Starting phenix.real_space_refine on Mon Jul 6 15:38:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chz_45605/07_2026/9chz_45605.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.221 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 224 5.16 5 C 23536 2.51 5 N 6416 2.21 5 O 6856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 103 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37056 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3645 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 442} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "J" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "K" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "L" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "M" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "O" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "P" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 965 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 11, 'TRANS': 106} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.29, per 1000 atoms: 0.22 Number of scatterers: 37056 At special positions: 0 Unit cell: (133.44, 134.83, 132.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 224 16.00 P 16 15.00 Mg 8 11.99 O 6856 8.00 N 6416 7.00 C 23536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.5 seconds 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8432 Finding SS restraints... Secondary structure from input PDB file: 202 helices and 40 sheets defined 41.1% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.936A pdb=" N LEU A 22 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR A 23 " --> pdb=" O TYR A 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 19 through 23' Processing helix chain 'A' and resid 54 through 63 removed outlier: 3.613A pdb=" N ALA A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER A 62 " --> pdb=" O ALA A 58 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 63 " --> pdb=" O ALA A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.911A pdb=" N ASP A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY A 73 " --> pdb=" O TRP A 70 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.762A pdb=" N LEU A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE A 108 " --> pdb=" O LEU A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 112 through 121 removed outlier: 4.252A pdb=" N MET A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.683A pdb=" N GLY A 126 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.507A pdb=" N SER A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 141 through 146' Processing helix chain 'A' and resid 157 through 162 removed outlier: 3.808A pdb=" N LYS A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 162 " --> pdb=" O GLU A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 162' Processing helix chain 'A' and resid 181 through 186 removed outlier: 3.857A pdb=" N GLY A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.744A pdb=" N TYR A 190 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 191 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N CYS A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 removed outlier: 3.630A pdb=" N ARG A 217 " --> pdb=" O ARG A 213 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 219 " --> pdb=" O ARG A 215 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 220 " --> pdb=" O ASP A 216 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA A 222 " --> pdb=" O PHE A 218 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 224 " --> pdb=" O PHE A 220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 227 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.747A pdb=" N GLN A 255 " --> pdb=" O MET A 251 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 256 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 260 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 288 removed outlier: 3.730A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS A 282 " --> pdb=" O THR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.808A pdb=" N VAL A 300 " --> pdb=" O MET A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.551A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS A 316 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 removed outlier: 3.966A pdb=" N ASP A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 removed outlier: 3.581A pdb=" N GLU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 393 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.600A pdb=" N VAL A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 421 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 449 Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.848A pdb=" N ALA A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 458 " --> pdb=" O GLU A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.931A pdb=" N LEU B 22 " --> pdb=" O ASP B 19 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 23 " --> pdb=" O TYR B 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 19 through 23' Processing helix chain 'B' and resid 49 through 63 removed outlier: 3.622A pdb=" N GLY B 54 " --> pdb=" O PRO B 50 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 62 " --> pdb=" O ALA B 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.910A pdb=" N ASP B 72 " --> pdb=" O VAL B 69 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY B 73 " --> pdb=" O TRP B 70 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 75 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.780A pdb=" N LEU B 107 " --> pdb=" O PRO B 104 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B 108 " --> pdb=" O LEU B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 104 through 108' Processing helix chain 'B' and resid 112 through 121 removed outlier: 4.238A pdb=" N MET B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.732A pdb=" N GLY B 126 " --> pdb=" O ASN B 123 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 127 " --> pdb=" O VAL B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.501A pdb=" N SER B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 141 through 146' Processing helix chain 'B' and resid 157 through 163 removed outlier: 3.707A pdb=" N LYS B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 162 " --> pdb=" O GLU B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 removed outlier: 3.583A pdb=" N ARG B 187 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 189 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR B 190 " --> pdb=" O GLY B 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLU B 191 " --> pdb=" O ARG B 187 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N CYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 removed outlier: 3.639A pdb=" N ARG B 217 " --> pdb=" O ARG B 213 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 219 " --> pdb=" O ARG B 215 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 222 " --> pdb=" O PHE B 218 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA B 224 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 226 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS B 227 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 230 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU B 231 " --> pdb=" O LYS B 227 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 254 through 260 removed outlier: 3.668A pdb=" N ARG B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.626A pdb=" N ASN B 277 " --> pdb=" O GLY B 273 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR B 278 " --> pdb=" O PHE B 274 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 279 " --> pdb=" O THR B 275 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 286 " --> pdb=" O HIS B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.876A pdb=" N ARG B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.569A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LYS B 316 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 317 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 removed outlier: 3.994A pdb=" N ASP B 347 " --> pdb=" O LEU B 343 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 348 " --> pdb=" O GLY B 344 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 removed outlier: 3.598A pdb=" N GLU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 393 " --> pdb=" O ALA B 389 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 414 through 432 removed outlier: 3.630A pdb=" N VAL B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 419 " --> pdb=" O PRO B 415 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASN B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 421 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU B 424 " --> pdb=" O ASN B 420 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N CYS B 427 " --> pdb=" O ALA B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 449 removed outlier: 3.550A pdb=" N ILE B 445 " --> pdb=" O GLY B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.779A pdb=" N ALA B 456 " --> pdb=" O SER B 452 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 458 " --> pdb=" O GLU B 454 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.927A pdb=" N LEU C 22 " --> pdb=" O ASP C 19 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR C 23 " --> pdb=" O TYR C 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 19 through 23' Processing helix chain 'C' and resid 49 through 63 removed outlier: 3.631A pdb=" N GLY C 54 " --> pdb=" O PRO C 50 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER C 61 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER C 62 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.885A pdb=" N ASP C 72 " --> pdb=" O VAL C 69 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY C 73 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 75 " --> pdb=" O ASP C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.777A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 108 " --> pdb=" O LEU C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 104 through 108' Processing helix chain 'C' and resid 112 through 121 removed outlier: 4.235A pdb=" N MET C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.729A pdb=" N GLY C 126 " --> pdb=" O ASN C 123 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE C 127 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.724A pdb=" N LYS C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 163 removed outlier: 3.712A pdb=" N LYS C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 162 " --> pdb=" O GLU C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 removed outlier: 3.580A pdb=" N ARG C 187 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA C 188 " --> pdb=" O ASN C 184 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 189 " --> pdb=" O TYR C 185 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 190 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N CYS C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 removed outlier: 3.616A pdb=" N ARG C 217 " --> pdb=" O ARG C 213 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 219 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C 222 " --> pdb=" O PHE C 218 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 225 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 232 " --> pdb=" O SER C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 254 removed outlier: 3.746A pdb=" N LYS C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 261 removed outlier: 3.647A pdb=" N ARG C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 288 removed outlier: 3.549A pdb=" N ASN C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR C 278 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 279 " --> pdb=" O THR C 275 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 281 " --> pdb=" O ASN C 277 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N HIS C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 303 removed outlier: 3.844A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.540A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS C 316 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N MET C 320 " --> pdb=" O LYS C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 removed outlier: 4.002A pdb=" N ASP C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU C 348 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 removed outlier: 3.590A pdb=" N GLU C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 414 through 432 removed outlier: 3.710A pdb=" N VAL C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 424 " --> pdb=" O ASN C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 449 removed outlier: 3.584A pdb=" N ILE C 445 " --> pdb=" O GLY C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 459 removed outlier: 3.775A pdb=" N ALA C 456 " --> pdb=" O SER C 452 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 457 " --> pdb=" O PRO C 453 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA C 458 " --> pdb=" O GLU C 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.938A pdb=" N LEU D 22 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR D 23 " --> pdb=" O TYR D 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 19 through 23' Processing helix chain 'D' and resid 49 through 63 removed outlier: 3.515A pdb=" N ALA D 53 " --> pdb=" O PRO D 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 54 " --> pdb=" O PRO D 50 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER D 61 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.909A pdb=" N ASP D 72 " --> pdb=" O VAL D 69 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY D 73 " --> pdb=" O TRP D 70 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR D 75 " --> pdb=" O ASP D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.778A pdb=" N LEU D 107 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 108 " --> pdb=" O LEU D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 112 through 121 removed outlier: 4.242A pdb=" N MET D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.735A pdb=" N GLY D 126 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 127 " --> pdb=" O VAL D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 127' Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.506A pdb=" N SER D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 141 through 146' Processing helix chain 'D' and resid 155 through 163 removed outlier: 3.777A pdb=" N ASP D 160 " --> pdb=" O GLN D 156 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 194 removed outlier: 3.579A pdb=" N ARG D 187 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 188 " --> pdb=" O ASN D 184 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 189 " --> pdb=" O TYR D 185 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR D 190 " --> pdb=" O GLY D 186 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLU D 191 " --> pdb=" O ARG D 187 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 233 removed outlier: 3.726A pdb=" N ARG D 217 " --> pdb=" O ARG D 213 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 219 " --> pdb=" O ARG D 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 222 " --> pdb=" O PHE D 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE D 225 " --> pdb=" O VAL D 221 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 260 removed outlier: 3.739A pdb=" N LYS D 252 " --> pdb=" O GLU D 248 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 254 " --> pdb=" O MET D 250 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN D 255 " --> pdb=" O MET D 251 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG D 258 " --> pdb=" O ALA D 254 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 260 " --> pdb=" O PHE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 288 removed outlier: 3.674A pdb=" N ASN D 277 " --> pdb=" O GLY D 273 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D 278 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR D 279 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 3.799A pdb=" N VAL D 300 " --> pdb=" O MET D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.540A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS D 316 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA D 317 " --> pdb=" O VAL D 313 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N MET D 320 " --> pdb=" O LYS D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 removed outlier: 3.998A pdb=" N ASP D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU D 348 " --> pdb=" O GLY D 344 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU D 349 " --> pdb=" O PHE D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 removed outlier: 3.750A pdb=" N GLU D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE D 393 " --> pdb=" O ALA D 389 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 414 through 432 removed outlier: 3.640A pdb=" N VAL D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASN D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 421 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU D 424 " --> pdb=" O ASN D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 449 removed outlier: 3.584A pdb=" N ILE D 445 " --> pdb=" O GLY D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 459 removed outlier: 3.772A pdb=" N ALA D 456 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 457 " --> pdb=" O PRO D 453 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.937A pdb=" N LEU E 22 " --> pdb=" O ASP E 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 23 " --> pdb=" O TYR E 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 19 through 23' Processing helix chain 'E' and resid 49 through 63 removed outlier: 3.628A pdb=" N GLY E 54 " --> pdb=" O PRO E 50 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU E 60 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 63 " --> pdb=" O ALA E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 75 removed outlier: 3.909A pdb=" N ASP E 72 " --> pdb=" O VAL E 69 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLY E 73 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.778A pdb=" N LEU E 107 " --> pdb=" O PRO E 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE E 108 " --> pdb=" O LEU E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 108' Processing helix chain 'E' and resid 112 through 121 removed outlier: 4.249A pdb=" N MET E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE E 117 " --> pdb=" O VAL E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.731A pdb=" N GLY E 126 " --> pdb=" O ASN E 123 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.724A pdb=" N LYS E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 163 removed outlier: 3.692A pdb=" N LYS E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 186 removed outlier: 3.854A pdb=" N GLY E 186 " --> pdb=" O ALA E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 194 removed outlier: 3.726A pdb=" N TYR E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU E 191 " --> pdb=" O ARG E 187 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N CYS E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 233 removed outlier: 3.720A pdb=" N ARG E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU E 219 " --> pdb=" O ARG E 215 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA E 222 " --> pdb=" O PHE E 218 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 223 " --> pdb=" O LEU E 219 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA E 224 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 225 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS E 227 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 230 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU E 231 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 260 removed outlier: 3.691A pdb=" N LYS E 252 " --> pdb=" O GLU E 248 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 254 " --> pdb=" O MET E 250 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA E 257 " --> pdb=" O ARG E 253 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG E 258 " --> pdb=" O ALA E 254 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 260 " --> pdb=" O PHE E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 286 removed outlier: 3.523A pdb=" N ASN E 277 " --> pdb=" O GLY E 273 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR E 278 " --> pdb=" O PHE E 274 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR E 279 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 280 " --> pdb=" O ALA E 276 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP E 286 " --> pdb=" O HIS E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 303 removed outlier: 3.869A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.543A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS E 316 " --> pdb=" O ARG E 312 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA E 317 " --> pdb=" O VAL E 313 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 removed outlier: 4.007A pdb=" N ASP E 347 " --> pdb=" O LEU E 343 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 348 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU E 349 " --> pdb=" O PHE E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 395 removed outlier: 3.748A pdb=" N GLU E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE E 393 " --> pdb=" O ALA E 389 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 408 Processing helix chain 'E' and resid 414 through 432 removed outlier: 3.623A pdb=" N VAL E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 419 " --> pdb=" O PRO E 415 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASN E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG E 421 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 424 " --> pdb=" O ASN E 420 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 449 removed outlier: 3.563A pdb=" N ILE E 445 " --> pdb=" O GLY E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 459 removed outlier: 3.786A pdb=" N ALA E 458 " --> pdb=" O GLU E 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.932A pdb=" N LEU F 22 " --> pdb=" O ASP F 19 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR F 23 " --> pdb=" O TYR F 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 19 through 23' Processing helix chain 'F' and resid 49 through 63 removed outlier: 3.515A pdb=" N ALA F 53 " --> pdb=" O PRO F 49 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY F 54 " --> pdb=" O PRO F 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.885A pdb=" N ASP F 72 " --> pdb=" O VAL F 69 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 73 " --> pdb=" O TRP F 70 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR F 75 " --> pdb=" O ASP F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.783A pdb=" N LEU F 107 " --> pdb=" O PRO F 104 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE F 108 " --> pdb=" O LEU F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 112 through 121 removed outlier: 4.241A pdb=" N MET F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.730A pdb=" N GLY F 126 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE F 127 " --> pdb=" O VAL F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 141 through 146 removed outlier: 3.506A pdb=" N SER F 145 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS F 146 " --> pdb=" O PRO F 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 141 through 146' Processing helix chain 'F' and resid 157 through 163 removed outlier: 3.706A pdb=" N LYS F 161 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU F 162 " --> pdb=" O GLU F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 186 removed outlier: 3.852A pdb=" N GLY F 186 " --> pdb=" O ALA F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 194 removed outlier: 3.729A pdb=" N TYR F 190 " --> pdb=" O GLY F 186 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 removed outlier: 3.722A pdb=" N ARG F 217 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU F 219 " --> pdb=" O ARG F 215 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 222 " --> pdb=" O PHE F 218 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 223 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA F 224 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE F 225 " --> pdb=" O VAL F 221 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU F 231 " --> pdb=" O LYS F 227 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 251 Processing helix chain 'F' and resid 254 through 261 removed outlier: 3.643A pdb=" N ARG F 258 " --> pdb=" O ALA F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 288 removed outlier: 3.545A pdb=" N ASN F 277 " --> pdb=" O GLY F 273 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR F 278 " --> pdb=" O PHE F 274 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 279 " --> pdb=" O THR F 275 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU F 280 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS F 282 " --> pdb=" O THR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 303 removed outlier: 3.869A pdb=" N ARG F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.551A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LYS F 316 " --> pdb=" O ARG F 312 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 317 " --> pdb=" O VAL F 313 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET F 320 " --> pdb=" O LYS F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 removed outlier: 3.998A pdb=" N ASP F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU F 348 " --> pdb=" O GLY F 344 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU F 349 " --> pdb=" O PHE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 removed outlier: 3.591A pdb=" N GLU F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE F 393 " --> pdb=" O ALA F 389 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 408 Processing helix chain 'F' and resid 414 through 432 removed outlier: 3.701A pdb=" N VAL F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA F 419 " --> pdb=" O PRO F 415 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASN F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG F 421 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU F 424 " --> pdb=" O ASN F 420 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS F 427 " --> pdb=" O ALA F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 449 removed outlier: 3.573A pdb=" N ILE F 445 " --> pdb=" O GLY F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 459 removed outlier: 3.771A pdb=" N ALA F 456 " --> pdb=" O SER F 452 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.932A pdb=" N LEU G 22 " --> pdb=" O ASP G 19 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR G 23 " --> pdb=" O TYR G 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 19 through 23' Processing helix chain 'G' and resid 49 through 63 removed outlier: 3.517A pdb=" N ALA G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY G 54 " --> pdb=" O PRO G 50 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER G 61 " --> pdb=" O VAL G 57 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 75 removed outlier: 3.885A pdb=" N ASP G 72 " --> pdb=" O VAL G 69 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY G 73 " --> pdb=" O TRP G 70 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR G 75 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 removed outlier: 3.774A pdb=" N LEU G 107 " --> pdb=" O PRO G 104 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE G 108 " --> pdb=" O LEU G 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 104 through 108' Processing helix chain 'G' and resid 112 through 121 removed outlier: 4.240A pdb=" N MET G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.729A pdb=" N GLY G 126 " --> pdb=" O ASN G 123 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE G 127 " --> pdb=" O VAL G 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 123 through 127' Processing helix chain 'G' and resid 141 through 146 removed outlier: 3.505A pdb=" N SER G 145 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS G 146 " --> pdb=" O PRO G 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 141 through 146' Processing helix chain 'G' and resid 157 through 163 removed outlier: 3.745A pdb=" N LYS G 161 " --> pdb=" O VAL G 157 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU G 162 " --> pdb=" O GLU G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 186 removed outlier: 3.840A pdb=" N GLY G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 194 removed outlier: 3.736A pdb=" N TYR G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N CYS G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 233 removed outlier: 3.722A pdb=" N ARG G 217 " --> pdb=" O ARG G 213 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU G 219 " --> pdb=" O ARG G 215 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 222 " --> pdb=" O PHE G 218 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU G 223 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA G 224 " --> pdb=" O PHE G 220 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE G 225 " --> pdb=" O VAL G 221 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE G 226 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS G 227 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G 230 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR G 232 " --> pdb=" O SER G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 260 removed outlier: 3.686A pdb=" N LYS G 252 " --> pdb=" O GLU G 248 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA G 254 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G 255 " --> pdb=" O MET G 251 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE G 256 " --> pdb=" O LYS G 252 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ALA G 257 " --> pdb=" O ARG G 253 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG G 258 " --> pdb=" O ALA G 254 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU G 259 " --> pdb=" O GLN G 255 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU G 260 " --> pdb=" O PHE G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 286 removed outlier: 3.531A pdb=" N ASN G 277 " --> pdb=" O GLY G 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR G 278 " --> pdb=" O PHE G 274 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR G 279 " --> pdb=" O THR G 275 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU G 280 " --> pdb=" O ALA G 276 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 281 " --> pdb=" O ASN G 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS G 282 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP G 286 " --> pdb=" O HIS G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 301 removed outlier: 3.847A pdb=" N VAL G 300 " --> pdb=" O MET G 297 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.535A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS G 316 " --> pdb=" O ARG G 312 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 317 " --> pdb=" O VAL G 313 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET G 320 " --> pdb=" O LYS G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 351 removed outlier: 4.027A pdb=" N ASP G 347 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU G 349 " --> pdb=" O PHE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 395 removed outlier: 3.614A pdb=" N GLU G 392 " --> pdb=" O PRO G 388 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE G 393 " --> pdb=" O ALA G 389 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE G 394 " --> pdb=" O LEU G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 403 through 408 Processing helix chain 'G' and resid 414 through 432 removed outlier: 3.713A pdb=" N VAL G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA G 419 " --> pdb=" O PRO G 415 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA G 423 " --> pdb=" O ALA G 419 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 424 " --> pdb=" O ASN G 420 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 449 removed outlier: 3.581A pdb=" N ILE G 445 " --> pdb=" O GLY G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 459 removed outlier: 3.784A pdb=" N ALA G 456 " --> pdb=" O SER G 452 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA G 457 " --> pdb=" O PRO G 453 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA G 458 " --> pdb=" O GLU G 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.917A pdb=" N LEU H 22 " --> pdb=" O ASP H 19 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR H 23 " --> pdb=" O TYR H 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 19 through 23' Processing helix chain 'H' and resid 49 through 63 removed outlier: 3.516A pdb=" N ALA H 53 " --> pdb=" O PRO H 49 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY H 54 " --> pdb=" O PRO H 50 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 58 " --> pdb=" O GLY H 54 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER H 61 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER H 62 " --> pdb=" O ALA H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 75 removed outlier: 3.909A pdb=" N ASP H 72 " --> pdb=" O VAL H 69 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY H 73 " --> pdb=" O TRP H 70 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR H 75 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.778A pdb=" N LEU H 107 " --> pdb=" O PRO H 104 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE H 108 " --> pdb=" O LEU H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 104 through 108' Processing helix chain 'H' and resid 112 through 121 removed outlier: 4.243A pdb=" N MET H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE H 117 " --> pdb=" O VAL H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 127 removed outlier: 3.729A pdb=" N GLY H 126 " --> pdb=" O ASN H 123 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE H 127 " --> pdb=" O VAL H 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 123 through 127' Processing helix chain 'H' and resid 141 through 146 removed outlier: 3.721A pdb=" N LYS H 146 " --> pdb=" O PRO H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 163 removed outlier: 3.693A pdb=" N LYS H 161 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU H 162 " --> pdb=" O GLU H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 removed outlier: 3.786A pdb=" N GLY H 186 " --> pdb=" O ALA H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 194 removed outlier: 3.732A pdb=" N TYR H 190 " --> pdb=" O GLY H 186 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU H 191 " --> pdb=" O ARG H 187 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 233 removed outlier: 3.723A pdb=" N ARG H 217 " --> pdb=" O ARG H 213 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H 219 " --> pdb=" O ARG H 215 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA H 222 " --> pdb=" O PHE H 218 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU H 223 " --> pdb=" O LEU H 219 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA H 224 " --> pdb=" O PHE H 220 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE H 225 " --> pdb=" O VAL H 221 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE H 226 " --> pdb=" O ALA H 222 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS H 227 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 230 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 251 Processing helix chain 'H' and resid 251 through 260 removed outlier: 3.787A pdb=" N GLN H 255 " --> pdb=" O MET H 251 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE H 256 " --> pdb=" O LYS H 252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA H 257 " --> pdb=" O ARG H 253 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG H 258 " --> pdb=" O ALA H 254 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 260 " --> pdb=" O PHE H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 286 removed outlier: 3.530A pdb=" N ASN H 277 " --> pdb=" O GLY H 273 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 278 " --> pdb=" O PHE H 274 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR H 279 " --> pdb=" O THR H 275 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU H 280 " --> pdb=" O ALA H 276 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA H 281 " --> pdb=" O ASN H 277 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS H 282 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP H 286 " --> pdb=" O HIS H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.823A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.537A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS H 316 " --> pdb=" O ARG H 312 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 317 " --> pdb=" O VAL H 313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N MET H 320 " --> pdb=" O LYS H 316 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 removed outlier: 3.988A pdb=" N ASP H 347 " --> pdb=" O LEU H 343 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU H 348 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU H 349 " --> pdb=" O PHE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 removed outlier: 3.754A pdb=" N GLU H 392 " --> pdb=" O PRO H 388 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE H 393 " --> pdb=" O ALA H 389 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE H 394 " --> pdb=" O LEU H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 403 through 408 Processing helix chain 'H' and resid 414 through 432 removed outlier: 3.710A pdb=" N VAL H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 419 " --> pdb=" O PRO H 415 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG H 421 " --> pdb=" O ALA H 417 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 423 " --> pdb=" O ALA H 419 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 424 " --> pdb=" O ASN H 420 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS H 427 " --> pdb=" O ALA H 423 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 449 removed outlier: 3.523A pdb=" N ILE H 445 " --> pdb=" O GLY H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 459 removed outlier: 3.859A pdb=" N ALA H 456 " --> pdb=" O SER H 452 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA H 457 " --> pdb=" O PRO H 453 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA H 458 " --> pdb=" O GLU H 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 27 removed outlier: 3.767A pdb=" N ALA I 27 " --> pdb=" O ASP I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 35 removed outlier: 3.740A pdb=" N MET I 33 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 92 removed outlier: 3.722A pdb=" N LEU I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 83 " --> pdb=" O GLY I 79 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU I 86 " --> pdb=" O LEU I 82 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA I 91 " --> pdb=" O HIS I 87 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR I 92 " --> pdb=" O CYS I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 27 removed outlier: 3.777A pdb=" N ALA J 27 " --> pdb=" O ASP J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 35 removed outlier: 3.758A pdb=" N MET J 33 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 92 removed outlier: 3.749A pdb=" N LEU J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG J 83 " --> pdb=" O GLY J 79 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU J 86 " --> pdb=" O LEU J 82 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA J 91 " --> pdb=" O HIS J 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR J 92 " --> pdb=" O CYS J 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 27 removed outlier: 3.777A pdb=" N ALA K 27 " --> pdb=" O ASP K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 35 removed outlier: 3.751A pdb=" N MET K 33 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 92 removed outlier: 3.719A pdb=" N LEU K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG K 83 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU K 86 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA K 91 " --> pdb=" O HIS K 87 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR K 92 " --> pdb=" O CYS K 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 27 removed outlier: 3.803A pdb=" N ALA L 27 " --> pdb=" O ASP L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 35 removed outlier: 3.732A pdb=" N MET L 33 " --> pdb=" O GLU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 92 removed outlier: 3.759A pdb=" N LEU L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG L 83 " --> pdb=" O GLY L 79 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU L 86 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA L 91 " --> pdb=" O HIS L 87 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR L 92 " --> pdb=" O CYS L 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 27 removed outlier: 3.626A pdb=" N ILE M 26 " --> pdb=" O ASP M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 35 removed outlier: 3.772A pdb=" N MET M 33 " --> pdb=" O GLU M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 92 removed outlier: 3.758A pdb=" N LEU M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG M 83 " --> pdb=" O GLY M 79 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU M 86 " --> pdb=" O LEU M 82 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR M 92 " --> pdb=" O CYS M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 27 removed outlier: 3.799A pdb=" N ALA N 27 " --> pdb=" O ASP N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 35 removed outlier: 3.748A pdb=" N MET N 33 " --> pdb=" O GLU N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 92 removed outlier: 3.779A pdb=" N GLU N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA N 91 " --> pdb=" O HIS N 87 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR N 92 " --> pdb=" O CYS N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 27 removed outlier: 3.782A pdb=" N ALA O 27 " --> pdb=" O ASP O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 35 removed outlier: 3.737A pdb=" N MET O 33 " --> pdb=" O GLU O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 78 through 92 removed outlier: 3.759A pdb=" N LEU O 82 " --> pdb=" O ALA O 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG O 83 " --> pdb=" O GLY O 79 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU O 86 " --> pdb=" O LEU O 82 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA O 91 " --> pdb=" O HIS O 87 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR O 92 " --> pdb=" O CYS O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 23 through 27 removed outlier: 3.628A pdb=" N ILE P 26 " --> pdb=" O ASP P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 35 removed outlier: 3.773A pdb=" N MET P 33 " --> pdb=" O GLU P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 78 through 92 removed outlier: 3.739A pdb=" N LEU P 82 " --> pdb=" O ALA P 78 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA P 91 " --> pdb=" O HIS P 87 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR P 92 " --> pdb=" O CYS P 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 6.194A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 97 " --> pdb=" O MET A 42 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 43 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ALA A 132 " --> pdb=" O THR A 43 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 308 " --> pdb=" O LEU A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.779A pdb=" N ILE A 326 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241 removed outlier: 6.842A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N HIS A 294 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA5, first strand: chain 'B' and resid 83 through 89 removed outlier: 6.184A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 97 " --> pdb=" O MET B 42 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR B 43 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA B 132 " --> pdb=" O THR B 43 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 308 " --> pdb=" O LEU B 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 171 removed outlier: 6.786A pdb=" N ILE B 326 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 240 through 241 removed outlier: 6.831A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AA9, first strand: chain 'C' and resid 83 through 89 removed outlier: 6.190A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR C 97 " --> pdb=" O MET C 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 43 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA C 132 " --> pdb=" O THR C 43 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 308 " --> pdb=" O LEU C 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 171 removed outlier: 6.782A pdb=" N ILE C 326 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 240 through 241 removed outlier: 6.627A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.704A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS C 294 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'D' and resid 83 through 89 removed outlier: 6.185A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR D 97 " --> pdb=" O MET D 42 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR D 43 " --> pdb=" O ALA D 132 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA D 132 " --> pdb=" O THR D 43 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY D 308 " --> pdb=" O LEU D 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 169 through 171 removed outlier: 6.777A pdb=" N ILE D 326 " --> pdb=" O VAL D 377 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 240 through 241 removed outlier: 6.635A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 89 removed outlier: 6.194A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR E 97 " --> pdb=" O MET E 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR E 43 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA E 132 " --> pdb=" O THR E 43 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 308 " --> pdb=" O LEU E 133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 169 through 171 removed outlier: 6.786A pdb=" N ILE E 326 " --> pdb=" O VAL E 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 240 through 241 removed outlier: 6.834A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N HIS E 294 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N HIS E 267 " --> pdb=" O HIS E 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AC3, first strand: chain 'F' and resid 83 through 89 removed outlier: 6.197A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 97 " --> pdb=" O MET F 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F 43 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA F 132 " --> pdb=" O THR F 43 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY F 308 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 171 removed outlier: 6.779A pdb=" N ILE F 326 " --> pdb=" O VAL F 377 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 240 through 241 removed outlier: 6.870A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS F 294 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC7, first strand: chain 'G' and resid 83 through 89 removed outlier: 6.181A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ASP G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR G 97 " --> pdb=" O MET G 42 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR G 43 " --> pdb=" O ALA G 132 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA G 132 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY G 308 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 169 through 171 removed outlier: 6.779A pdb=" N ILE G 326 " --> pdb=" O VAL G 377 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 240 through 241 removed outlier: 6.615A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N HIS G 294 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AD2, first strand: chain 'H' and resid 83 through 89 removed outlier: 6.187A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR H 97 " --> pdb=" O MET H 42 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR H 43 " --> pdb=" O ALA H 132 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA H 132 " --> pdb=" O THR H 43 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY H 308 " --> pdb=" O LEU H 133 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 169 through 171 removed outlier: 6.781A pdb=" N ILE H 326 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 240 through 241 removed outlier: 6.623A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N HIS H 294 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AD6, first strand: chain 'I' and resid 66 through 67 removed outlier: 6.795A pdb=" N ILE I 97 " --> pdb=" O VAL I 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE I 113 " --> pdb=" O VAL I 99 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY I 101 " --> pdb=" O CYS I 111 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N CYS I 111 " --> pdb=" O GLY I 101 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ASP I 103 " --> pdb=" O GLN I 109 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN I 109 " --> pdb=" O ASP I 103 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 66 through 67 removed outlier: 6.782A pdb=" N ILE J 97 " --> pdb=" O VAL J 115 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY J 101 " --> pdb=" O CYS J 111 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS J 111 " --> pdb=" O GLY J 101 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ASP J 103 " --> pdb=" O GLN J 109 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN J 109 " --> pdb=" O ASP J 103 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 66 through 67 removed outlier: 6.779A pdb=" N ILE K 97 " --> pdb=" O VAL K 115 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE K 113 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY K 101 " --> pdb=" O CYS K 111 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N CYS K 111 " --> pdb=" O GLY K 101 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASP K 103 " --> pdb=" O GLN K 109 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N GLN K 109 " --> pdb=" O ASP K 103 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 66 through 67 removed outlier: 6.784A pdb=" N ILE L 97 " --> pdb=" O VAL L 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE L 113 " --> pdb=" O VAL L 99 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY L 101 " --> pdb=" O CYS L 111 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS L 111 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 103 " --> pdb=" O GLN L 109 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLN L 109 " --> pdb=" O ASP L 103 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 66 through 67 removed outlier: 6.777A pdb=" N ILE M 97 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE M 113 " --> pdb=" O VAL M 99 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY M 101 " --> pdb=" O CYS M 111 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N CYS M 111 " --> pdb=" O GLY M 101 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ASP M 103 " --> pdb=" O GLN M 109 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN M 109 " --> pdb=" O ASP M 103 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'N' and resid 66 through 67 removed outlier: 6.783A pdb=" N ILE N 97 " --> pdb=" O VAL N 115 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY N 101 " --> pdb=" O CYS N 111 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS N 111 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP N 103 " --> pdb=" O GLN N 109 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN N 109 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 66 through 67 removed outlier: 6.779A pdb=" N ILE O 97 " --> pdb=" O VAL O 115 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE O 113 " --> pdb=" O VAL O 99 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY O 101 " --> pdb=" O CYS O 111 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N CYS O 111 " --> pdb=" O GLY O 101 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP O 103 " --> pdb=" O GLN O 109 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLN O 109 " --> pdb=" O ASP O 103 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 66 through 67 removed outlier: 6.773A pdb=" N ILE P 97 " --> pdb=" O VAL P 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE P 113 " --> pdb=" O VAL P 99 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY P 101 " --> pdb=" O CYS P 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N CYS P 111 " --> pdb=" O GLY P 101 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASP P 103 " --> pdb=" O GLN P 109 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN P 109 " --> pdb=" O ASP P 103 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2253 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: 6.97 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12112 1.34 - 1.46: 7328 1.46 - 1.58: 18216 1.58 - 1.69: 16 1.69 - 1.81: 344 Bond restraints: 38016 Sorted by residual: bond pdb=" O1 CAP H 502 " pdb=" P1 CAP H 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" O1 CAP E 502 " pdb=" P1 CAP E 502 " ideal model delta sigma weight residual 1.708 1.608 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" O1 CAP F 502 " pdb=" P1 CAP F 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O1 CAP G 502 " pdb=" P1 CAP G 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O1 CAP C 502 " pdb=" P1 CAP C 502 " ideal model delta sigma weight residual 1.708 1.609 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 49070 1.78 - 3.56: 2073 3.56 - 5.34: 359 5.34 - 7.12: 63 7.12 - 8.90: 43 Bond angle restraints: 51608 Sorted by residual: angle pdb=" N ILE P 26 " pdb=" CA ILE P 26 " pdb=" C ILE P 26 " ideal model delta sigma weight residual 113.71 105.33 8.38 9.50e-01 1.11e+00 7.78e+01 angle pdb=" N ILE M 26 " pdb=" CA ILE M 26 " pdb=" C ILE M 26 " ideal model delta sigma weight residual 113.71 105.37 8.34 9.50e-01 1.11e+00 7.71e+01 angle pdb=" N ARG N 28 " pdb=" CA ARG N 28 " pdb=" C ARG N 28 " ideal model delta sigma weight residual 114.56 108.68 5.88 1.27e+00 6.20e-01 2.14e+01 angle pdb=" N ARG L 28 " pdb=" CA ARG L 28 " pdb=" C ARG L 28 " ideal model delta sigma weight residual 114.56 108.70 5.86 1.27e+00 6.20e-01 2.13e+01 angle pdb=" N ARG J 28 " pdb=" CA ARG J 28 " pdb=" C ARG J 28 " ideal model delta sigma weight residual 114.56 108.75 5.81 1.27e+00 6.20e-01 2.09e+01 ... (remaining 51603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18809 17.98 - 35.97: 2523 35.97 - 53.95: 899 53.95 - 71.93: 183 71.93 - 89.91: 82 Dihedral angle restraints: 22496 sinusoidal: 9224 harmonic: 13272 Sorted by residual: dihedral pdb=" CA ILE B 301 " pdb=" C ILE B 301 " pdb=" N ASP B 302 " pdb=" CA ASP B 302 " ideal model delta harmonic sigma weight residual 180.00 -159.87 -20.13 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA ILE E 301 " pdb=" C ILE E 301 " pdb=" N ASP E 302 " pdb=" CA ASP E 302 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA ILE F 301 " pdb=" C ILE F 301 " pdb=" N ASP F 302 " pdb=" CA ASP F 302 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 22493 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3751 0.048 - 0.095: 1365 0.095 - 0.143: 282 0.143 - 0.191: 31 0.191 - 0.238: 11 Chirality restraints: 5440 Sorted by residual: chirality pdb=" C3 CAP G 502 " pdb=" C2 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" O3 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.43 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C3 CAP H 502 " pdb=" C2 CAP H 502 " pdb=" C4 CAP H 502 " pdb=" O3 CAP H 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.43 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C3 CAP F 502 " pdb=" C2 CAP F 502 " pdb=" C4 CAP F 502 " pdb=" O3 CAP F 502 " both_signs ideal model delta sigma weight residual False -2.19 -2.43 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 5437 not shown) Planarity restraints: 6728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 432 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C ASN A 432 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN A 432 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU A 433 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 432 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C ASN B 432 " 0.047 2.00e-02 2.50e+03 pdb=" O ASN B 432 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU B 433 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 432 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ASN F 432 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN F 432 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU F 433 " 0.015 2.00e-02 2.50e+03 ... (remaining 6725 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 266 2.62 - 3.19: 26824 3.19 - 3.76: 47842 3.76 - 4.33: 72218 4.33 - 4.90: 126194 Nonbonded interactions: 273344 Sorted by model distance: nonbonded pdb=" OQ2 KCX D 201 " pdb="MG MG D 501 " model vdw 2.055 2.170 nonbonded pdb=" OQ2 KCX C 201 " pdb="MG MG C 501 " model vdw 2.057 2.170 nonbonded pdb=" OQ2 KCX B 201 " pdb="MG MG B 501 " model vdw 2.059 2.170 nonbonded pdb=" OQ2 KCX H 201 " pdb="MG MG H 501 " model vdw 2.060 2.170 nonbonded pdb=" OQ2 KCX G 201 " pdb="MG MG G 501 " model vdw 2.060 2.170 ... (remaining 273339 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 0.590 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.040 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 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:7.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 : 0.005 0.100 38016 Z= 0.248 Angle : 0.866 8.900 51608 Z= 0.484 Chirality : 0.050 0.238 5440 Planarity : 0.007 0.062 6728 Dihedral : 19.150 89.914 14064 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.07 % Favored : 93.52 % Rotamer: Outliers : 4.61 % Allowed : 25.34 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.10), residues: 4600 helix: -3.43 (0.09), residues: 1552 sheet: -1.04 (0.18), residues: 712 loop : -2.50 (0.10), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 295 TYR 0.011 0.002 TYR E 20 PHE 0.026 0.002 PHE H 345 TRP 0.007 0.001 TRP C 214 HIS 0.007 0.002 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.25 (38016) covalent geometry : angle 0.86603 / 0.48 (51608) hydrogen bonds : bond 0.33026 / 21.90 ( 812) hydrogen bonds : angle 8.82526 / 6.16 ( 2253) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 341 time to evaluate : 1.668 Fit side-chains REVERT: C 81 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.6681 (ptpp) REVERT: D 202 ASP cc_start: 0.8013 (m-30) cc_final: 0.7610 (m-30) REVERT: H 202 ASP cc_start: 0.7970 (m-30) cc_final: 0.7528 (m-30) REVERT: N 50 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7555 (mm) outliers start: 177 outliers final: 147 residues processed: 489 average time/residue: 0.8143 time to fit residues: 473.4358 Evaluate side-chains 482 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 333 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 252 LYS Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 146 LYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 265 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 265 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 146 LYS Chi-restraints excluded: chain E residue 158 GLU Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 146 LYS Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 396 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 146 LYS Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 265 VAL Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 396 ASP Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 146 LYS Chi-restraints excluded: chain H residue 175 LYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 265 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 452 SER Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 76 ASN Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 16 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 89 LYS Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 89 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.7980 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 298 HIS B 294 HIS D 298 HIS E 294 HIS I 90 ASN J 90 ASN L 90 ASN M 90 ASN N 90 ASN O 90 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.135385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.115721 restraints weight = 40596.207| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.37 r_work: 0.3136 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.0652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 38016 Z= 0.158 Angle : 0.670 6.945 51608 Z= 0.360 Chirality : 0.047 0.163 5440 Planarity : 0.007 0.057 6728 Dihedral : 10.480 76.853 5720 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.50 % Favored : 94.09 % Rotamer: Outliers : 5.31 % Allowed : 24.19 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.50 (0.10), residues: 4600 helix: -2.87 (0.11), residues: 1536 sheet: -0.48 (0.19), residues: 688 loop : -2.53 (0.10), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 258 TYR 0.009 0.002 TYR H 24 PHE 0.025 0.002 PHE D 345 TRP 0.014 0.001 TRP B 214 HIS 0.007 0.002 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (38016) covalent geometry : angle 0.66974 / 0.36 (51608) hydrogen bonds : bond 0.07010 / 4.66 ( 812) hydrogen bonds : angle 5.50832 / 3.88 ( 2253) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 332 time to evaluate : 1.610 Fit side-chains REVERT: A 81 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.6982 (ptpt) REVERT: A 175 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8439 (mmtp) REVERT: A 338 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: A 371 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8238 (ttp) REVERT: B 81 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.6950 (ptpt) REVERT: B 83 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8312 (ptt180) REVERT: B 175 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8428 (mmtp) REVERT: B 338 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: B 371 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8203 (ttp) REVERT: C 371 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8192 (ttp) REVERT: D 81 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.6970 (ptpt) REVERT: D 83 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8295 (ptt180) REVERT: D 338 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: E 81 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.6998 (ptpt) REVERT: E 156 GLN cc_start: 0.7680 (mt0) cc_final: 0.6976 (pt0) REVERT: E 360 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: E 371 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8181 (ttp) REVERT: F 81 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.6658 (ptpp) REVERT: F 175 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8387 (mmtp) REVERT: F 318 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8276 (tm) REVERT: F 371 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8174 (ttp) REVERT: G 318 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8258 (tm) REVERT: G 360 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.6398 (mtp180) REVERT: H 81 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.6943 (ptpt) REVERT: H 83 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8290 (ptt180) REVERT: H 371 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: I 50 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7394 (mm) REVERT: J 5 ASN cc_start: 0.8415 (t0) cc_final: 0.8214 (t0) REVERT: J 50 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7307 (mm) REVERT: L 5 ASN cc_start: 0.8403 (t0) cc_final: 0.8198 (t0) REVERT: L 50 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7442 (mm) REVERT: M 50 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7403 (mm) REVERT: P 50 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7439 (mm) outliers start: 204 outliers final: 116 residues processed: 486 average time/residue: 0.8182 time to fit residues: 472.6308 Evaluate side-chains 464 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 318 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 175 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 83 ARG Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 371 MET Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 175 LYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 371 MET Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 371 MET Chi-restraints excluded: chain H residue 450 LYS Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 473 ASP Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 67 MET Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 51 optimal weight: 7.9990 chunk 272 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 434 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 401 optimal weight: 0.8980 chunk 252 optimal weight: 6.9990 chunk 425 optimal weight: 7.9990 chunk 332 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 ASN C 432 ASN F 432 ASN G 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.132598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.113031 restraints weight = 40772.638| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.37 r_work: 0.3098 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 38016 Z= 0.219 Angle : 0.766 8.193 51608 Z= 0.409 Chirality : 0.051 0.196 5440 Planarity : 0.007 0.066 6728 Dihedral : 10.086 83.597 5589 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.13 % Favored : 93.46 % Rotamer: Outliers : 6.67 % Allowed : 23.26 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.10), residues: 4600 helix: -2.81 (0.11), residues: 1560 sheet: -0.56 (0.20), residues: 688 loop : -2.71 (0.10), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 258 TYR 0.012 0.002 TYR E 20 PHE 0.028 0.003 PHE B 345 TRP 0.012 0.002 TRP B 214 HIS 0.007 0.002 HIS G 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (38016) covalent geometry : angle 0.76621 / 0.41 (51608) hydrogen bonds : bond 0.07676 / 5.12 ( 812) hydrogen bonds : angle 5.17707 / 3.64 ( 2253) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 342 time to evaluate : 1.550 Fit side-chains REVERT: A 81 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.7170 (ptpt) REVERT: A 209 GLN cc_start: 0.8889 (OUTLIER) cc_final: 0.7835 (mt0) REVERT: A 259 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7501 (mt-10) REVERT: A 318 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8277 (tm) REVERT: A 338 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.6720 (tt0) REVERT: A 454 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: B 51 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: B 81 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7078 (ptpt) REVERT: B 209 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: B 318 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8305 (tm) REVERT: B 338 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7605 (tm-30) REVERT: B 360 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.6922 (mtt180) REVERT: B 454 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: C 51 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: C 156 GLN cc_start: 0.7748 (mt0) cc_final: 0.7089 (pt0) REVERT: C 209 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: C 318 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8280 (tm) REVERT: D 51 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 81 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7085 (ptpt) REVERT: D 209 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: D 318 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8260 (tm) REVERT: D 338 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: E 51 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: E 81 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7110 (ptpt) REVERT: E 156 GLN cc_start: 0.7754 (mt0) cc_final: 0.7045 (pt0) REVERT: E 209 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7854 (mt0) REVERT: E 318 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8277 (tm) REVERT: E 454 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: E 470 GLU cc_start: 0.6815 (mp0) cc_final: 0.6606 (mp0) REVERT: F 51 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: F 81 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.7104 (ptpt) REVERT: F 209 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: F 318 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8325 (tm) REVERT: F 454 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: G 51 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7639 (mp0) REVERT: G 81 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8142 (pttt) REVERT: G 209 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: G 318 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8291 (tm) REVERT: G 371 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8272 (ttp) REVERT: H 18 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.6907 (ttpt) REVERT: H 51 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7653 (mp0) REVERT: H 81 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7067 (ptpt) REVERT: H 209 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.7790 (mt0) REVERT: H 259 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7494 (mt-10) REVERT: H 318 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8294 (tm) REVERT: H 466 LYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6793 (mttm) REVERT: I 29 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: I 50 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7376 (mm) REVERT: J 50 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7500 (mm) REVERT: J 100 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8794 (pt) REVERT: K 29 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.6707 (mt-10) REVERT: K 50 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7483 (mm) REVERT: K 72 MET cc_start: 0.8818 (mtp) cc_final: 0.8609 (mtt) REVERT: L 29 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6727 (mt-10) REVERT: L 50 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7513 (mm) REVERT: M 50 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7429 (mm) REVERT: N 29 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6686 (mt-10) REVERT: N 100 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8821 (pt) REVERT: O 29 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7418 (mt-10) REVERT: O 50 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7542 (mm) REVERT: P 50 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7515 (mm) outliers start: 256 outliers final: 129 residues processed: 523 average time/residue: 0.8375 time to fit residues: 518.6022 Evaluate side-chains 495 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 311 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 473 ASP Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 98 ILE Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 98 ILE Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 172 CYS Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain F residue 461 VAL Chi-restraints excluded: chain F residue 473 ASP Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 98 ILE Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 172 CYS Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 371 MET Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 396 ASP Chi-restraints excluded: chain H residue 450 LYS Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 466 LYS Chi-restraints excluded: chain H residue 473 ASP Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 100 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 100 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 28 ARG Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 333 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 267 optimal weight: 0.0980 chunk 309 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 325 optimal weight: 0.8980 chunk 373 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 ASN B 432 ASN C 432 ASN F 432 ASN G 432 ASN J 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.119019 restraints weight = 40438.063| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.37 r_work: 0.3139 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 38016 Z= 0.100 Angle : 0.541 5.741 51608 Z= 0.288 Chirality : 0.044 0.149 5440 Planarity : 0.006 0.051 6728 Dihedral : 8.254 81.953 5550 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.54 % Favored : 94.22 % Rotamer: Outliers : 5.00 % Allowed : 24.43 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.11), residues: 4600 helix: -2.15 (0.12), residues: 1520 sheet: -0.45 (0.20), residues: 688 loop : -2.46 (0.10), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 258 TYR 0.007 0.001 TYR D 239 PHE 0.023 0.001 PHE E 345 TRP 0.010 0.001 TRP B 214 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.10 (38016) covalent geometry : angle 0.54117 / 0.29 (51608) hydrogen bonds : bond 0.04026 / 2.70 ( 812) hydrogen bonds : angle 4.66406 / 3.29 ( 2253) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 347 time to evaluate : 1.535 Fit side-chains REVERT: A 71 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8427 (m) REVERT: A 81 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.6905 (ptpt) REVERT: A 106 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: A 318 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8319 (tm) REVERT: A 338 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6606 (tt0) REVERT: A 454 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: B 71 THR cc_start: 0.8852 (OUTLIER) cc_final: 0.8433 (m) REVERT: B 106 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: B 318 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8381 (tm) REVERT: C 71 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8341 (m) REVERT: C 106 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: C 156 GLN cc_start: 0.7663 (mt0) cc_final: 0.7094 (pt0) REVERT: C 318 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8341 (tm) REVERT: D 18 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6957 (ttpt) REVERT: D 71 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8420 (m) REVERT: D 106 ASP cc_start: 0.8527 (OUTLIER) cc_final: 0.8157 (m-30) REVERT: D 318 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8322 (tm) REVERT: E 18 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6937 (ttpt) REVERT: E 71 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8383 (m) REVERT: E 106 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: E 156 GLN cc_start: 0.7670 (mt0) cc_final: 0.7070 (pt0) REVERT: E 158 GLU cc_start: 0.8725 (tt0) cc_final: 0.8496 (tt0) REVERT: E 318 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8309 (tm) REVERT: E 338 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6388 (tt0) REVERT: E 360 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6395 (mtp180) REVERT: E 454 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7818 (mp0) REVERT: F 71 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8346 (m) REVERT: F 106 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8168 (m-30) REVERT: F 158 GLU cc_start: 0.8806 (tt0) cc_final: 0.8542 (tt0) REVERT: F 203 ASP cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (t0) REVERT: F 318 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8354 (tm) REVERT: F 360 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.6354 (mtp180) REVERT: F 454 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: G 71 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8384 (m) REVERT: G 106 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: G 156 GLN cc_start: 0.7666 (mt0) cc_final: 0.7042 (pt0) REVERT: G 318 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8302 (tm) REVERT: H 71 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8410 (m) REVERT: H 106 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: H 318 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8345 (tm) REVERT: I 29 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6599 (mt-10) REVERT: I 50 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7330 (mm) REVERT: J 50 ILE cc_start: 0.7582 (OUTLIER) cc_final: 0.7279 (mm) REVERT: K 29 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: L 29 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6588 (mt-10) REVERT: L 50 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7394 (mm) REVERT: N 29 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: P 50 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7391 (mm) outliers start: 192 outliers final: 66 residues processed: 481 average time/residue: 0.7770 time to fit residues: 443.5228 Evaluate side-chains 423 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 314 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 371 MET Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 112 SER Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 360 ARG Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 112 SER Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain P residue 28 ARG Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 331 optimal weight: 7.9990 chunk 366 optimal weight: 0.9980 chunk 203 optimal weight: 0.0570 chunk 222 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 216 optimal weight: 8.9990 chunk 344 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 278 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 overall best weight: 4.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 432 ASN C 432 ASN D 432 ASN F 432 ASN G 432 ASN I 90 ASN L 90 ASN M 90 ASN N 90 ASN O 90 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115473 restraints weight = 40588.925| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.35 r_work: 0.3109 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 38016 Z= 0.203 Angle : 0.720 7.640 51608 Z= 0.383 Chirality : 0.050 0.189 5440 Planarity : 0.007 0.058 6728 Dihedral : 8.673 86.902 5517 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.20 % Favored : 93.57 % Rotamer: Outliers : 5.73 % Allowed : 24.40 % Favored : 69.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.11), residues: 4600 helix: -2.32 (0.11), residues: 1560 sheet: -0.43 (0.20), residues: 688 loop : -2.64 (0.10), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 215 TYR 0.011 0.002 TYR D 20 PHE 0.028 0.003 PHE C 345 TRP 0.008 0.002 TRP B 214 HIS 0.006 0.002 HIS H 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (38016) covalent geometry : angle 0.72049 / 0.38 (51608) hydrogen bonds : bond 0.06799 / 4.53 ( 812) hydrogen bonds : angle 4.83435 / 3.41 ( 2253) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 338 time to evaluate : 1.426 Fit side-chains REVERT: A 71 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (m) REVERT: A 81 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.7289 (ptpt) REVERT: A 209 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.7539 (mt0) REVERT: A 259 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 318 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8327 (tm) REVERT: A 338 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6713 (tt0) REVERT: A 454 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: B 51 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: B 71 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8441 (m) REVERT: B 81 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7145 (ptpt) REVERT: B 106 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8276 (m-30) REVERT: B 209 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7574 (mt0) REVERT: B 318 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8357 (tm) REVERT: C 18 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7100 (ttpt) REVERT: C 71 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8371 (m) REVERT: C 81 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.6978 (ptpt) REVERT: C 106 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8294 (m-30) REVERT: C 203 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8461 (t0) REVERT: C 209 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7591 (mt0) REVERT: C 318 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8331 (tm) REVERT: D 18 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6917 (ttpt) REVERT: D 51 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: D 71 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8415 (m) REVERT: D 81 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7169 (ptpt) REVERT: D 106 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.8274 (m-30) REVERT: D 209 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7585 (mt0) REVERT: D 318 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (tm) REVERT: E 18 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.6883 (ttpt) REVERT: E 51 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: E 71 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8393 (m) REVERT: E 81 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7122 (ptpt) REVERT: E 106 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: E 158 GLU cc_start: 0.8782 (tt0) cc_final: 0.8580 (tt0) REVERT: E 209 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.7562 (mt0) REVERT: E 318 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8327 (tm) REVERT: E 338 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6598 (tt0) REVERT: E 454 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7872 (mp0) REVERT: F 51 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: F 71 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8386 (m) REVERT: F 81 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7123 (ptpt) REVERT: F 106 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8243 (m-30) REVERT: F 158 GLU cc_start: 0.8837 (tt0) cc_final: 0.8615 (tt0) REVERT: F 203 ASP cc_start: 0.8710 (OUTLIER) cc_final: 0.8499 (t0) REVERT: F 209 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: F 454 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: G 51 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: G 71 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8424 (m) REVERT: G 81 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7585 (ptpt) REVERT: G 106 ASP cc_start: 0.8629 (OUTLIER) cc_final: 0.8212 (m-30) REVERT: G 209 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: G 318 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8313 (tm) REVERT: H 18 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.6932 (ttpt) REVERT: H 51 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: H 71 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8402 (m) REVERT: H 81 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7104 (ptpt) REVERT: H 106 ASP cc_start: 0.8639 (OUTLIER) cc_final: 0.8268 (m-30) REVERT: H 209 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7566 (mt0) REVERT: H 259 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7480 (mt-10) REVERT: H 318 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8323 (tm) REVERT: I 29 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6587 (mt-10) REVERT: I 50 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7417 (mm) REVERT: J 29 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6636 (mt-10) REVERT: J 50 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7502 (mm) REVERT: K 5 ASN cc_start: 0.8462 (t0) cc_final: 0.8258 (t0) REVERT: K 29 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: K 50 ILE cc_start: 0.7796 (OUTLIER) cc_final: 0.7490 (mm) REVERT: L 5 ASN cc_start: 0.8339 (t0) cc_final: 0.8125 (t0) REVERT: L 29 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6630 (mt-10) REVERT: L 50 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7497 (mm) REVERT: N 29 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6541 (mt-10) REVERT: O 29 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: O 50 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7447 (mm) REVERT: P 5 ASN cc_start: 0.8413 (t0) cc_final: 0.8197 (t0) REVERT: P 50 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7566 (mm) outliers start: 220 outliers final: 110 residues processed: 495 average time/residue: 0.7966 time to fit residues: 468.1601 Evaluate side-chains 499 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 322 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 203 ASP Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain E residue 461 VAL Chi-restraints excluded: chain E residue 473 ASP Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 318 LEU Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 28 ARG Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 82 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 246 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 317 optimal weight: 7.9990 chunk 306 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 410 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN I 90 ASN L 90 ASN O 90 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.115812 restraints weight = 40601.497| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.38 r_work: 0.3113 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 38016 Z= 0.189 Angle : 0.700 7.499 51608 Z= 0.373 Chirality : 0.049 0.188 5440 Planarity : 0.007 0.059 6728 Dihedral : 8.786 89.980 5515 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.72 % Favored : 94.04 % Rotamer: Outliers : 6.04 % Allowed : 23.88 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.10), residues: 4600 helix: -2.38 (0.11), residues: 1632 sheet: -0.40 (0.20), residues: 672 loop : -2.72 (0.10), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 258 TYR 0.009 0.002 TYR H 20 PHE 0.027 0.002 PHE D 345 TRP 0.009 0.002 TRP B 214 HIS 0.006 0.002 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (38016) covalent geometry : angle 0.69953 / 0.37 (51608) hydrogen bonds : bond 0.06484 / 4.32 ( 812) hydrogen bonds : angle 4.79930 / 3.38 ( 2253) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 232 poor density : 322 time to evaluate : 1.198 Fit side-chains REVERT: A 71 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8386 (m) REVERT: A 81 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.6977 (ptpt) REVERT: A 106 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8198 (m-30) REVERT: A 209 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7592 (mt0) REVERT: A 259 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7408 (mt-10) REVERT: A 318 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8292 (tm) REVERT: A 338 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6642 (tt0) REVERT: A 360 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6627 (mtt180) REVERT: A 454 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 51 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: B 71 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8373 (m) REVERT: B 81 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.7072 (ptpt) REVERT: B 106 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8332 (m-30) REVERT: B 209 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7617 (mt0) REVERT: B 318 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8307 (tm) REVERT: B 360 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.6694 (mtt180) REVERT: B 454 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: C 18 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7080 (ttpt) REVERT: C 71 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8294 (m) REVERT: C 81 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.6899 (ptpt) REVERT: C 106 ASP cc_start: 0.8703 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: C 116 MET cc_start: 0.8652 (ttp) cc_final: 0.8368 (ttp) REVERT: C 209 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7552 (mt0) REVERT: C 318 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8296 (tm) REVERT: C 360 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.6587 (mtt180) REVERT: D 18 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6865 (ttpt) REVERT: D 51 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7619 (mp0) REVERT: D 71 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8364 (m) REVERT: D 81 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7091 (ptpt) REVERT: D 106 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8333 (m-30) REVERT: D 209 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7649 (mt0) REVERT: D 318 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (tm) REVERT: E 18 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.6888 (ttpt) REVERT: E 51 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: E 71 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8334 (m) REVERT: E 81 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7076 (ptpt) REVERT: E 106 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8354 (m-30) REVERT: E 209 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7538 (mt0) REVERT: E 318 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8280 (tm) REVERT: E 338 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6560 (tt0) REVERT: E 454 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: F 51 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: F 71 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8329 (m) REVERT: F 81 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7078 (ptpt) REVERT: F 106 ASP cc_start: 0.8647 (OUTLIER) cc_final: 0.8264 (m-30) REVERT: F 158 GLU cc_start: 0.8846 (tt0) cc_final: 0.8629 (tt0) REVERT: F 209 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.7638 (mt0) REVERT: F 454 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7908 (mp0) REVERT: G 51 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7601 (mp0) REVERT: G 71 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8372 (m) REVERT: G 81 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.7530 (ptpt) REVERT: G 106 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: G 116 MET cc_start: 0.8624 (ttp) cc_final: 0.8323 (ttp) REVERT: G 209 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7555 (mt0) REVERT: G 360 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6627 (mtt180) REVERT: H 18 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.6911 (ttpt) REVERT: H 51 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: H 71 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8355 (m) REVERT: H 81 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7024 (ptpt) REVERT: H 106 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: H 209 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: H 259 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7413 (mt-10) REVERT: H 318 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (tm) REVERT: H 360 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.6595 (mtt180) REVERT: I 29 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6590 (mt-10) REVERT: I 50 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7372 (mm) REVERT: J 29 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6621 (mt-10) REVERT: J 50 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7474 (mm) REVERT: K 29 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6576 (mt-10) REVERT: K 50 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7419 (mm) REVERT: K 100 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8720 (pt) REVERT: L 5 ASN cc_start: 0.8369 (t0) cc_final: 0.8158 (t0) REVERT: L 29 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6602 (mt-10) REVERT: L 50 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7491 (mm) REVERT: M 50 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7487 (mm) REVERT: N 29 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6515 (mt-10) REVERT: O 29 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6489 (mt-10) REVERT: O 50 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7572 (mm) REVERT: P 5 ASN cc_start: 0.8397 (t0) cc_final: 0.8192 (t0) REVERT: P 50 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7535 (mm) outliers start: 232 outliers final: 117 residues processed: 489 average time/residue: 0.7497 time to fit residues: 433.2667 Evaluate side-chains 502 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 312 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 106 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 209 GLN Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 51 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 209 GLN Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 106 ASP Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 209 GLN Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 297 MET Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 336 GLU Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain D residue 473 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 209 GLN Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain E residue 318 LEU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 106 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 209 GLN Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 297 MET Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 336 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 209 GLN Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 473 ASP Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 209 GLN Chi-restraints excluded: chain H residue 297 MET Chi-restraints excluded: chain H residue 318 LEU Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 336 GLU Chi-restraints excluded: chain H residue 360 ARG Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 29 GLU Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain J residue 82 LEU Chi-restraints excluded: chain K residue 1 MET Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 100 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain O residue 82 LEU Chi-restraints excluded: chain O residue 100 LEU Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 28 ARG Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Chi-restraints excluded: chain P residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 433 optimal weight: 8.9990 chunk 278 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 231 optimal weight: 4.9990 chunk 25 optimal weight: 0.0030 chunk 293 optimal weight: 4.9990 chunk 243 optimal weight: 2.9990 chunk 425 optimal weight: 0.0270 chunk 447 optimal weight: 0.0370 chunk 49 optimal weight: 0.7980 chunk 369 optimal weight: 0.0670 overall best weight: 0.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN L 90 ASN O 90 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122905 restraints weight = 40205.952| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.39 r_work: 0.3177 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 38016 Z= 0.094 Angle : 0.511 6.944 51608 Z= 0.270 Chirality : 0.043 0.150 5440 Planarity : 0.005 0.050 6728 Dihedral : 7.462 85.320 5515 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.63 % Favored : 95.17 % Rotamer: Outliers : 3.57 % Allowed : 25.96 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.11), residues: 4600 helix: -1.67 (0.12), residues: 1600 sheet: -0.00 (0.20), residues: 752 loop : -2.38 (0.11), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 258 TYR 0.005 0.001 TYR F 24 PHE 0.025 0.001 PHE B 345 TRP 0.010 0.001 TRP B 214 HIS 0.004 0.001 HIS G 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 (38016) covalent geometry : angle 0.51120 / 0.27 (51608) hydrogen bonds : bond 0.03048 / 2.04 ( 812) hydrogen bonds : angle 4.30994 / 3.07 ( 2253) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 362 time to evaluate : 1.025 Fit side-chains REVERT: A 338 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.6468 (tt0) REVERT: A 360 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.6586 (mtt180) REVERT: B 78 ASP cc_start: 0.8255 (p0) cc_final: 0.8049 (p0) REVERT: B 81 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.6363 (ptpp) REVERT: B 360 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.6546 (mtt180) REVERT: B 454 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: C 156 GLN cc_start: 0.7621 (mt0) cc_final: 0.7065 (pt0) REVERT: C 355 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: C 360 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6505 (mtt180) REVERT: D 81 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.6379 (ptpp) REVERT: D 202 ASP cc_start: 0.7218 (m-30) cc_final: 0.7008 (m-30) REVERT: E 81 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.6479 (ptpp) REVERT: E 156 GLN cc_start: 0.7648 (mt0) cc_final: 0.7050 (pt0) REVERT: E 355 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: F 81 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.6402 (ptpp) REVERT: F 454 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: G 156 GLN cc_start: 0.7658 (mt0) cc_final: 0.7049 (pt0) REVERT: G 360 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.6510 (mtt180) REVERT: H 81 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.6382 (ptpp) REVERT: H 202 ASP cc_start: 0.7166 (m-30) cc_final: 0.6950 (m-30) REVERT: H 360 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6501 (mtt180) REVERT: I 50 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7265 (mm) REVERT: J 50 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7270 (mm) REVERT: K 50 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7318 (mm) REVERT: L 5 ASN cc_start: 0.8320 (t0) cc_final: 0.8037 (t0) REVERT: L 50 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7339 (mm) REVERT: M 50 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7313 (mm) REVERT: O 29 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: P 50 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7288 (mm) outliers start: 137 outliers final: 56 residues processed: 452 average time/residue: 0.7310 time to fit residues: 392.8599 Evaluate side-chains 422 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 344 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 127 PHE Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 127 PHE Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 203 ASP Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 203 ASP Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 127 PHE Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain G residue 371 MET Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 127 PHE Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 360 ARG Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 350 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 427 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 277 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 422 optimal weight: 5.9990 chunk 367 optimal weight: 0.0040 overall best weight: 4.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN C 432 ASN E 432 ASN F 432 ASN H 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.115049 restraints weight = 40234.655| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.38 r_work: 0.3110 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 38016 Z= 0.217 Angle : 0.739 7.933 51608 Z= 0.392 Chirality : 0.051 0.191 5440 Planarity : 0.007 0.059 6728 Dihedral : 8.339 89.590 5466 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.22 % Favored : 93.61 % Rotamer: Outliers : 3.78 % Allowed : 26.25 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.11), residues: 4600 helix: -2.06 (0.11), residues: 1584 sheet: -0.33 (0.20), residues: 688 loop : -2.63 (0.10), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 319 TYR 0.011 0.002 TYR F 20 PHE 0.027 0.003 PHE A 345 TRP 0.008 0.002 TRP F 214 HIS 0.007 0.002 HIS F 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (38016) covalent geometry : angle 0.73856 / 0.39 (51608) hydrogen bonds : bond 0.06728 / 4.48 ( 812) hydrogen bonds : angle 4.66834 / 3.29 ( 2253) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 332 time to evaluate : 1.423 Fit side-chains REVERT: A 81 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.6437 (ptpp) REVERT: A 259 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 338 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: A 360 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.6686 (mtt180) REVERT: A 454 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: B 81 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7091 (ptpt) REVERT: B 360 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6881 (mtt180) REVERT: B 454 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: C 81 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.6408 (ptpp) REVERT: C 360 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.6608 (mtt180) REVERT: D 18 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.6902 (ttpt) REVERT: D 51 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: D 81 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7124 (ptpt) REVERT: E 18 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.6898 (ttpt) REVERT: E 81 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7286 (ptpt) REVERT: E 175 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.6480 (mttt) REVERT: F 51 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7690 (mp0) REVERT: F 81 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7100 (ptpt) REVERT: F 158 GLU cc_start: 0.8849 (tt0) cc_final: 0.8635 (tt0) REVERT: F 454 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.7938 (mp0) REVERT: G 51 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: G 360 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6664 (mtt180) REVERT: H 81 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7071 (ptpt) REVERT: H 259 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7392 (mt-10) REVERT: H 360 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.6664 (mtt180) REVERT: I 50 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7365 (mm) REVERT: J 50 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7469 (mm) REVERT: K 50 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7371 (mm) REVERT: L 5 ASN cc_start: 0.8399 (t0) cc_final: 0.8196 (t0) REVERT: L 50 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7560 (mm) REVERT: M 50 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7392 (mm) REVERT: O 29 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6432 (mt-10) REVERT: P 5 ASN cc_start: 0.8400 (t0) cc_final: 0.8190 (t0) REVERT: P 50 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7537 (mm) outliers start: 145 outliers final: 77 residues processed: 427 average time/residue: 0.7600 time to fit residues: 382.7593 Evaluate side-chains 427 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 321 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 336 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 355 GLU Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 360 ARG Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain J residue 21 LEU Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 7.9990 chunk 443 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 333 optimal weight: 9.9990 chunk 417 optimal weight: 0.6980 chunk 439 optimal weight: 0.0270 chunk 361 optimal weight: 7.9990 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 376 optimal weight: 5.9990 overall best weight: 2.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN C 432 ASN E 432 ASN F 432 ASN H 432 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.117356 restraints weight = 40495.264| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.37 r_work: 0.3140 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 38016 Z= 0.141 Angle : 0.630 6.933 51608 Z= 0.335 Chirality : 0.046 0.178 5440 Planarity : 0.006 0.061 6728 Dihedral : 8.134 89.953 5466 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.17 % Favored : 94.65 % Rotamer: Outliers : 3.26 % Allowed : 26.90 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.11), residues: 4600 helix: -1.97 (0.11), residues: 1632 sheet: -0.24 (0.21), residues: 672 loop : -2.59 (0.10), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 258 TYR 0.008 0.001 TYR F 239 PHE 0.024 0.002 PHE E 345 TRP 0.009 0.001 TRP B 214 HIS 0.006 0.001 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (38016) covalent geometry : angle 0.63007 / 0.34 (51608) hydrogen bonds : bond 0.05217 / 3.48 ( 812) hydrogen bonds : angle 4.53088 / 3.20 ( 2253) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 339 time to evaluate : 0.922 Fit side-chains REVERT: A 259 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7335 (mt-10) REVERT: A 338 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: A 360 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.6642 (mtt180) REVERT: A 454 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: B 81 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.6959 (ptpt) REVERT: B 360 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6634 (mtt180) REVERT: B 454 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.7953 (mp0) REVERT: C 81 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.6365 (ptpp) REVERT: C 360 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.6587 (mtt180) REVERT: D 18 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.6908 (ttpt) REVERT: D 81 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.6982 (ptpt) REVERT: E 18 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.6929 (ttpt) REVERT: E 81 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.6978 (ptpt) REVERT: E 338 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6218 (tt0) REVERT: E 360 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.6366 (mtp180) REVERT: F 81 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.6967 (ptpt) REVERT: F 158 GLU cc_start: 0.8804 (tt0) cc_final: 0.8591 (tt0) REVERT: F 454 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: G 360 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.6596 (mtt180) REVERT: H 81 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.6881 (ptpt) REVERT: H 259 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7362 (mt-10) REVERT: H 360 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.6614 (mtt180) REVERT: I 29 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6475 (mt-10) REVERT: I 50 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7317 (mm) REVERT: J 50 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7324 (mm) REVERT: K 29 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: K 50 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7347 (mm) REVERT: L 5 ASN cc_start: 0.8385 (t0) cc_final: 0.8149 (t0) REVERT: L 29 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6512 (mt-10) REVERT: L 50 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7398 (mm) REVERT: M 50 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7438 (mm) REVERT: N 29 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: O 29 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6406 (mt-10) REVERT: P 5 ASN cc_start: 0.8401 (t0) cc_final: 0.8175 (t0) REVERT: P 50 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7375 (mm) outliers start: 125 outliers final: 67 residues processed: 422 average time/residue: 0.8010 time to fit residues: 399.4006 Evaluate side-chains 430 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 333 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 127 PHE Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 360 ARG Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 127 PHE Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 300 VAL Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 360 ARG Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 21 LEU Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 71 optimal weight: 20.0000 chunk 255 optimal weight: 30.0000 chunk 281 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 256 optimal weight: 4.9990 chunk 403 optimal weight: 3.9990 chunk 352 optimal weight: 7.9990 chunk 275 optimal weight: 10.0000 chunk 384 optimal weight: 0.4980 chunk 179 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN C 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115249 restraints weight = 40536.897| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.38 r_work: 0.3114 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 38016 Z= 0.194 Angle : 0.721 7.641 51608 Z= 0.383 Chirality : 0.050 0.204 5440 Planarity : 0.007 0.063 6728 Dihedral : 8.352 86.969 5466 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.48 % Favored : 93.35 % Rotamer: Outliers : 3.07 % Allowed : 27.24 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.11), residues: 4600 helix: -2.06 (0.11), residues: 1584 sheet: -0.36 (0.20), residues: 688 loop : -2.71 (0.10), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 215 TYR 0.009 0.002 TYR F 20 PHE 0.028 0.002 PHE B 345 TRP 0.009 0.002 TRP B 214 HIS 0.006 0.002 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (38016) covalent geometry : angle 0.72057 / 0.38 (51608) hydrogen bonds : bond 0.06454 / 4.30 ( 812) hydrogen bonds : angle 4.65672 / 3.28 ( 2253) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9200 Ramachandran restraints generated. 4600 Oldfield, 0 Emsley, 4600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 336 time to evaluate : 1.154 Fit side-chains REVERT: A 81 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.6425 (ptpp) REVERT: A 259 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 338 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6651 (tt0) REVERT: A 360 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.6689 (mtt180) REVERT: A 454 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: B 81 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7020 (ptpt) REVERT: B 360 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6675 (mtt180) REVERT: B 454 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7914 (mp0) REVERT: C 81 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.6406 (ptpp) REVERT: C 360 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.6594 (mtt180) REVERT: D 18 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.6872 (ttpt) REVERT: D 81 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7031 (ptpt) REVERT: E 18 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.6889 (ttpt) REVERT: E 81 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7094 (ptpt) REVERT: E 338 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6286 (tt0) REVERT: F 51 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: F 81 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.7031 (ptpt) REVERT: F 454 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: G 360 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6648 (mtt180) REVERT: H 18 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.6877 (ttpt) REVERT: H 81 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.6939 (ptpt) REVERT: H 259 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7374 (mt-10) REVERT: H 360 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6614 (mtt180) REVERT: I 29 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6496 (mt-10) REVERT: I 50 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7464 (mm) REVERT: J 50 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7483 (mm) REVERT: K 29 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6540 (mt-10) REVERT: K 50 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7499 (mm) REVERT: L 5 ASN cc_start: 0.8367 (t0) cc_final: 0.8154 (t0) REVERT: L 29 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6560 (mt-10) REVERT: L 50 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7475 (mm) REVERT: M 50 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7391 (mm) REVERT: N 29 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.6504 (mt-10) REVERT: O 29 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6466 (mt-10) REVERT: P 5 ASN cc_start: 0.8448 (t0) cc_final: 0.8236 (t0) REVERT: P 50 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7550 (mm) outliers start: 118 outliers final: 70 residues processed: 417 average time/residue: 0.7865 time to fit residues: 385.1827 Evaluate side-chains 430 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 328 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 286 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 360 ARG Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 172 CYS Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 454 GLU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 158 GLU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 286 ASP Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 360 ARG Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain D residue 18 LYS Chi-restraints excluded: chain D residue 81 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 172 CYS Chi-restraints excluded: chain D residue 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 81 LYS Chi-restraints excluded: chain E residue 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain F residue 51 GLU Chi-restraints excluded: chain F residue 81 LYS Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 172 CYS Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 204 GLU Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 454 GLU Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain H residue 18 LYS Chi-restraints excluded: chain H residue 81 LYS Chi-restraints excluded: chain H residue 158 GLU Chi-restraints excluded: chain H residue 172 CYS Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 204 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 360 ARG Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 29 GLU Chi-restraints excluded: chain I residue 33 MET Chi-restraints excluded: chain I residue 50 ILE Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 29 GLU Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 50 ILE Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 33 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 76 ASN Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain M residue 21 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 76 ASN Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 29 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain N residue 82 LEU Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 29 GLU Chi-restraints excluded: chain O residue 33 MET Chi-restraints excluded: chain O residue 76 ASN Chi-restraints excluded: chain P residue 21 LEU Chi-restraints excluded: chain P residue 33 MET Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 378 optimal weight: 5.9990 chunk 414 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 chunk 178 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 408 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 432 ASN B 432 ASN C 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.113585 restraints weight = 40444.010| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 1.37 r_work: 0.3084 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 38016 Z= 0.255 Angle : 0.831 8.948 51608 Z= 0.440 Chirality : 0.054 0.213 5440 Planarity : 0.008 0.067 6728 Dihedral : 8.644 81.785 5466 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.59 % Favored : 93.24 % Rotamer: Outliers : 3.78 % Allowed : 26.43 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.42 (0.10), residues: 4600 helix: -2.32 (0.11), residues: 1584 sheet: -0.50 (0.20), residues: 688 loop : -2.84 (0.10), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 215 TYR 0.013 0.002 TYR F 20 PHE 0.032 0.003 PHE E 345 TRP 0.009 0.002 TRP B 214 HIS 0.007 0.003 HIS D 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.25 (38016) covalent geometry : angle 0.83057 / 0.44 (51608) hydrogen bonds : bond 0.07739 / 5.15 ( 812) hydrogen bonds : angle 4.85565 / 3.42 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10799.06 seconds wall clock time: 184 minutes 39.19 seconds (11079.19 seconds total)