (30668) hydrogen bonds : bond 0.04992 ( 988) hydrogen bonds : angle 4.75910 ( 2793) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 456 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8437 (tp30) cc_final: 0.8143 (tp30) REVERT: A 283 ARG cc_start: 0.8323 (tpp-160) cc_final: 0.8110 (tpp-160) REVERT: B 182 LEU cc_start: 0.9194 (mt) cc_final: 0.8799 (tt) REVERT: B 232 TRP cc_start: 0.9050 (t-100) cc_final: 0.8791 (t-100) REVERT: B 233 PHE cc_start: 0.9079 (m-10) cc_final: 0.8832 (m-80) REVERT: B 290 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: B 311 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: B 321 MET cc_start: 0.8046 (tmm) cc_final: 0.7815 (tmm) REVERT: B 363 TRP cc_start: 0.8874 (t60) cc_final: 0.8613 (t60) REVERT: B 368 MET cc_start: 0.8732 (ttm) cc_final: 0.8190 (mmt) REVERT: B 376 MET cc_start: 0.8606 (ptp) cc_final: 0.8118 (ptm) REVERT: C 283 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7956 (tpp-160) REVERT: D 114 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8395 (mtm110) REVERT: D 311 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: D 321 MET cc_start: 0.8077 (tmm) cc_final: 0.7836 (tmm) REVERT: D 368 MET cc_start: 0.8705 (ttm) cc_final: 0.8047 (tpp) REVERT: F 114 ARG cc_start: 0.8711 (mtt180) cc_final: 0.8282 (mtm110) REVERT: F 120 GLU cc_start: 0.8282 (tp30) cc_final: 0.7954 (tp30) REVERT: F 124 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8222 (mt-10) REVERT: F 182 LEU cc_start: 0.9166 (mt) cc_final: 0.8725 (tt) REVERT: F 244 CYS cc_start: 0.8274 (p) cc_final: 0.7723 (p) REVERT: F 311 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8579 (pm20) REVERT: F 326 LEU cc_start: 0.9720 (tp) cc_final: 0.9340 (tp) REVERT: F 330 PHE cc_start: 0.9477 (m-10) cc_final: 0.9032 (m-80) REVERT: F 344 PHE cc_start: 0.8709 (m-80) cc_final: 0.8424 (m-80) REVERT: F 351 ASP cc_start: 0.8443 (p0) cc_final: 0.8237 (p0) REVERT: G 283 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8089 (tpp-160) REVERT: H 182 LEU cc_start: 0.9106 (mm) cc_final: 0.8436 (tt) REVERT: H 232 TRP cc_start: 0.9056 (t-100) cc_final: 0.8831 (t-100) REVERT: H 292 PHE cc_start: 0.9426 (m-10) cc_final: 0.9087 (m-10) REVERT: H 311 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: H 353 GLN cc_start: 0.8099 (pp30) cc_final: 0.7793 (pp30) REVERT: H 376 MET cc_start: 0.8503 (ptp) cc_final: 0.7953 (ptm) outliers start: 75 outliers final: 46 residues processed: 492 average time/residue: 0.1671 time to fit residues: 125.2190 Evaluate side-chains 461 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 410 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 351 ILE Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 402 VAL Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 27 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 232 optimal weight: 0.9990 chunk 253 optimal weight: 40.0000 chunk 66 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 GLN F 53 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.129296 restraints weight = 29405.243| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.32 r_work: 0.3079 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22600 Z= 0.143 Angle : 0.686 12.956 30668 Z= 0.331 Chirality : 0.044 0.242 3416 Planarity : 0.004 0.048 3892 Dihedral : 9.485 66.378 3361 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.25 % Allowed : 15.02 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.16), residues: 2832 helix: 0.07 (0.13), residues: 1576 sheet: -0.28 (0.39), residues: 176 loop : -0.99 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 284 TYR 0.010 0.001 TYR H 266 PHE 0.048 0.002 PHE D 237 TRP 0.022 0.002 TRP D 232 HIS 0.007 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00320 (22600) covalent geometry : angle 0.68630 (30668) hydrogen bonds : bond 0.04273 ( 988) hydrogen bonds : angle 4.65542 ( 2793) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 439 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8260 (tp30) cc_final: 0.7999 (tp30) REVERT: B 66 MET cc_start: 0.8669 (ttp) cc_final: 0.8448 (ttp) REVERT: B 182 LEU cc_start: 0.9120 (mt) cc_final: 0.8734 (tt) REVERT: B 311 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8650 (pm20) REVERT: B 321 MET cc_start: 0.7954 (tmm) cc_final: 0.7680 (tmm) REVERT: B 363 TRP cc_start: 0.8949 (t60) cc_final: 0.8715 (t60) REVERT: B 368 MET cc_start: 0.8796 (ttm) cc_final: 0.8255 (mmt) REVERT: B 376 MET cc_start: 0.8254 (ptp) cc_final: 0.7818 (ptm) REVERT: D 232 TRP cc_start: 0.8974 (t-100) cc_final: 0.8650 (t-100) REVERT: D 311 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: D 321 MET cc_start: 0.8007 (tmm) cc_final: 0.7675 (tmm) REVERT: D 368 MET cc_start: 0.8733 (ttm) cc_final: 0.8154 (mmt) REVERT: F 124 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8187 (mt-10) REVERT: F 182 LEU cc_start: 0.9094 (mt) cc_final: 0.8681 (tt) REVERT: F 232 TRP cc_start: 0.8947 (t-100) cc_final: 0.8727 (t-100) REVERT: F 244 CYS cc_start: 0.8410 (p) cc_final: 0.8025 (p) REVERT: F 311 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8612 (pm20) REVERT: F 326 LEU cc_start: 0.9728 (tp) cc_final: 0.9325 (tp) REVERT: F 329 PHE cc_start: 0.9278 (t80) cc_final: 0.9005 (m-80) REVERT: F 330 PHE cc_start: 0.9451 (m-10) cc_final: 0.8787 (m-80) REVERT: F 344 PHE cc_start: 0.8541 (m-80) cc_final: 0.8326 (m-80) REVERT: H 182 LEU cc_start: 0.9085 (mm) cc_final: 0.8454 (tt) REVERT: H 232 TRP cc_start: 0.9024 (t-100) cc_final: 0.8795 (t-100) REVERT: H 311 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8540 (pm20) REVERT: H 321 MET cc_start: 0.7983 (tmm) cc_final: 0.7645 (tmm) REVERT: H 353 GLN cc_start: 0.8125 (pp30) cc_final: 0.7835 (pp30) REVERT: H 376 MET cc_start: 0.8401 (ptp) cc_final: 0.7885 (ptm) REVERT: H 384 LYS cc_start: 0.8553 (mmtm) cc_final: 0.8337 (mmtp) outliers start: 50 outliers final: 36 residues processed: 463 average time/residue: 0.1646 time to fit residues: 117.4333 Evaluate side-chains 443 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 403 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 351 ILE Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 288 VAL Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 42 optimal weight: 8.9990 chunk 70 optimal weight: 3.9990 chunk 231 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 269 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 chunk 194 optimal weight: 30.0000 chunk 179 optimal weight: 0.4980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 290 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 = 0.4311 r_free = 0.4311 target = 0.195678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123550 restraints weight = 29849.092| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.50 r_work: 0.2984 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.079 22600 Z= 0.362 Angle : 0.790 12.215 30668 Z= 0.390 Chirality : 0.050 0.280 3416 Planarity : 0.005 0.063 3892 Dihedral : 10.131 69.437 3361 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.24 % Allowed : 14.66 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.16), residues: 2832 helix: 0.07 (0.13), residues: 1576 sheet: -1.16 (0.37), residues: 180 loop : -0.99 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 283 TYR 0.022 0.002 TYR B 116 PHE 0.050 0.002 PHE D 237 TRP 0.024 0.002 TRP B 232 HIS 0.010 0.002 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00855 (22600) covalent geometry : angle 0.79048 (30668) hydrogen bonds : bond 0.04815 ( 988) hydrogen bonds : angle 4.80159 ( 2793) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 423 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 182 LEU cc_start: 0.9122 (mt) cc_final: 0.8763 (tt) REVERT: B 311 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8643 (pm20) REVERT: B 321 MET cc_start: 0.7943 (tmm) cc_final: 0.7603 (tmm) REVERT: B 344 PHE cc_start: 0.8695 (m-80) cc_final: 0.8360 (m-80) REVERT: B 368 MET cc_start: 0.8786 (ttm) cc_final: 0.8257 (mmt) REVERT: B 376 MET cc_start: 0.8292 (ptp) cc_final: 0.7933 (ptm) REVERT: D 114 ARG cc_start: 0.8800 (mtt180) cc_final: 0.8472 (mtm110) REVERT: D 232 TRP cc_start: 0.9040 (t-100) cc_final: 0.8719 (t-100) REVERT: D 311 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: D 321 MET cc_start: 0.8072 (tmm) cc_final: 0.7656 (tmm) REVERT: D 326 LEU cc_start: 0.9760 (tp) cc_final: 0.9397 (tp) REVERT: D 330 PHE cc_start: 0.9452 (m-80) cc_final: 0.8976 (m-80) REVERT: D 344 PHE cc_start: 0.8649 (m-80) cc_final: 0.8402 (m-80) REVERT: D 368 MET cc_start: 0.8746 (ttm) cc_final: 0.8328 (mmt) REVERT: F 114 ARG cc_start: 0.8791 (mtt180) cc_final: 0.8406 (mtm110) REVERT: F 124 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8272 (mt-10) REVERT: F 151 LEU cc_start: 0.9468 (tt) cc_final: 0.9063 (mt) REVERT: F 182 LEU cc_start: 0.9119 (mt) cc_final: 0.8725 (tt) REVERT: F 232 TRP cc_start: 0.8950 (t-100) cc_final: 0.8709 (t-100) REVERT: F 290 GLN cc_start: 0.8053 (pp30) cc_final: 0.7845 (pm20) REVERT: F 311 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: F 326 LEU cc_start: 0.9730 (tp) cc_final: 0.9318 (tp) REVERT: F 329 PHE cc_start: 0.9331 (t80) cc_final: 0.8999 (m-80) REVERT: F 330 PHE cc_start: 0.9491 (m-10) cc_final: 0.8799 (m-80) REVERT: F 331 LEU cc_start: 0.9311 (pp) cc_final: 0.9073 (tp) REVERT: F 344 PHE cc_start: 0.8567 (m-80) cc_final: 0.8330 (m-80) REVERT: G 352 ASP cc_start: 0.8756 (p0) cc_final: 0.8440 (p0) REVERT: H 182 LEU cc_start: 0.9132 (mm) cc_final: 0.8541 (tt) REVERT: H 311 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8639 (pm20) REVERT: H 321 MET cc_start: 0.7986 (tmm) cc_final: 0.7624 (tmm) REVERT: H 376 MET cc_start: 0.8409 (ptp) cc_final: 0.8077 (ptm) outliers start: 72 outliers final: 47 residues processed: 466 average time/residue: 0.1738 time to fit residues: 122.5362 Evaluate side-chains 459 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 408 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 411 TYR Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 348 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 158 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 162 optimal weight: 0.0980 chunk 82 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 183 optimal weight: 20.0000 chunk 231 optimal weight: 0.4980 chunk 188 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 315 GLN E 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.152966 restraints weight = 29397.901| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.07 r_work: 0.3142 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22600 Z= 0.127 Angle : 0.682 14.068 30668 Z= 0.332 Chirality : 0.044 0.205 3416 Planarity : 0.004 0.048 3892 Dihedral : 9.942 68.533 3361 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.25 % Allowed : 16.32 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.16), residues: 2832 helix: 0.31 (0.13), residues: 1572 sheet: -0.34 (0.40), residues: 176 loop : -0.94 (0.20), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 296 TYR 0.008 0.001 TYR E 255 PHE 0.048 0.002 PHE D 237 TRP 0.030 0.002 TRP B 232 HIS 0.006 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00276 (22600) covalent geometry : angle 0.68162 (30668) hydrogen bonds : bond 0.04091 ( 988) hydrogen bonds : angle 4.66612 ( 2793) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 438 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7591 (mp0) REVERT: B 182 LEU cc_start: 0.9095 (mt) cc_final: 0.8747 (tt) REVERT: B 311 GLN cc_start: 0.8932 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: B 321 MET cc_start: 0.7757 (tmm) cc_final: 0.7398 (tmm) REVERT: B 338 PHE cc_start: 0.8940 (m-80) cc_final: 0.8659 (m-80) REVERT: B 368 MET cc_start: 0.8689 (ttm) cc_final: 0.8289 (mmt) REVERT: B 376 MET cc_start: 0.8255 (ptp) cc_final: 0.7908 (ptm) REVERT: D 232 TRP cc_start: 0.9085 (t-100) cc_final: 0.8782 (t-100) REVERT: D 311 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8476 (pm20) REVERT: D 321 MET cc_start: 0.7863 (tmm) cc_final: 0.7437 (tmm) REVERT: D 326 LEU cc_start: 0.9742 (tp) cc_final: 0.9245 (tp) REVERT: D 330 PHE cc_start: 0.9383 (m-80) cc_final: 0.8678 (m-80) REVERT: D 368 MET cc_start: 0.8468 (ttm) cc_final: 0.8228 (mmt) REVERT: F 63 LYS cc_start: 0.9100 (mmtt) cc_final: 0.8864 (tppt) REVERT: F 114 ARG cc_start: 0.8471 (mtt180) cc_final: 0.8183 (mtm110) REVERT: F 120 GLU cc_start: 0.8032 (tp30) cc_final: 0.7823 (tp30) REVERT: F 124 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8167 (mt-10) REVERT: F 151 LEU cc_start: 0.9407 (tt) cc_final: 0.9057 (mm) REVERT: F 182 LEU cc_start: 0.9091 (mt) cc_final: 0.8698 (tt) REVERT: F 232 TRP cc_start: 0.9011 (t-100) cc_final: 0.8760 (t-100) REVERT: F 244 CYS cc_start: 0.8164 (p) cc_final: 0.7834 (p) REVERT: F 311 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: F 326 LEU cc_start: 0.9731 (tp) cc_final: 0.9270 (tp) REVERT: F 329 PHE cc_start: 0.9266 (t80) cc_final: 0.9002 (m-80) REVERT: F 330 PHE cc_start: 0.9434 (m-10) cc_final: 0.8781 (m-80) REVERT: F 331 LEU cc_start: 0.9267 (pp) cc_final: 0.9050 (tp) REVERT: F 351 ASP cc_start: 0.8338 (p0) cc_final: 0.8125 (p0) REVERT: G 352 ASP cc_start: 0.8621 (p0) cc_final: 0.8329 (p0) REVERT: H 151 LEU cc_start: 0.9505 (tp) cc_final: 0.9193 (pp) REVERT: H 171 MET cc_start: 0.9397 (mmp) cc_final: 0.9053 (mmm) REVERT: H 182 LEU cc_start: 0.9088 (mm) cc_final: 0.8509 (tt) REVERT: H 311 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8648 (pm20) REVERT: H 321 MET cc_start: 0.7842 (tmm) cc_final: 0.7419 (tmm) REVERT: H 322 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7835 (mtt-85) REVERT: H 353 GLN cc_start: 0.8079 (pp30) cc_final: 0.7846 (pp30) REVERT: H 376 MET cc_start: 0.8320 (ptp) cc_final: 0.7846 (ptm) REVERT: H 384 LYS cc_start: 0.8599 (mmtm) cc_final: 0.8315 (mmtp) outliers start: 50 outliers final: 37 residues processed: 466 average time/residue: 0.1652 time to fit residues: 117.8248 Evaluate side-chains 452 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 411 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 237 PHE Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 106 LEU Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 259 optimal weight: 0.0370 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 258 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 192 optimal weight: 20.0000 chunk 228 optimal weight: 4.9990 chunk 47 optimal weight: 0.0370 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.196382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152103 restraints weight = 29313.540| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.20 r_work: 0.3116 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22600 Z= 0.139 Angle : 0.685 13.110 30668 Z= 0.335 Chirality : 0.044 0.189 3416 Planarity : 0.004 0.046 3892 Dihedral : 9.678 64.826 3360 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.25 % Allowed : 16.86 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2832 helix: 0.42 (0.13), residues: 1572 sheet: -0.68 (0.36), residues: 216 loop : -0.71 (0.21), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 284 TYR 0.009 0.001 TYR F 90 PHE 0.048 0.002 PHE H 292 TRP 0.040 0.002 TRP B 232 HIS 0.006 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00310 (22600) covalent geometry : angle 0.68506 (30668) hydrogen bonds : bond 0.04047 ( 988) hydrogen bonds : angle 4.63865 ( 2793) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 437 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7640 (mp0) REVERT: A 150 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 182 LEU cc_start: 0.9105 (mt) cc_final: 0.8762 (tt) REVERT: B 311 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8573 (pm20) REVERT: B 321 MET cc_start: 0.7807 (tmm) cc_final: 0.7423 (tmm) REVERT: B 338 PHE cc_start: 0.8977 (m-80) cc_final: 0.8700 (m-80) REVERT: B 344 PHE cc_start: 0.8784 (m-80) cc_final: 0.8473 (m-10) REVERT: B 368 MET cc_start: 0.8707 (ttm) cc_final: 0.8297 (mmt) REVERT: B 376 MET cc_start: 0.8208 (ptp) cc_final: 0.7871 (ptm) REVERT: B 406 VAL cc_start: 0.9484 (OUTLIER) cc_final: 0.9245 (m) REVERT: D 232 TRP cc_start: 0.9097 (t-100) cc_final: 0.8883 (t-100) REVERT: D 311 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: D 321 MET cc_start: 0.7882 (tmm) cc_final: 0.7472 (tmm) REVERT: D 326 LEU cc_start: 0.9701 (tp) cc_final: 0.9218 (tp) REVERT: D 330 PHE cc_start: 0.9370 (m-80) cc_final: 0.8643 (m-80) REVERT: D 344 PHE cc_start: 0.8627 (m-80) cc_final: 0.8357 (m-10) REVERT: F 63 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8859 (tppt) REVERT: F 114 ARG cc_start: 0.8571 (mtt180) cc_final: 0.8245 (mtm110) REVERT: F 124 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8253 (pp20) REVERT: F 151 LEU cc_start: 0.9397 (tt) cc_final: 0.9040 (mm) REVERT: F 182 LEU cc_start: 0.9103 (mt) cc_final: 0.8709 (tt) REVERT: F 232 TRP cc_start: 0.9059 (t-100) cc_final: 0.8797 (t-100) REVERT: F 244 CYS cc_start: 0.8052 (p) cc_final: 0.7803 (p) REVERT: F 290 GLN cc_start: 0.8210 (pp30) cc_final: 0.7729 (pm20) REVERT: F 311 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8614 (pm20) REVERT: F 326 LEU cc_start: 0.9737 (tp) cc_final: 0.9275 (tp) REVERT: F 329 PHE cc_start: 0.9255 (t80) cc_final: 0.9007 (m-80) REVERT: F 330 PHE cc_start: 0.9454 (m-10) cc_final: 0.8537 (m-80) REVERT: F 331 LEU cc_start: 0.9278 (pp) cc_final: 0.9069 (tp) REVERT: G 283 ARG cc_start: 0.8355 (mmp-170) cc_final: 0.8151 (mmm160) REVERT: G 352 ASP cc_start: 0.8624 (p0) cc_final: 0.8298 (p0) REVERT: H 124 GLU cc_start: 0.8054 (pp20) cc_final: 0.7820 (pp20) REVERT: H 151 LEU cc_start: 0.9503 (tp) cc_final: 0.9198 (pp) REVERT: H 171 MET cc_start: 0.9349 (mmp) cc_final: 0.8981 (mmm) REVERT: H 182 LEU cc_start: 0.9088 (mm) cc_final: 0.8514 (tt) REVERT: H 297 ILE cc_start: 0.9721 (pt) cc_final: 0.9438 (mm) REVERT: H 311 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: H 321 MET cc_start: 0.7778 (tmm) cc_final: 0.7362 (tmm) REVERT: H 322 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7824 (mtt-85) REVERT: H 376 MET cc_start: 0.8278 (ptp) cc_final: 0.7994 (ptm) REVERT: H 384 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8320 (mmtp) outliers start: 50 outliers final: 39 residues processed: 467 average time/residue: 0.1645 time to fit residues: 117.7558 Evaluate side-chains 468 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 424 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 272 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 276 optimal weight: 0.5980 chunk 239 optimal weight: 0.9980 chunk 156 optimal weight: 0.5980 chunk 258 optimal weight: 50.0000 chunk 184 optimal weight: 1.9990 chunk 32 optimal weight: 0.0770 chunk 223 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 305 GLN E 305 GLN H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.196852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151442 restraints weight = 29494.876| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.14 r_work: 0.3138 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22600 Z= 0.135 Angle : 0.705 14.063 30668 Z= 0.343 Chirality : 0.044 0.359 3416 Planarity : 0.004 0.045 3892 Dihedral : 9.533 61.825 3360 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.38 % Allowed : 16.95 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2832 helix: 0.50 (0.13), residues: 1576 sheet: -0.67 (0.35), residues: 216 loop : -0.56 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.008 0.001 TYR F 266 PHE 0.052 0.001 PHE D 237 TRP 0.047 0.002 TRP B 232 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00300 (22600) covalent geometry : angle 0.70534 (30668) hydrogen bonds : bond 0.03959 ( 988) hydrogen bonds : angle 4.64833 ( 2793) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 453 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7597 (mp0) REVERT: A 150 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7974 (mm-30) REVERT: B 182 LEU cc_start: 0.9107 (mt) cc_final: 0.8764 (tt) REVERT: B 297 ILE cc_start: 0.9535 (pt) cc_final: 0.9127 (mm) REVERT: B 311 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8599 (pm20) REVERT: B 321 MET cc_start: 0.7814 (tmm) cc_final: 0.7440 (tmm) REVERT: B 338 PHE cc_start: 0.8975 (m-80) cc_final: 0.8670 (m-80) REVERT: B 344 PHE cc_start: 0.8779 (m-80) cc_final: 0.8476 (m-10) REVERT: B 368 MET cc_start: 0.8714 (ttm) cc_final: 0.8424 (mmt) REVERT: B 376 MET cc_start: 0.8198 (ptp) cc_final: 0.7877 (ptm) REVERT: B 384 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8175 (mmtp) REVERT: B 406 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9233 (m) REVERT: D 114 ARG cc_start: 0.8574 (mtt180) cc_final: 0.8305 (mtm110) REVERT: D 124 GLU cc_start: 0.8048 (pp20) cc_final: 0.7804 (pp20) REVERT: D 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8621 (pm20) REVERT: D 321 MET cc_start: 0.7906 (tmm) cc_final: 0.7492 (tmm) REVERT: D 326 LEU cc_start: 0.9705 (tp) cc_final: 0.9257 (tp) REVERT: D 330 PHE cc_start: 0.9341 (m-80) cc_final: 0.8628 (m-80) REVERT: D 344 PHE cc_start: 0.8604 (m-80) cc_final: 0.8279 (m-10) REVERT: D 376 MET cc_start: 0.8091 (ptm) cc_final: 0.7872 (pmm) REVERT: F 63 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8815 (tppt) REVERT: F 114 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8265 (mtm110) REVERT: F 120 GLU cc_start: 0.8282 (tp30) cc_final: 0.7817 (tp30) REVERT: F 124 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8165 (mt-10) REVERT: F 151 LEU cc_start: 0.9358 (tt) cc_final: 0.8973 (mm) REVERT: F 182 LEU cc_start: 0.9101 (mt) cc_final: 0.8714 (tt) REVERT: F 232 TRP cc_start: 0.9073 (t-100) cc_final: 0.8824 (t-100) REVERT: F 244 CYS cc_start: 0.8034 (p) cc_final: 0.7746 (p) REVERT: F 311 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8678 (pm20) REVERT: F 326 LEU cc_start: 0.9753 (tp) cc_final: 0.9268 (tp) REVERT: F 329 PHE cc_start: 0.9276 (t80) cc_final: 0.9044 (m-80) REVERT: F 330 PHE cc_start: 0.9352 (m-10) cc_final: 0.8780 (m-80) REVERT: G 352 ASP cc_start: 0.8597 (p0) cc_final: 0.8280 (p0) REVERT: H 151 LEU cc_start: 0.9508 (tp) cc_final: 0.9206 (pp) REVERT: H 171 MET cc_start: 0.9363 (mmp) cc_final: 0.8995 (mmm) REVERT: H 182 LEU cc_start: 0.9092 (mm) cc_final: 0.8529 (tt) REVERT: H 297 ILE cc_start: 0.9715 (pt) cc_final: 0.9429 (mm) REVERT: H 311 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8689 (pm20) REVERT: H 321 MET cc_start: 0.7772 (tmm) cc_final: 0.7348 (tmm) REVERT: H 322 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7847 (mtt-85) REVERT: H 353 GLN cc_start: 0.8112 (pp30) cc_final: 0.7819 (pp30) REVERT: H 362 TRP cc_start: 0.9214 (t-100) cc_final: 0.8738 (t-100) REVERT: H 376 MET cc_start: 0.8191 (ptp) cc_final: 0.7764 (ptm) REVERT: H 384 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8323 (mmtp) outliers start: 53 outliers final: 41 residues processed: 482 average time/residue: 0.1743 time to fit residues: 128.3349 Evaluate side-chains 481 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 435 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 402 VAL Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 324 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 238 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 243 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 198 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 189 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN D 315 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.195499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.151357 restraints weight = 29634.485| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 2.16 r_work: 0.3118 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22600 Z= 0.172 Angle : 0.731 12.795 30668 Z= 0.358 Chirality : 0.046 0.303 3416 Planarity : 0.004 0.044 3892 Dihedral : 9.532 61.228 3360 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.29 % Allowed : 17.09 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.16), residues: 2832 helix: 0.47 (0.13), residues: 1592 sheet: -0.69 (0.35), residues: 216 loop : -0.51 (0.21), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 284 TYR 0.011 0.001 TYR F 90 PHE 0.053 0.002 PHE H 292 TRP 0.052 0.003 TRP B 232 HIS 0.008 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00398 (22600) covalent geometry : angle 0.73059 (30668) hydrogen bonds : bond 0.04086 ( 988) hydrogen bonds : angle 4.65854 ( 2793) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5664 Ramachandran restraints generated. 2832 Oldfield, 0 Emsley, 2832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 439 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7646 (mp0) REVERT: A 150 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 231 GLU cc_start: 0.8350 (tp30) cc_final: 0.8067 (tp30) REVERT: B 182 LEU cc_start: 0.9117 (mt) cc_final: 0.8781 (tt) REVERT: B 297 ILE cc_start: 0.9557 (pt) cc_final: 0.9161 (mm) REVERT: B 321 MET cc_start: 0.7809 (tmm) cc_final: 0.7427 (tmm) REVERT: B 338 PHE cc_start: 0.9000 (m-80) cc_final: 0.8681 (m-80) REVERT: B 344 PHE cc_start: 0.8792 (m-80) cc_final: 0.8500 (m-10) REVERT: B 368 MET cc_start: 0.8734 (ttm) cc_final: 0.8417 (mmt) REVERT: B 376 MET cc_start: 0.8147 (ptp) cc_final: 0.7797 (ptm) REVERT: B 406 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9247 (m) REVERT: D 114 ARG cc_start: 0.8605 (mtt180) cc_final: 0.8320 (mtm110) REVERT: D 124 GLU cc_start: 0.8102 (pp20) cc_final: 0.7862 (pp20) REVERT: D 311 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8641 (pm20) REVERT: D 321 MET cc_start: 0.7873 (tmm) cc_final: 0.7474 (tmm) REVERT: D 326 LEU cc_start: 0.9703 (tp) cc_final: 0.9270 (tp) REVERT: D 330 PHE cc_start: 0.9354 (m-80) cc_final: 0.8606 (m-80) REVERT: D 344 PHE cc_start: 0.8634 (m-80) cc_final: 0.8290 (m-80) REVERT: F 63 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8804 (tppt) REVERT: F 114 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8263 (mtm110) REVERT: F 120 GLU cc_start: 0.8307 (tp30) cc_final: 0.7856 (tp30) REVERT: F 124 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8192 (mt-10) REVERT: F 151 LEU cc_start: 0.9366 (tt) cc_final: 0.9066 (pp) REVERT: F 182 LEU cc_start: 0.9111 (mt) cc_final: 0.8726 (tt) REVERT: F 232 TRP cc_start: 0.9082 (t-100) cc_final: 0.8840 (t-100) REVERT: F 244 CYS cc_start: 0.8009 (p) cc_final: 0.7590 (p) REVERT: F 295 MET cc_start: 0.8968 (ptp) cc_final: 0.8613 (ppp) REVERT: F 311 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8712 (pm20) REVERT: F 326 LEU cc_start: 0.9749 (tp) cc_final: 0.9249 (tp) REVERT: F 329 PHE cc_start: 0.9287 (t80) cc_final: 0.9035 (m-80) REVERT: F 330 PHE cc_start: 0.9360 (m-10) cc_final: 0.8746 (m-80) REVERT: G 352 ASP cc_start: 0.8619 (p0) cc_final: 0.8286 (p0) REVERT: H 151 LEU cc_start: 0.9508 (tp) cc_final: 0.9217 (pp) REVERT: H 171 MET cc_start: 0.9386 (mmp) cc_final: 0.9010 (mmm) REVERT: H 182 LEU cc_start: 0.9099 (mm) cc_final: 0.8541 (tt) REVERT: H 295 MET cc_start: 0.9092 (ptp) cc_final: 0.8712 (pmm) REVERT: H 297 ILE cc_start: 0.9717 (pt) cc_final: 0.9459 (mm) REVERT: H 311 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8668 (pm20) REVERT: H 321 MET cc_start: 0.7803 (tmm) cc_final: 0.7387 (tmm) REVERT: H 322 ARG cc_start: 0.8232 (mtt-85) cc_final: 0.7848 (mtt-85) outliers start: 51 outliers final: 41 residues processed: 472 average time/residue: 0.1680 time to fit residues: 121.4963 Evaluate side-chains 476 residues out of total 2480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 431 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain C residue 73 MET Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 343 LEU Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 TYR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 225 VAL Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 311 GLN Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 406 VAL Chi-restraints excluded: chain F residue 411 TYR Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 163 ASN Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 293 GLN Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 311 GLN Chi-restraints excluded: chain H residue 317 LEU Chi-restraints excluded: chain H residue 406 VAL Chi-restraints excluded: chain H residue 411 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 224 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 198 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 219 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 194 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 315 GLN E 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.196360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.151698 restraints weight = 29507.927| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.27 r_work: 0.3126 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22600 Z= 0.141 Angle : 0.728 12.944 30668 Z= 0.354 Chirality : 0.045 0.266 3416 Planarity : 0.004 0.047 3892 Dihedral : 9.481 60.734 3360 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.43 % Allowed : 17.18 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.16), residues: 2832 helix: 0.50 (0.13), residues: 1576 sheet: -0.68 (0.35), residues: 216 loop : -0.43 (0.21), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.013 0.001 TYR B 90 PHE 0.052 0.002 PHE H 292 TRP 0.053 0.002 TRP B 232 HIS 0.006 0.001 HIS G 135 Details of bonding type rmsd covalent geometry : bond 0.00317 (22600) covalent geometry : angle 0.72817 (30668) hydrogen bonds : bond 0.03980 ( 988) hydrogen bonds : angle 4.66230 ( 2793) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8957.22 seconds wall clock time: 152 minutes 52.11 seconds (9172.11 seconds total)