Starting phenix.real_space_refine on Sun Sep 29 11:41:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_9024_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_9024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_9024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_9024_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ebk_9024/09_2024/6ebk_9024_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} 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: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 4} 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: 14.63, per 1000 atoms: 0.66 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: 5.71 Conformation dependent library (CDL) restraints added in 3.2 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: 2.33 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: 7.01 Time building geometry restraints manager: 6.72 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: 0.00 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: 4.520 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: 0.020 Extract box with map and model: 1.100 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 50.970 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.400 ------------------------------------------------------------------------------- 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= 0.746 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.63 (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 TRP 0.036 0.003 TRP C 185 HIS 0.012 0.004 HIS F 306 PHE 0.031 0.004 PHE E 84 TYR 0.045 0.004 TYR H 116 ARG 0.022 0.002 ARG D 80 *********************** 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 fitting. rotamer outliers: 3 poor density : 723 time to evaluate : 2.491 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: 0.8613 (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: 0.8476 (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: 0.8428 (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: 0.3658 time to fit residues: 395.6536 Evaluate side-chains 495 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 493 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 236 optimal weight: 0.8980 chunk 212 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 40.0000 chunk 219 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 chunk 133 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 254 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 414 HIS C 135 HIS C 175 HIS C 204 GLN C 314 ASN D 53 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 290 GLN H 414 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.3309 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= 0.225 Angle : 0.729 11.579 30668 Z= 0.367 Chirality : 0.045 0.241 3416 Planarity : 0.006 0.047 3892 Dihedral : 9.503 66.560 3363 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.65 % Allowed : 9.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.14), residues: 2832 helix: -1.61 (0.11), residues: 1636 sheet: -0.43 (0.36), residues: 176 loop : -1.53 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 232 HIS 0.004 0.001 HIS C 135 PHE 0.027 0.002 PHE F 361 TYR 0.015 0.002 TYR H 90 ARG 0.006 0.001 ARG B 296 *********************** 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 611 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 552 time to evaluate : 2.573 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: B 331 LEU cc_start: 0.7154 (tp) cc_final: 0.6179 (pp) REVERT: C 75 LEU cc_start: 0.9050 (tp) cc_final: 0.8838 (tp) REVERT: C 277 ILE cc_start: 0.8370 (mt) cc_final: 0.8136 (mt) REVERT: D 331 LEU cc_start: 0.7010 (tp) cc_final: 0.6227 (pp) REVERT: F 175 ILE cc_start: 0.8305 (mt) cc_final: 0.8036 (tp) REVERT: F 244 CYS cc_start: 0.7936 (p) cc_final: 0.7360 (p) outliers start: 59 outliers final: 27 residues processed: 577 average time/residue: 0.3571 time to fit residues: 309.4976 Evaluate side-chains 467 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 440 time to evaluate : 2.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 SER 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 53 GLN Chi-restraints excluded: chain D residue 313 LEU 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 313 LEU Chi-restraints excluded: chain F residue 392 ILE 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 313 LEU 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 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 211 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 30.0000 chunk 275 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 252 optimal weight: 0.0870 chunk 86 optimal weight: 1.9990 chunk 204 optimal weight: 30.0000 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 286 GLN B 53 GLN B 353 GLN C 271 GLN C 286 GLN C 333 ASN D 53 GLN ** D 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 GLN E 271 GLN E 333 ASN F 53 GLN G 271 GLN G 286 GLN G 333 ASN H 53 GLN H 315 GLN H 353 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22600 Z= 0.234 Angle : 0.695 12.832 30668 Z= 0.342 Chirality : 0.045 0.264 3416 Planarity : 0.005 0.042 3892 Dihedral : 8.798 62.005 3361 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.52 % Allowed : 12.46 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.15), residues: 2832 helix: -0.86 (0.12), residues: 1640 sheet: -0.40 (0.37), residues: 176 loop : -1.23 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 150 HIS 0.007 0.001 HIS G 135 PHE 0.029 0.002 PHE D 330 TYR 0.012 0.002 TYR F 266 ARG 0.005 0.000 ARG E 284 *********************** 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 532 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 476 time to evaluate : 2.557 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 313 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8313 (tp) REVERT: D 129 ASP cc_start: 0.7782 (t0) cc_final: 0.7541 (t0) REVERT: D 313 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8254 (tp) REVERT: E 75 LEU cc_start: 0.9074 (tp) cc_final: 0.8708 (tp) REVERT: F 151 LEU cc_start: 0.8527 (pp) cc_final: 0.8221 (pp) REVERT: F 313 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8278 (tp) REVERT: H 313 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8417 (tp) outliers start: 56 outliers final: 30 residues processed: 502 average time/residue: 0.3544 time to fit residues: 272.3234 Evaluate side-chains 451 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 417 time to evaluate : 2.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 313 LEU Chi-restraints excluded: chain B residue 376 MET 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 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 313 LEU Chi-restraints excluded: chain D residue 376 MET 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 313 LEU Chi-restraints excluded: chain F residue 376 MET 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 338 GLN Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 251 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 255 optimal weight: 20.0000 chunk 270 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 242 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D 53 GLN D 353 GLN E 286 GLN F 53 GLN G 314 ASN H 53 GLN H 353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 22600 Z= 0.421 Angle : 0.754 14.424 30668 Z= 0.369 Chirality : 0.048 0.282 3416 Planarity : 0.005 0.042 3892 Dihedral : 9.758 69.519 3361 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.37 % Allowed : 13.80 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.16), residues: 2832 helix: -0.27 (0.13), residues: 1580 sheet: -0.47 (0.43), residues: 136 loop : -0.96 (0.19), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 232 HIS 0.011 0.001 HIS C 135 PHE 0.041 0.002 PHE F 237 TYR 0.020 0.002 TYR B 116 ARG 0.006 0.001 ARG F 82 *********************** 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 522 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 447 time to evaluate : 2.569 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: B 120 GLU cc_start: 0.6834 (tp30) cc_final: 0.5738 (tp30) REVERT: B 290 GLN cc_start: 0.7570 (pp30) cc_final: 0.7327 (pm20) REVERT: B 313 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8292 (tp) REVERT: D 313 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8302 (tp) REVERT: F 151 LEU cc_start: 0.8584 (pp) cc_final: 0.8317 (pp) REVERT: H 313 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8462 (tp) outliers start: 75 outliers final: 45 residues processed: 482 average time/residue: 0.3445 time to fit residues: 251.3615 Evaluate side-chains 463 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 415 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 292 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 313 LEU Chi-restraints excluded: chain B residue 376 MET 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 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 D residue 98 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 331 LEU 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 351 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 402 VAL 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 155 VAL 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 343 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 225 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 187 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 138 optimal weight: 0.2980 chunk 242 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D 353 GLN H 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22600 Z= 0.218 Angle : 0.677 11.220 30668 Z= 0.331 Chirality : 0.044 0.242 3416 Planarity : 0.004 0.043 3892 Dihedral : 9.852 68.240 3361 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.70 % Allowed : 15.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2832 helix: 0.03 (0.13), residues: 1568 sheet: -0.31 (0.39), residues: 176 loop : -0.83 (0.20), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 363 HIS 0.007 0.001 HIS G 135 PHE 0.042 0.002 PHE H 292 TYR 0.009 0.001 TYR H 266 ARG 0.005 0.000 ARG A 284 *********************** 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 499 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 439 time to evaluate : 2.544 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: D 313 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8336 (tp) REVERT: H 290 GLN cc_start: 0.7903 (pp30) cc_final: 0.7484 (pm20) REVERT: H 313 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8384 (tp) outliers start: 60 outliers final: 39 residues processed: 465 average time/residue: 0.3501 time to fit residues: 245.8964 Evaluate side-chains 452 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 411 time to evaluate : 2.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 352 ASP Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 408 ASN 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 313 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 376 MET 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 315 GLU Chi-restraints excluded: chain G residue 348 VAL Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 91 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 53 optimal weight: 30.0000 chunk 158 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 270 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 305 GLN D 353 GLN F 315 GLN H 353 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.4893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22600 Z= 0.395 Angle : 0.737 14.543 30668 Z= 0.364 Chirality : 0.047 0.259 3416 Planarity : 0.005 0.065 3892 Dihedral : 10.095 69.091 3361 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.28 % Allowed : 15.65 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.16), residues: 2832 helix: 0.09 (0.13), residues: 1576 sheet: -0.65 (0.43), residues: 136 loop : -0.84 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 363 HIS 0.009 0.001 HIS C 135 PHE 0.026 0.002 PHE D 330 TYR 0.015 0.002 TYR B 116 ARG 0.004 0.000 ARG B 80 *********************** 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 501 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 428 time to evaluate : 2.695 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: B 313 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8162 (tp) REVERT: D 313 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8143 (tp) REVERT: D 384 LYS cc_start: 0.7288 (mmtt) cc_final: 0.6721 (mmtt) outliers start: 73 outliers final: 51 residues processed: 466 average time/residue: 0.3620 time to fit residues: 255.2564 Evaluate side-chains 462 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 409 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 187 THR 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 98 LEU Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 408 ASN 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 98 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 313 LEU 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 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 313 LEU Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain F residue 376 MET 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 106 LEU Chi-restraints excluded: chain H residue 237 PHE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 261 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 269 optimal weight: 8.9990 chunk 168 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 124 optimal weight: 0.6980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D 353 GLN E 305 GLN H 353 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22600 Z= 0.238 Angle : 0.702 14.531 30668 Z= 0.343 Chirality : 0.045 0.292 3416 Planarity : 0.004 0.040 3892 Dihedral : 9.988 67.825 3361 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.79 % Allowed : 16.64 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2832 helix: 0.17 (0.13), residues: 1596 sheet: -0.80 (0.35), residues: 216 loop : -0.74 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 363 HIS 0.007 0.001 HIS G 135 PHE 0.041 0.002 PHE D 292 TYR 0.010 0.001 TYR F 155 ARG 0.008 0.000 ARG C 284 *********************** 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 500 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 438 time to evaluate : 2.412 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: A 231 GLU cc_start: 0.7583 (tp30) cc_final: 0.7263 (tp30) REVERT: B 290 GLN cc_start: 0.7534 (pp30) cc_final: 0.7099 (pm20) REVERT: D 313 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8262 (tp) REVERT: E 331 MET cc_start: 0.7993 (mmm) cc_final: 0.7745 (mmm) REVERT: F 351 ASP cc_start: 0.6845 (p0) cc_final: 0.6581 (p0) REVERT: H 298 LEU cc_start: 0.8379 (mp) cc_final: 0.8058 (mp) outliers start: 62 outliers final: 48 residues processed: 473 average time/residue: 0.3453 time to fit residues: 249.3688 Evaluate side-chains 460 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 411 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 315 GLU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 67 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 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 106 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 353 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 106 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 324 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 315 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 166 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 161 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 52 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 183 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN B 256 ASN B 353 GLN D 353 GLN H 53 GLN H 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22600 Z= 0.328 Angle : 0.733 14.135 30668 Z= 0.360 Chirality : 0.046 0.192 3416 Planarity : 0.004 0.039 3892 Dihedral : 9.962 67.109 3360 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.70 % Allowed : 17.22 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2832 helix: 0.16 (0.13), residues: 1600 sheet: -1.09 (0.37), residues: 176 loop : -0.72 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 363 HIS 0.008 0.001 HIS C 135 PHE 0.036 0.002 PHE D 344 TYR 0.013 0.001 TYR F 90 ARG 0.008 0.000 ARG A 284 *********************** 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 485 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 425 time to evaluate : 2.561 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 231 GLU cc_start: 0.7572 (tp30) cc_final: 0.7201 (tp30) REVERT: D 313 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8242 (tp) REVERT: F 151 LEU cc_start: 0.8645 (tp) cc_final: 0.8371 (pp) REVERT: F 351 ASP cc_start: 0.6972 (p0) cc_final: 0.6718 (p0) REVERT: H 290 GLN cc_start: 0.7859 (pp30) cc_final: 0.7568 (pm20) outliers start: 60 outliers final: 48 residues processed: 459 average time/residue: 0.3431 time to fit residues: 239.6624 Evaluate side-chains 459 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 410 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 106 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 408 ASN 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 98 LEU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 324 LEU 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 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 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 67 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 237 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 353 GLN Chi-restraints excluded: chain H residue 376 MET 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 245 optimal weight: 1.9990 chunk 258 optimal weight: 50.0000 chunk 235 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 151 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 227 optimal weight: 0.9990 chunk 237 optimal weight: 0.3980 chunk 250 optimal weight: 0.4980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 305 GLN D 353 GLN E 305 GLN F 315 GLN H 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22600 Z= 0.212 Angle : 0.719 12.172 30668 Z= 0.351 Chirality : 0.044 0.243 3416 Planarity : 0.004 0.039 3892 Dihedral : 9.812 65.954 3360 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.34 % Allowed : 18.21 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2832 helix: 0.26 (0.13), residues: 1596 sheet: -0.78 (0.35), residues: 216 loop : -0.65 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 150 HIS 0.006 0.001 HIS G 135 PHE 0.056 0.002 PHE F 330 TYR 0.010 0.001 TYR H 343 ARG 0.008 0.000 ARG C 284 *********************** 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 480 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 428 time to evaluate : 2.586 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: A 231 GLU cc_start: 0.7542 (tp30) cc_final: 0.7320 (tp30) REVERT: D 151 LEU cc_start: 0.8689 (pp) cc_final: 0.8449 (pp) REVERT: D 313 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 331 MET cc_start: 0.7848 (mmm) cc_final: 0.7615 (mmm) REVERT: F 151 LEU cc_start: 0.8679 (tp) cc_final: 0.8401 (pp) REVERT: H 151 LEU cc_start: 0.8725 (tp) cc_final: 0.8420 (pp) outliers start: 52 outliers final: 44 residues processed: 458 average time/residue: 0.3464 time to fit residues: 241.5904 Evaluate side-chains 460 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 415 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 106 LEU 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 C residue 78 ASP 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 106 LEU Chi-restraints excluded: chain D residue 313 LEU 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 293 GLN Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG 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 315 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 237 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 165 optimal weight: 1.9990 chunk 265 optimal weight: 6.9990 chunk 162 optimal weight: 0.0670 chunk 126 optimal weight: 50.0000 chunk 184 optimal weight: 30.0000 chunk 278 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 222 optimal weight: 0.0670 chunk 23 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN A 305 GLN ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 22600 Z= 0.343 Angle : 0.862 59.198 30668 Z= 0.451 Chirality : 0.047 0.561 3416 Planarity : 0.004 0.058 3892 Dihedral : 9.805 65.953 3360 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.16 % Allowed : 18.35 % Favored : 79.50 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2832 helix: 0.26 (0.13), residues: 1596 sheet: -0.77 (0.35), residues: 216 loop : -0.64 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.003 TRP D 150 HIS 0.006 0.001 HIS G 135 PHE 0.034 0.002 PHE F 330 TYR 0.010 0.001 TYR H 343 ARG 0.004 0.000 ARG D 240 ********************** 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 462 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 414 time to evaluate : 2.394 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: D 151 LEU cc_start: 0.8674 (pp) cc_final: 0.8456 (pp) REVERT: D 313 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8280 (tp) REVERT: F 151 LEU cc_start: 0.8677 (tp) cc_final: 0.8403 (pp) REVERT: H 151 LEU cc_start: 0.8728 (tp) cc_final: 0.8433 (pp) outliers start: 48 outliers final: 43 residues processed: 444 average time/residue: 0.3420 time to fit residues: 231.9083 Evaluate side-chains 459 residues out of total 2480 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 415 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET 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 106 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 340 SER 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 106 LEU Chi-restraints excluded: chain D residue 313 LEU 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 293 GLN Chi-restraints excluded: chain E residue 352 ASP Chi-restraints excluded: chain F residue 99 ARG Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 331 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 315 GLU Chi-restraints excluded: chain G residue 343 LEU Chi-restraints excluded: chain H residue 67 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 237 PHE Chi-restraints excluded: chain H residue 288 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 376 MET 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 176 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 204 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 222 optimal weight: 0.0870 chunk 93 optimal weight: 4.9990 chunk 228 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 353 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 = 0.4309 r_free = 0.4309 target = 0.195521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145033 restraints weight = 29331.630| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.13 r_work: 0.3120 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.275 22600 Z= 0.343 Angle : 0.862 59.198 30668 Z= 0.451 Chirality : 0.047 0.561 3416 Planarity : 0.004 0.058 3892 Dihedral : 9.805 65.953 3360 Min Nonbonded Distance : 1.665 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.98 % Allowed : 18.66 % Favored : 79.36 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2832 helix: 0.26 (0.13), residues: 1596 sheet: -0.77 (0.35), residues: 216 loop : -0.64 (0.21), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.097 0.003 TRP D 150 HIS 0.006 0.001 HIS G 135 PHE 0.034 0.002 PHE F 330 TYR 0.010 0.001 TYR H 343 ARG 0.004 0.000 ARG D 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6342.12 seconds wall clock time: 111 minutes 56.60 seconds (6716.60 seconds total)