Starting phenix.real_space_refine on Tue Aug 26 12:10:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chz_45605/08_2025/9chz_45605_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chz_45605/08_2025/9chz_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_45605/08_2025/9chz_45605_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chz_45605/08_2025/9chz_45605_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9chz_45605/08_2025/9chz_45605.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chz_45605/08_2025/9chz_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: 7.76, per 1000 atoms: 0.21 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: 2.59 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.38 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: 7.69 Time building geometry restraints manager: 3.60 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=" NZ KCX D 201 " pdb=" CX KCX D 201 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" NZ KCX F 201 " pdb=" CX KCX F 201 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX G 201 " pdb=" CX KCX G 201 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" NZ KCX A 201 " pdb=" CX KCX A 201 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" NZ KCX C 201 " pdb=" CX KCX C 201 " ideal model delta sigma weight residual 1.411 1.325 0.086 2.00e-02 2.50e+03 1.85e+01 ... (remaining 38011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 48867 1.68 - 3.35: 2336 3.35 - 5.03: 346 5.03 - 6.70: 46 6.70 - 8.38: 13 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 - 35.02: 21127 35.02 - 70.04: 1108 70.04 - 105.06: 94 105.06 - 140.09: 5 140.09 - 175.11: 2 Dihedral angle restraints: 22336 sinusoidal: 9064 harmonic: 13272 Sorted by residual: dihedral pdb=" C3 CAP B 502 " pdb=" C CAP B 502 " pdb=" C2 CAP B 502 " pdb=" O6 CAP B 502 " ideal model delta sinusoidal sigma weight residual 81.86 -93.24 175.11 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP C 502 " pdb=" C CAP C 502 " pdb=" C2 CAP C 502 " pdb=" O6 CAP C 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.44 174.30 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5 CAP G 502 " pdb=" O5 CAP G 502 " pdb=" P2 CAP G 502 " pdb=" O4P CAP G 502 " ideal model delta sinusoidal sigma weight residual 160.56 27.49 133.07 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 22333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 3077 0.039 - 0.077: 1785 0.077 - 0.116: 432 0.116 - 0.154: 115 0.154 - 0.193: 23 Chirality restraints: 5432 Sorted by residual: chirality pdb=" CA ASN B 432 " pdb=" N ASN B 432 " pdb=" C ASN B 432 " pdb=" CB ASN B 432 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ASN E 432 " pdb=" N ASN E 432 " pdb=" C ASN E 432 " pdb=" CB ASN E 432 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" CA ASN C 432 " pdb=" N ASN C 432 " pdb=" C ASN C 432 " pdb=" CB ASN C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 5429 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: 0.01 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: 0.770 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 31.690 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 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 : 0.004 0.087 38016 Z= 0.218 Angle : 0.811 8.380 51608 Z= 0.473 Chirality : 0.049 0.193 5432 Planarity : 0.007 0.062 6728 Dihedral : 19.295 175.107 13904 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 aren 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 covalent geometry : bond 0.00440 (38016) covalent geometry : angle 0.81135 (51608) hydrogen bonds : bond 0.33026 ( 812) hydrogen bonds : angle 8.82526 ( 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 : 1.474 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: 0.6796 time to fit residues: 394.4270 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 : 1.274 ------------------------------------------------------------------------------- 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: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 401 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3490 r_free = 0.3490 target = 0.134864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.115210 restraints weight = 40589.431| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.37 r_work: 0.3129 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 38016 Z= 0.174 Angle : 0.702 7.130 51608 Z= 0.377 Chirality : 0.049 0.167 5432 Planarity : 0.007 0.058 6728 Dihedral : 11.256 175.220 5560 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.59 % Favored : 94.00 % Rotamer: Outliers : 5.47 % Allowed : 24.14 % Favored : 70.39 % 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 aren not related in a simple way. whole: -3.55 (0.10), residues: 4600 helix: -2.90 (0.11), residues: 1536 sheet: -0.50 (0.19), residues: 688 loop : -2.56 (0.10), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 295 TYR 0.009 0.002 TYR E 20 PHE 0.026 0.002 PHE F 345 TRP 0.015 0.001 TRP B 214 HIS 0.007 0.002 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00375 (38016) covalent geometry : angle 0.70193 (51608) hydrogen bonds : bond 0.07265 ( 812) hydrogen bonds : angle 5.51861 ( 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 542 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 332 time to evaluate : 0.977 Fit side-chains REVERT: A 81 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7039 (ptpt) REVERT: A 338 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: A 371 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8272 (ttp) REVERT: B 81 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.6961 (ptpt) REVERT: B 175 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8434 (mmtp) REVERT: B 338 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: B 371 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8240 (ttp) REVERT: C 371 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8230 (ttp) REVERT: D 81 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7022 (ptpt) REVERT: D 121 VAL cc_start: 0.8156 (m) cc_final: 0.7766 (m) REVERT: D 338 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7450 (tp30) REVERT: E 81 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.6685 (ptpp) REVERT: E 156 GLN cc_start: 0.7688 (mt0) cc_final: 0.6974 (pt0) REVERT: E 371 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8255 (ttp) REVERT: E 433 GLU cc_start: 0.7193 (tt0) cc_final: 0.6993 (tt0) REVERT: F 81 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7034 (ptpt) REVERT: F 318 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (tm) REVERT: F 371 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8209 (ttp) REVERT: G 318 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8228 (tm) REVERT: H 81 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.6613 (ptpp) REVERT: H 83 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8333 (ptt180) REVERT: H 371 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8230 (ttp) REVERT: I 50 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7413 (mm) REVERT: J 50 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7326 (mm) REVERT: L 50 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7470 (mm) REVERT: M 50 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7423 (mm) REVERT: P 50 ILE cc_start: 0.7741 (OUTLIER) cc_final: 0.7464 (mm) outliers start: 210 outliers final: 121 residues processed: 489 average time/residue: 0.6594 time to fit residues: 382.0606 Evaluate side-chains 461 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 316 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 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 396 ASP 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 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 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 396 ASP Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 473 ASP 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 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 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 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 297 MET Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 355 GLU 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 172 CYS 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 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 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 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: 9.9990 chunk 272 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 434 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 401 optimal weight: 0.5980 chunk 252 optimal weight: 6.9990 chunk 425 optimal weight: 6.9990 chunk 332 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 432 ASN C 432 ASN D 432 ASN H 432 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.132810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.113252 restraints weight = 40809.943| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.37 r_work: 0.3101 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 38016 Z= 0.217 Angle : 0.763 7.938 51608 Z= 0.407 Chirality : 0.051 0.194 5432 Planarity : 0.007 0.066 6728 Dihedral : 10.547 171.751 5429 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.02 % Favored : 93.57 % Rotamer: Outliers : 6.54 % Allowed : 23.78 % 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 aren not related in a simple way. whole: -3.63 (0.10), residues: 4600 helix: -2.81 (0.11), residues: 1560 sheet: -0.57 (0.20), residues: 688 loop : -2.72 (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 G 345 TRP 0.012 0.002 TRP B 214 HIS 0.007 0.002 HIS G 238 Details of bonding type rmsd covalent geometry : bond 0.00492 (38016) covalent geometry : angle 0.76268 (51608) hydrogen bonds : bond 0.07589 ( 812) hydrogen bonds : angle 5.17503 ( 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 592 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 251 poor density : 341 time to evaluate : 1.071 Fit side-chains REVERT: A 81 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7110 (ptpt) REVERT: A 209 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7841 (mt0) REVERT: A 259 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7504 (mt-10) REVERT: A 318 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8280 (tm) REVERT: A 338 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: A 454 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7941 (mp0) REVERT: B 51 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7917 (mp0) REVERT: B 81 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.7103 (ptpt) REVERT: B 209 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.7847 (mt0) REVERT: B 318 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8304 (tm) REVERT: B 338 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7609 (tm-30) REVERT: B 360 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.6915 (mtt180) REVERT: B 454 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: C 51 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7907 (mp0) REVERT: C 156 GLN cc_start: 0.7759 (mt0) cc_final: 0.7089 (pt0) REVERT: C 209 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: C 318 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8278 (tm) REVERT: D 18 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.6851 (ttpt) REVERT: D 51 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: D 81 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.7118 (ptpt) REVERT: D 209 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7860 (mt0) REVERT: D 318 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8264 (tm) REVERT: D 338 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: E 18 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.6898 (ttpt) REVERT: E 51 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: E 81 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7107 (ptpt) REVERT: E 156 GLN cc_start: 0.7735 (mt0) cc_final: 0.7025 (pt0) REVERT: E 209 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: E 318 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8280 (tm) REVERT: E 454 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: E 470 GLU cc_start: 0.6815 (mp0) cc_final: 0.6601 (mp0) REVERT: F 51 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7543 (mp0) REVERT: F 81 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7058 (ptpt) REVERT: F 209 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: F 318 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8320 (tm) REVERT: F 454 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7935 (mp0) REVERT: G 51 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: G 209 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: G 318 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8284 (tm) REVERT: G 371 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8276 (ttp) REVERT: H 18 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.6866 (ttpt) REVERT: H 51 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: H 81 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.7063 (ptpt) REVERT: H 209 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7851 (mt0) REVERT: H 259 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7488 (mt-10) REVERT: H 318 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8258 (tm) REVERT: H 466 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6799 (mttm) REVERT: I 29 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6720 (mt-10) REVERT: I 50 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7348 (mm) REVERT: J 50 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7579 (mm) REVERT: J 100 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8794 (pt) REVERT: K 29 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: K 50 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7453 (mm) REVERT: K 72 MET cc_start: 0.8810 (mtp) cc_final: 0.8603 (mtt) REVERT: L 29 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6732 (mt-10) REVERT: L 50 ILE cc_start: 0.7632 (OUTLIER) cc_final: 0.7426 (mm) REVERT: M 50 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7425 (mm) REVERT: N 29 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6715 (mt-10) REVERT: N 100 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8819 (pt) REVERT: O 50 ILE cc_start: 0.7749 (OUTLIER) cc_final: 0.7526 (mm) REVERT: P 50 ILE cc_start: 0.7720 (OUTLIER) cc_final: 0.7511 (mm) outliers start: 251 outliers final: 118 residues processed: 517 average time/residue: 0.6802 time to fit residues: 414.3383 Evaluate side-chains 487 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 314 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 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 221 VAL 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 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 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 473 ASP 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 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 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 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 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 473 ASP Chi-restraints excluded: chain G residue 51 GLU 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 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 336 GLU 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 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 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 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 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 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: 3.9990 chunk 393 optimal weight: 8.9990 chunk 190 optimal weight: 8.9990 chunk 267 optimal weight: 0.4980 chunk 309 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 402 optimal weight: 7.9990 chunk 325 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 287 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN H 432 ASN J 90 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.117678 restraints weight = 40559.329| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 1.39 r_work: 0.3141 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 38016 Z= 0.136 Angle : 0.621 6.845 51608 Z= 0.332 Chirality : 0.046 0.159 5432 Planarity : 0.006 0.057 6728 Dihedral : 9.579 174.377 5392 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.89 % Favored : 93.87 % Rotamer: Outliers : 5.86 % Allowed : 23.93 % Favored : 70.21 % 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 aren not related in a simple way. whole: -3.36 (0.10), residues: 4600 helix: -2.44 (0.11), residues: 1560 sheet: -0.50 (0.20), residues: 688 loop : -2.66 (0.10), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 258 TYR 0.008 0.001 TYR H 239 PHE 0.024 0.002 PHE C 345 TRP 0.011 0.001 TRP B 214 HIS 0.005 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00283 (38016) covalent geometry : angle 0.62123 (51608) hydrogen bonds : bond 0.05421 ( 812) hydrogen bonds : angle 4.86183 ( 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 560 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 335 time to evaluate : 1.215 Fit side-chains REVERT: A 81 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7081 (ptpt) REVERT: A 209 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7635 (mt0) REVERT: A 259 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7374 (mt-10) REVERT: A 318 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8271 (tm) REVERT: A 338 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: A 454 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7789 (mp0) REVERT: B 81 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.7002 (ptpt) REVERT: B 106 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: B 209 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 318 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8299 (tm) REVERT: B 454 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.7838 (mp0) REVERT: C 18 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7068 (ttpt) REVERT: C 81 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.6459 (ptpp) REVERT: C 106 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: C 121 VAL cc_start: 0.8070 (m) cc_final: 0.7625 (m) REVERT: C 156 GLN cc_start: 0.7724 (mt0) cc_final: 0.7050 (pt0) REVERT: C 203 ASP cc_start: 0.8740 (OUTLIER) cc_final: 0.8510 (t0) REVERT: C 209 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7723 (mt0) REVERT: C 318 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8260 (tm) REVERT: D 18 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6824 (ttpt) REVERT: D 51 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: D 81 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.7030 (ptpt) REVERT: D 106 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: D 209 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: D 318 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8259 (tm) REVERT: E 18 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.6862 (ttpt) REVERT: E 51 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: E 81 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7018 (ptpt) REVERT: E 106 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: E 156 GLN cc_start: 0.7716 (mt0) cc_final: 0.7034 (pt0) REVERT: E 209 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: E 318 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8254 (tm) REVERT: E 338 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.6464 (tt0) REVERT: E 360 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.6355 (mtp180) REVERT: E 454 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7798 (mp0) REVERT: F 51 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7540 (mp0) REVERT: F 81 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.7010 (ptpt) REVERT: F 121 VAL cc_start: 0.8040 (m) cc_final: 0.7603 (m) REVERT: F 209 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: F 318 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8270 (tm) REVERT: F 454 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.7796 (mp0) REVERT: G 51 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: G 106 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: G 121 VAL cc_start: 0.8063 (m) cc_final: 0.7623 (m) REVERT: G 209 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: G 318 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8224 (tm) REVERT: G 355 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: G 360 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.6359 (mtp180) REVERT: H 18 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.6835 (ttpt) REVERT: H 81 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.7012 (ptpt) REVERT: H 106 ASP cc_start: 0.8630 (OUTLIER) cc_final: 0.8130 (m-30) REVERT: H 209 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: H 259 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7372 (mt-10) REVERT: H 318 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8283 (tm) REVERT: I 29 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6583 (mt-10) REVERT: I 50 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7392 (mm) REVERT: J 50 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7334 (mm) REVERT: K 29 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: K 50 ILE cc_start: 0.7715 (OUTLIER) cc_final: 0.7406 (mm) REVERT: L 5 ASN cc_start: 0.8323 (t0) cc_final: 0.8075 (t0) REVERT: L 29 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: L 50 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7464 (mm) REVERT: M 50 ILE cc_start: 0.7664 (OUTLIER) cc_final: 0.7407 (mm) REVERT: N 29 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6638 (mt-10) REVERT: O 50 ILE cc_start: 0.7747 (OUTLIER) cc_final: 0.7474 (mm) REVERT: P 50 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7364 (mm) outliers start: 225 outliers final: 108 residues processed: 492 average time/residue: 0.6882 time to fit residues: 401.7193 Evaluate side-chains 481 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 315 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 127 PHE 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 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 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 127 PHE 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 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 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 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 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 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 98 ILE 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 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 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 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 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 200 THR Chi-restraints excluded: chain E residue 204 GLU Chi-restraints excluded: chain E residue 209 GLN 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 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 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 286 ASP 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 454 GLU Chi-restraints excluded: chain G residue 51 GLU 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 127 PHE 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 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 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 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 127 PHE 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 318 LEU Chi-restraints excluded: chain H residue 335 LEU 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 I residue 100 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 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 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 N residue 1 MET 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 33 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 100 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 Chi-restraints excluded: chain P residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 331 optimal weight: 8.9990 chunk 366 optimal weight: 4.9990 chunk 203 optimal weight: 10.0000 chunk 222 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 216 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 361 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 J 90 ASN L 90 ASN M 90 ASN O 90 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.113499 restraints weight = 40614.711| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.36 r_work: 0.3101 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 38016 Z= 0.205 Angle : 0.735 7.696 51608 Z= 0.391 Chirality : 0.050 0.200 5432 Planarity : 0.007 0.064 6728 Dihedral : 9.627 171.184 5379 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 1.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.74 % Favored : 93.02 % Rotamer: Outliers : 6.51 % Allowed : 23.91 % Favored : 69.58 % 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 aren not related in a simple way. whole: -3.43 (0.10), residues: 4600 helix: -2.44 (0.11), residues: 1560 sheet: -0.51 (0.20), residues: 688 loop : -2.75 (0.10), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 258 TYR 0.011 0.002 TYR H 20 PHE 0.028 0.003 PHE B 345 TRP 0.011 0.002 TRP B 214 HIS 0.007 0.002 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00465 (38016) covalent geometry : angle 0.73480 (51608) hydrogen bonds : bond 0.06962 ( 812) hydrogen bonds : angle 4.91761 ( 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 579 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 250 poor density : 329 time to evaluate : 1.135 Fit side-chains REVERT: A 81 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7027 (ptpt) REVERT: A 209 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: A 259 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 318 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8343 (tm) REVERT: A 454 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7857 (mp0) REVERT: B 51 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: B 81 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.7020 (ptpt) REVERT: B 106 ASP cc_start: 0.8650 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: B 209 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: B 318 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8358 (tm) REVERT: B 360 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.6950 (mtt180) REVERT: B 454 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7896 (mp0) REVERT: C 18 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7108 (ttpt) REVERT: C 51 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7913 (mp0) REVERT: C 81 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.6702 (ptpp) REVERT: C 106 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8251 (m-30) REVERT: C 156 GLN cc_start: 0.7774 (mt0) cc_final: 0.7143 (pt0) REVERT: C 209 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7888 (mt0) REVERT: C 318 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8345 (tm) REVERT: D 18 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.6929 (ttpt) REVERT: D 51 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: D 81 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.7045 (ptpt) REVERT: D 106 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8231 (m-30) REVERT: D 209 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: D 318 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (tm) REVERT: E 51 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: E 81 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.7029 (ptpt) REVERT: E 106 ASP cc_start: 0.8693 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: E 156 GLN cc_start: 0.7761 (mt0) cc_final: 0.7120 (pt0) REVERT: E 209 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.7859 (mt0) REVERT: E 338 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6594 (tt0) REVERT: E 433 GLU cc_start: 0.7395 (tt0) cc_final: 0.7154 (tt0) REVERT: E 454 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7976 (mp0) REVERT: F 51 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: F 81 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7020 (ptpt) REVERT: F 209 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7874 (mt0) REVERT: F 318 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8337 (tm) REVERT: F 454 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7956 (mp0) REVERT: G 51 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (mp0) REVERT: G 106 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: G 209 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: G 318 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8299 (tm) REVERT: G 371 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8118 (ttp) REVERT: H 18 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.6906 (ttpt) REVERT: H 51 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: H 81 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.7015 (ptpt) REVERT: H 106 ASP cc_start: 0.8682 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: H 209 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: H 259 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7496 (mt-10) REVERT: H 318 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8316 (tm) REVERT: I 29 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: I 50 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7418 (mm) REVERT: J 29 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6679 (mt-10) REVERT: J 50 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7535 (mm) REVERT: K 29 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6612 (mt-10) REVERT: K 50 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7529 (mm) REVERT: K 72 MET cc_start: 0.8811 (mtp) cc_final: 0.8595 (mtt) REVERT: L 29 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6656 (mt-10) REVERT: L 50 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7510 (mm) REVERT: M 50 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7444 (mm) REVERT: N 29 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6554 (mt-10) REVERT: O 29 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6666 (mt-10) REVERT: O 50 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7468 (mm) REVERT: P 50 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7578 (mm) outliers start: 250 outliers final: 137 residues processed: 518 average time/residue: 0.6836 time to fit residues: 420.8201 Evaluate side-chains 506 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 311 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 158 GLU 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 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 112 SER 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 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 51 GLU 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 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 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 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 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 172 CYS 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 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 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 221 VAL 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 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 172 CYS 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 318 LEU 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 106 ASP Chi-restraints excluded: chain G residue 112 SER Chi-restraints excluded: chain G residue 158 GLU 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 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 G residue 371 MET 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 106 ASP Chi-restraints excluded: chain H residue 112 SER 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 203 ASP 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 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 1 MET 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 33 MET Chi-restraints excluded: chain P residue 50 ILE 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: 0.6980 chunk 24 optimal weight: 6.9990 chunk 317 optimal weight: 6.9990 chunk 306 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 402 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 410 optimal weight: 5.9990 chunk 215 optimal weight: 10.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN J 90 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115221 restraints weight = 40572.348| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.38 r_work: 0.3109 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 38016 Z= 0.187 Angle : 0.702 7.460 51608 Z= 0.375 Chirality : 0.049 0.185 5432 Planarity : 0.007 0.061 6728 Dihedral : 9.482 170.292 5362 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.91 % Favored : 93.85 % Rotamer: Outliers : 6.15 % Allowed : 23.96 % Favored : 69.90 % 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 aren not related in a simple way. whole: -3.46 (0.10), residues: 4600 helix: -2.39 (0.11), residues: 1584 sheet: -0.53 (0.20), residues: 688 loop : -2.83 (0.10), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 258 TYR 0.009 0.002 TYR F 20 PHE 0.026 0.002 PHE E 345 TRP 0.010 0.002 TRP B 214 HIS 0.006 0.002 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00419 (38016) covalent geometry : angle 0.70205 (51608) hydrogen bonds : bond 0.06465 ( 812) hydrogen bonds : angle 4.84763 ( 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 549 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 313 time to evaluate : 1.146 Fit side-chains REVERT: A 71 THR cc_start: 0.8727 (OUTLIER) cc_final: 0.8363 (m) REVERT: A 81 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7072 (ptpt) REVERT: A 106 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8129 (m-30) REVERT: A 121 VAL cc_start: 0.8060 (m) cc_final: 0.7682 (m) REVERT: A 209 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: A 259 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7390 (mt-10) REVERT: A 318 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8290 (tm) REVERT: A 454 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7790 (mp0) REVERT: B 51 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 71 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8361 (m) REVERT: B 81 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.7113 (ptpt) REVERT: B 106 ASP cc_start: 0.8611 (OUTLIER) cc_final: 0.8248 (m-30) REVERT: B 209 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: B 318 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8296 (tm) REVERT: B 360 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.6880 (mtt180) REVERT: B 454 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: C 18 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7070 (ttpt) REVERT: C 51 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: C 71 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8276 (m) REVERT: C 81 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.6982 (ptpt) REVERT: C 106 ASP cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: C 156 GLN cc_start: 0.7768 (mt0) cc_final: 0.7083 (pt0) REVERT: C 209 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: C 318 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8283 (tm) REVERT: D 18 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.6845 (ttpt) REVERT: D 51 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: D 71 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8338 (m) REVERT: D 81 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7142 (ptpt) REVERT: D 106 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: D 209 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: D 318 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8277 (tm) REVERT: E 18 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.6905 (ttpt) REVERT: E 51 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: E 71 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8314 (m) REVERT: E 81 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.7069 (ptpt) REVERT: E 106 ASP cc_start: 0.8673 (OUTLIER) cc_final: 0.8311 (m-30) REVERT: E 158 GLU cc_start: 0.8799 (tt0) cc_final: 0.8578 (tt0) REVERT: E 209 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 318 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8311 (tm) REVERT: E 338 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.6590 (tt0) REVERT: E 454 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7921 (mp0) REVERT: F 51 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: F 71 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8288 (m) REVERT: F 81 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7067 (ptpt) REVERT: F 106 ASP cc_start: 0.8649 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: F 209 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7793 (mt0) REVERT: F 454 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7942 (mp0) REVERT: G 51 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: G 71 THR cc_start: 0.8709 (OUTLIER) cc_final: 0.8345 (m) REVERT: G 106 ASP cc_start: 0.8658 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: G 209 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: G 371 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: H 18 LYS cc_start: 0.7773 (OUTLIER) cc_final: 0.6874 (ttpt) REVERT: H 51 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: H 71 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8330 (m) REVERT: H 81 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7056 (ptpt) REVERT: H 106 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8255 (m-30) REVERT: H 209 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7784 (mt0) REVERT: H 259 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7415 (mt-10) REVERT: H 318 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8274 (tm) REVERT: I 29 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6559 (mt-10) REVERT: I 50 ILE cc_start: 0.7650 (OUTLIER) cc_final: 0.7359 (mm) REVERT: J 29 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6647 (mt-10) REVERT: J 50 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7487 (mm) REVERT: K 29 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6575 (mt-10) REVERT: K 50 ILE cc_start: 0.7782 (OUTLIER) cc_final: 0.7503 (mm) REVERT: L 29 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: L 50 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7571 (mm) REVERT: M 50 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7384 (mm) REVERT: N 29 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: O 29 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6609 (mt-10) REVERT: O 50 ILE cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (mm) REVERT: P 50 ILE cc_start: 0.7769 (OUTLIER) cc_final: 0.7491 (mm) outliers start: 236 outliers final: 130 residues processed: 488 average time/residue: 0.7086 time to fit residues: 408.9733 Evaluate side-chains 505 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 307 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 GLU 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 112 SER Chi-restraints excluded: chain A residue 158 GLU 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 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 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 112 SER 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 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 51 GLU 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 172 CYS 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 297 MET 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 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 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 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 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 98 ILE 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 221 VAL 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 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 106 ASP Chi-restraints excluded: chain F residue 112 SER 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 297 MET 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 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 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 203 ASP 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 335 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 371 MET Chi-restraints excluded: chain G residue 452 SER 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 98 ILE 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 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 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 1 MET 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 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: 6.9990 chunk 278 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 425 optimal weight: 0.0980 chunk 447 optimal weight: 0.9990 chunk 49 optimal weight: 0.0980 chunk 369 optimal weight: 0.8980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN J 90 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.120110 restraints weight = 40300.150| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.36 r_work: 0.3150 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 38016 Z= 0.095 Angle : 0.531 7.331 51608 Z= 0.282 Chirality : 0.043 0.149 5432 Planarity : 0.006 0.057 6728 Dihedral : 8.621 177.123 5355 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.15 % Favored : 94.65 % Rotamer: Outliers : 3.78 % Allowed : 25.89 % Favored : 70.34 % 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 aren not related in a simple way. whole: -2.83 (0.11), residues: 4600 helix: -1.87 (0.12), residues: 1632 sheet: -0.03 (0.20), residues: 752 loop : -2.56 (0.10), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 258 TYR 0.006 0.001 TYR B 239 PHE 0.024 0.001 PHE G 345 TRP 0.011 0.001 TRP B 214 HIS 0.005 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00195 (38016) covalent geometry : angle 0.53124 (51608) hydrogen bonds : bond 0.03456 ( 812) hydrogen bonds : angle 4.40055 ( 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 490 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 345 time to evaluate : 1.553 Fit side-chains REVERT: A 338 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6263 (tt0) REVERT: B 81 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.6392 (ptpp) REVERT: B 318 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8325 (tm) REVERT: C 81 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.6566 (ptpp) REVERT: C 156 GLN cc_start: 0.7650 (mt0) cc_final: 0.7072 (pt0) REVERT: C 355 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: D 81 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.6420 (ptpp) REVERT: E 156 GLN cc_start: 0.7651 (mt0) cc_final: 0.7058 (pt0) REVERT: E 158 GLU cc_start: 0.8709 (tt0) cc_final: 0.8481 (tt0) REVERT: E 175 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.6342 (mttt) REVERT: E 338 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6417 (tt0) REVERT: E 355 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7786 (tt0) REVERT: E 454 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: F 81 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.6415 (ptpp) REVERT: F 158 GLU cc_start: 0.8777 (tt0) cc_final: 0.8520 (tt0) REVERT: F 454 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: G 156 GLN cc_start: 0.7659 (mt0) cc_final: 0.7038 (pt0) REVERT: H 51 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: H 81 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.6416 (ptpp) REVERT: H 318 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8286 (tm) REVERT: I 50 ILE cc_start: 0.7616 (OUTLIER) cc_final: 0.7291 (mm) REVERT: J 50 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7249 (mm) REVERT: K 50 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7351 (mm) REVERT: L 50 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7382 (mm) REVERT: N 29 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6462 (mt-10) REVERT: P 50 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7343 (mm) outliers start: 145 outliers final: 55 residues processed: 437 average time/residue: 0.7942 time to fit residues: 408.9190 Evaluate side-chains 400 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 324 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 PHE 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 300 VAL Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 81 LYS 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 371 MET Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 81 LYS 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 355 GLU Chi-restraints excluded: chain C residue 382 ILE 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 158 GLU 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 127 PHE 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 338 GLU Chi-restraints excluded: chain E residue 355 GLU Chi-restraints excluded: chain E residue 454 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 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 172 CYS 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 450 LYS Chi-restraints excluded: chain H residue 51 GLU Chi-restraints excluded: chain H residue 81 LYS 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 454 GLU Chi-restraints excluded: chain I residue 33 MET 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 33 MET 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 350 optimal weight: 9.9990 chunk 96 optimal weight: 30.0000 chunk 427 optimal weight: 0.0870 chunk 86 optimal weight: 9.9990 chunk 167 optimal weight: 9.9990 chunk 277 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 422 optimal weight: 0.3980 chunk 367 optimal weight: 0.0970 overall best weight: 2.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 287 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.136480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.117150 restraints weight = 40080.278| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.37 r_work: 0.3135 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 38016 Z= 0.156 Angle : 0.649 7.019 51608 Z= 0.343 Chirality : 0.047 0.184 5432 Planarity : 0.006 0.058 6728 Dihedral : 8.802 175.401 5311 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 3.46 % Allowed : 26.77 % Favored : 69.77 % 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 aren not related in a simple way. whole: -3.00 (0.11), residues: 4600 helix: -1.97 (0.11), residues: 1632 sheet: -0.20 (0.21), residues: 672 loop : -2.60 (0.10), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 258 TYR 0.009 0.002 TYR F 20 PHE 0.025 0.002 PHE E 345 TRP 0.008 0.001 TRP B 214 HIS 0.006 0.002 HIS H 238 Details of bonding type rmsd covalent geometry : bond 0.00339 (38016) covalent geometry : angle 0.64873 (51608) hydrogen bonds : bond 0.05496 ( 812) hydrogen bonds : angle 4.53210 ( 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 466 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 333 time to evaluate : 1.642 Fit side-chains REVERT: A 259 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 338 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6310 (tt0) REVERT: A 454 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: B 81 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.7091 (ptpt) REVERT: B 360 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.6811 (mtt180) REVERT: C 81 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.6948 (ptpt) REVERT: C 360 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.6337 (mtp180) REVERT: D 81 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.7124 (ptpt) REVERT: E 158 GLU cc_start: 0.8773 (tt0) cc_final: 0.8557 (tt0) REVERT: E 175 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.6437 (mttt) REVERT: E 318 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8243 (tm) REVERT: E 338 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: E 454 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.7867 (mp0) REVERT: F 81 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7087 (ptpt) REVERT: F 158 GLU cc_start: 0.8829 (tt0) cc_final: 0.8585 (tt0) REVERT: F 454 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: G 51 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: G 355 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7815 (tt0) REVERT: G 360 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.6359 (mtp180) REVERT: H 51 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: H 81 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7076 (ptpt) REVERT: H 259 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7354 (mt-10) REVERT: H 318 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8266 (tm) REVERT: I 50 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7302 (mm) REVERT: J 50 ILE cc_start: 0.7612 (OUTLIER) cc_final: 0.7337 (mm) REVERT: K 50 ILE cc_start: 0.7622 (OUTLIER) cc_final: 0.7326 (mm) REVERT: L 50 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7385 (mm) REVERT: M 50 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7390 (mm) REVERT: O 5 ASN cc_start: 0.8370 (t0) cc_final: 0.8163 (t0) REVERT: P 50 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7349 (mm) outliers start: 133 outliers final: 80 residues processed: 417 average time/residue: 0.7828 time to fit residues: 385.0731 Evaluate side-chains 434 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 329 time to evaluate : 1.303 ------------------------------------------------------------------------------- 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 172 CYS 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 338 GLU 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 112 SER 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 251 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE 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 172 CYS 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 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 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 127 PHE Chi-restraints excluded: chain E residue 172 CYS 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 318 LEU 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 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 221 VAL 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 172 CYS Chi-restraints excluded: chain G residue 200 THR Chi-restraints excluded: chain G residue 203 ASP 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 300 VAL Chi-restraints excluded: chain G residue 355 GLU Chi-restraints excluded: chain G residue 360 ARG Chi-restraints excluded: chain H residue 51 GLU 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 318 LEU Chi-restraints excluded: chain H residue 454 GLU 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 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 21 LEU 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 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 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 21 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 9.9990 chunk 443 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 417 optimal weight: 9.9990 chunk 439 optimal weight: 0.9980 chunk 361 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 376 optimal weight: 4.9990 overall best weight: 4.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.114449 restraints weight = 40792.383| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.38 r_work: 0.3098 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 38016 Z= 0.220 Angle : 0.765 7.945 51608 Z= 0.406 Chirality : 0.051 0.202 5432 Planarity : 0.007 0.065 6728 Dihedral : 9.055 169.393 5311 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.41 % Favored : 93.41 % Rotamer: Outliers : 3.70 % Allowed : 26.56 % Favored : 69.74 % 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 aren not related in a simple way. whole: -3.26 (0.10), residues: 4600 helix: -2.17 (0.11), residues: 1584 sheet: -0.37 (0.20), residues: 688 loop : -2.77 (0.10), residues: 2328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 319 TYR 0.011 0.002 TYR F 20 PHE 0.029 0.003 PHE E 345 TRP 0.010 0.002 TRP B 214 HIS 0.007 0.002 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00503 (38016) covalent geometry : angle 0.76480 (51608) hydrogen bonds : bond 0.07035 ( 812) hydrogen bonds : angle 4.74115 ( 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 472 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 330 time to evaluate : 1.491 Fit side-chains REVERT: A 259 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7488 (mt-10) REVERT: A 338 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.6473 (tt0) REVERT: A 454 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 81 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.7098 (ptpt) REVERT: B 360 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.6919 (mtt180) REVERT: C 18 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7078 (ttpt) REVERT: C 81 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7016 (ptpt) REVERT: D 51 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7871 (mp0) REVERT: D 81 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7134 (ptpt) REVERT: E 18 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.6867 (ttpt) REVERT: E 175 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.6485 (mttt) REVERT: E 338 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6592 (tt0) REVERT: E 454 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7925 (mp0) REVERT: F 51 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: F 78 ASP cc_start: 0.8770 (p0) cc_final: 0.8343 (p0) REVERT: F 81 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7059 (ptpt) REVERT: F 454 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7905 (mp0) REVERT: G 51 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: H 51 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: H 81 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7025 (ptpt) REVERT: H 259 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7409 (mt-10) REVERT: I 29 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6535 (mt-10) REVERT: I 50 ILE cc_start: 0.7660 (OUTLIER) cc_final: 0.7398 (mm) REVERT: J 50 ILE cc_start: 0.7731 (OUTLIER) cc_final: 0.7503 (mm) REVERT: K 29 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6561 (mt-10) REVERT: K 50 ILE cc_start: 0.7685 (OUTLIER) cc_final: 0.7434 (mm) REVERT: L 29 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.6606 (mt-10) REVERT: L 50 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7494 (mm) REVERT: M 50 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7350 (mm) REVERT: P 50 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7560 (mm) outliers start: 142 outliers final: 82 residues processed: 433 average time/residue: 0.7809 time to fit residues: 397.2398 Evaluate side-chains 420 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 311 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU 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 286 ASP Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 454 GLU Chi-restraints excluded: chain A residue 461 VAL Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 112 SER 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 251 MET Chi-restraints excluded: chain B residue 360 ARG Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain C residue 18 LYS 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 172 CYS 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 382 ILE Chi-restraints excluded: chain C residue 452 SER 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 200 THR Chi-restraints excluded: chain D residue 204 GLU Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain E residue 18 LYS Chi-restraints excluded: chain E residue 172 CYS 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 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 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 221 VAL 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 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 355 GLU Chi-restraints excluded: chain H residue 51 GLU 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 297 MET 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 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 21 LEU 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 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 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 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 33 MET 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 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: 30.0000 chunk 255 optimal weight: 4.9990 chunk 281 optimal weight: 8.9990 chunk 138 optimal weight: 0.0980 chunk 256 optimal weight: 5.9990 chunk 403 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 384 optimal weight: 0.0970 chunk 179 optimal weight: 1.9990 chunk 267 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 96 GLN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.118279 restraints weight = 40353.357| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.39 r_work: 0.3111 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 38016 Z= 0.124 Angle : 0.600 6.964 51608 Z= 0.319 Chirality : 0.046 0.171 5432 Planarity : 0.006 0.059 6728 Dihedral : 8.690 171.901 5311 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 2.99 % Allowed : 27.21 % 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 aren not related in a simple way. whole: -2.99 (0.11), residues: 4600 helix: -1.90 (0.11), residues: 1632 sheet: -0.22 (0.21), residues: 672 loop : -2.63 (0.10), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 258 TYR 0.007 0.001 TYR H 190 PHE 0.026 0.002 PHE G 345 TRP 0.010 0.001 TRP B 214 HIS 0.005 0.001 HIS B 238 Details of bonding type rmsd covalent geometry : bond 0.00258 (38016) covalent geometry : angle 0.60039 (51608) hydrogen bonds : bond 0.04652 ( 812) hydrogen bonds : angle 4.48711 ( 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 433 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 318 time to evaluate : 1.221 Fit side-chains REVERT: A 259 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7285 (mt-10) REVERT: A 338 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: B 81 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.6931 (ptpt) REVERT: B 360 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.6861 (mtt180) REVERT: C 81 LYS cc_start: 0.8572 (OUTLIER) cc_final: 0.6481 (ptpp) REVERT: D 51 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: D 81 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6958 (ptpt) REVERT: E 18 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.6931 (ttpt) REVERT: E 158 GLU cc_start: 0.8737 (tt0) cc_final: 0.8515 (tt0) REVERT: E 175 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.6432 (mttt) REVERT: E 338 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6531 (tt0) REVERT: E 454 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7920 (mp0) REVERT: F 51 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: F 81 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.6928 (ptpt) REVERT: F 158 GLU cc_start: 0.8774 (tt0) cc_final: 0.8525 (tt0) REVERT: F 355 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7949 (tt0) REVERT: F 454 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: G 51 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7603 (mp0) REVERT: G 355 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: H 51 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: H 81 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.6921 (ptpt) REVERT: H 259 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7327 (mt-10) REVERT: I 50 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7315 (mm) REVERT: J 50 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7359 (mm) REVERT: K 29 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6494 (mt-10) REVERT: K 50 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7331 (mm) REVERT: L 50 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7353 (mm) REVERT: M 50 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7438 (mm) REVERT: P 50 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7337 (mm) outliers start: 115 outliers final: 59 residues processed: 393 average time/residue: 0.7249 time to fit residues: 335.8170 Evaluate side-chains 399 residues out of total 3840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 1.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 30 GLU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 112 SER 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 C residue 81 LYS Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 355 GLU Chi-restraints excluded: chain C residue 382 ILE 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 E residue 18 LYS Chi-restraints excluded: chain E residue 172 CYS 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 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 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 221 VAL 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 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 355 GLU Chi-restraints excluded: chain H residue 51 GLU 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 454 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 21 LEU 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 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 33 MET Chi-restraints excluded: chain N residue 76 ASN Chi-restraints excluded: chain O residue 21 LEU 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: 0.0070 chunk 414 optimal weight: 1.9990 chunk 297 optimal weight: 7.9990 chunk 85 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 279 optimal weight: 0.0040 chunk 178 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 408 optimal weight: 0.5980 overall best weight: 1.3214 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN B 432 ASN C 432 ASN D 432 ASN E 432 ASN F 432 ASN G 432 ASN H 432 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.119940 restraints weight = 40053.468| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.38 r_work: 0.3174 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 38016 Z= 0.109 Angle : 0.560 6.261 51608 Z= 0.297 Chirality : 0.044 0.174 5432 Planarity : 0.006 0.056 6728 Dihedral : 8.437 175.063 5311 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.15 % Favored : 94.67 % Rotamer: Outliers : 2.94 % Allowed : 27.11 % Favored : 69.95 % 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 aren not related in a simple way. whole: -2.70 (0.11), residues: 4600 helix: -1.62 (0.12), residues: 1640 sheet: -0.08 (0.21), residues: 672 loop : -2.49 (0.10), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 258 TYR 0.006 0.001 TYR F 20 PHE 0.024 0.001 PHE B 345 TRP 0.010 0.001 TRP B 214 HIS 0.005 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00227 (38016) covalent geometry : angle 0.55974 (51608) hydrogen bonds : bond 0.03989 ( 812) hydrogen bonds : angle 4.32571 ( 2253) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9593.30 seconds wall clock time: 164 minutes 9.49 seconds (9849.49 seconds total)