Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 16:44:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/04_2023/5u76_8517.pdb" } resolution = 3.76 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 ------------------------------------------------------------------------------- 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= -0.176 sd= 0.627 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: 4 Type Number sf(0) Gaussians S 220 5.16 5 C 18376 2.51 5 N 4748 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 396": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 443": "NH1" <-> "NH2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 592": "NH1" <-> "NH2" Residue "A TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 801": "NH1" <-> "NH2" Residue "A TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 883": "NH1" <-> "NH2" Residue "A PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 941": "NH1" <-> "NH2" Residue "A PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 997": "NH1" <-> "NH2" Residue "A PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1108": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1155": "NH1" <-> "NH2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 396": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 443": "NH1" <-> "NH2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 592": "NH1" <-> "NH2" Residue "B TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 801": "NH1" <-> "NH2" Residue "B TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 883": "NH1" <-> "NH2" Residue "B PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 941": "NH1" <-> "NH2" Residue "B PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 997": "NH1" <-> "NH2" Residue "B PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1108": "NH1" <-> "NH2" Residue "B ARG 1122": "NH1" <-> "NH2" Residue "B TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1155": "NH1" <-> "NH2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 396": "NH1" <-> "NH2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 592": "NH1" <-> "NH2" Residue "C TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 801": "NH1" <-> "NH2" Residue "C TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 883": "NH1" <-> "NH2" Residue "C PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 941": "NH1" <-> "NH2" Residue "C PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 997": "NH1" <-> "NH2" Residue "C PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1108": "NH1" <-> "NH2" Residue "C ARG 1122": "NH1" <-> "NH2" Residue "C TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1155": "NH1" <-> "NH2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 396": "NH1" <-> "NH2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 443": "NH1" <-> "NH2" Residue "D PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 592": "NH1" <-> "NH2" Residue "D TYR 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 732": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 801": "NH1" <-> "NH2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 849": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 883": "NH1" <-> "NH2" Residue "D PHE 933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 941": "NH1" <-> "NH2" Residue "D PHE 943": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 979": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 997": "NH1" <-> "NH2" Residue "D PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1108": "NH1" <-> "NH2" Residue "D ARG 1122": "NH1" <-> "NH2" Residue "D TYR 1145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1155": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 28364 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7091 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 7091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7091 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 7091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7091 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 7091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 7091 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 38, 'TRANS': 839} Chain breaks: 6 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 46 Time building chain proxies: 15.02, per 1000 atoms: 0.53 Number of scatterers: 28364 At special positions: 0 Unit cell: (152.1, 152.1, 139.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 220 16.00 O 5020 8.00 N 4748 7.00 C 18376 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 - 3.50 Amino acid : False - 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: 10.77 Conformation dependent library (CDL) restraints added in 4.0 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6752 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 54.3% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE A 83 " --> pdb=" O ARG A 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 117 " --> pdb=" O VAL A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR A 175 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU A 193 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 199 " --> pdb=" O MET A 195 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.672A pdb=" N ILE A 205 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN A 230 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE A 252 " --> pdb=" O ASN A 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU A 308 " --> pdb=" O TRP A 304 " (cutoff:3.500A) Proline residue: A 322 - end of helix removed outlier: 3.587A pdb=" N LEU A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR A 349 " --> pdb=" O HIS A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG A 397 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 398 " --> pdb=" O GLN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN A 406 " --> pdb=" O PRO A 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA A 424 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA A 446 " --> pdb=" O ASP A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU A 512 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS A 617 " --> pdb=" O ALA A 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN A 618 " --> pdb=" O PHE A 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 613 through 618' Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU A 752 " --> pdb=" O PRO A 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 753 " --> pdb=" O PHE A 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 748 through 753' Processing helix chain 'A' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR A 769 " --> pdb=" O ASP A 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 765 through 770' Processing helix chain 'A' and resid 785 through 795 Proline residue: A 793 - end of helix Processing helix chain 'A' and resid 800 through 804 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 Processing helix chain 'A' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE A 875 " --> pdb=" O ASP A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN A 899 " --> pdb=" O HIS A 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET A 900 " --> pdb=" O PRO A 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A 901 " --> pdb=" O SER A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 896 through 901' Processing helix chain 'A' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU A 913 " --> pdb=" O ASP A 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER A 916 " --> pdb=" O SER A 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS A 917 " --> pdb=" O LEU A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE A 933 " --> pdb=" O ALA A 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 930 through 933' Processing helix chain 'A' and resid 934 through 939 Processing helix chain 'A' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 957 No H-bonds generated for 'chain 'A' and resid 956 through 957' Processing helix chain 'A' and resid 958 through 959 No H-bonds generated for 'chain 'A' and resid 958 through 959' Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU A 969 " --> pdb=" O THR A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 991 " --> pdb=" O ASP A 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 992 " --> pdb=" O ASP A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 987 through 992' Processing helix chain 'A' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A1006 " --> pdb=" O LEU A1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A1007 " --> pdb=" O CYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER A1105 " --> pdb=" O GLN A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1110 through 1127 Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY A1132 " --> pdb=" O PRO A1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR A1133 " --> pdb=" O THR A1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1129 through 1133' Processing helix chain 'B' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE B 83 " --> pdb=" O ARG B 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE B 85 " --> pdb=" O LYS B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG B 95 " --> pdb=" O SER B 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS B 102 " --> pdb=" O ASN B 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 106 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN B 117 " --> pdb=" O VAL B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL B 158 " --> pdb=" O PRO B 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 159 " --> pdb=" O LEU B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR B 175 " --> pdb=" O MET B 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 194 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL B 199 " --> pdb=" O MET B 195 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.672A pdb=" N ILE B 205 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 206 " --> pdb=" O ILE B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 230 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN B 233 " --> pdb=" O GLU B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE B 252 " --> pdb=" O ASN B 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU B 308 " --> pdb=" O TRP B 304 " (cutoff:3.500A) Proline residue: B 322 - end of helix removed outlier: 3.587A pdb=" N LEU B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU B 334 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR B 349 " --> pdb=" O HIS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP B 367 " --> pdb=" O ASP B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG B 397 " --> pdb=" O ILE B 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL B 398 " --> pdb=" O GLN B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU B 512 " --> pdb=" O LEU B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG B 530 " --> pdb=" O GLU B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS B 565 " --> pdb=" O TYR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS B 617 " --> pdb=" O ALA B 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 618 " --> pdb=" O PHE B 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 613 through 618' Processing helix chain 'B' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU B 752 " --> pdb=" O PRO B 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG B 753 " --> pdb=" O PHE B 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 748 through 753' Processing helix chain 'B' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR B 769 " --> pdb=" O ASP B 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 765 through 770' Processing helix chain 'B' and resid 785 through 795 Proline residue: B 793 - end of helix Processing helix chain 'B' and resid 800 through 804 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS B 845 " --> pdb=" O SER B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 Processing helix chain 'B' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE B 875 " --> pdb=" O ASP B 871 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN B 899 " --> pdb=" O HIS B 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET B 900 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 901 " --> pdb=" O SER B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 896 through 901' Processing helix chain 'B' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU B 913 " --> pdb=" O ASP B 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS B 917 " --> pdb=" O LEU B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE B 933 " --> pdb=" O ALA B 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 930 through 933' Processing helix chain 'B' and resid 934 through 939 Processing helix chain 'B' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 957 No H-bonds generated for 'chain 'B' and resid 956 through 957' Processing helix chain 'B' and resid 958 through 959 No H-bonds generated for 'chain 'B' and resid 958 through 959' Processing helix chain 'B' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU B 969 " --> pdb=" O THR B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU B 990 " --> pdb=" O GLU B 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP B 991 " --> pdb=" O ASP B 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 992 " --> pdb=" O ASP B 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 987 through 992' Processing helix chain 'B' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B1004 " --> pdb=" O GLN B1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B1006 " --> pdb=" O LEU B1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B1007 " --> pdb=" O CYS B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER B1105 " --> pdb=" O GLN B1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 1110 through 1127 Processing helix chain 'B' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY B1132 " --> pdb=" O PRO B1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR B1133 " --> pdb=" O THR B1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1129 through 1133' Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE C 85 " --> pdb=" O LYS C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG C 95 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN C 117 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL C 158 " --> pdb=" O PRO C 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 159 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 175 " --> pdb=" O MET C 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU C 193 " --> pdb=" O ILE C 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU C 194 " --> pdb=" O SER C 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Proline residue: C 200 - end of helix removed outlier: 3.672A pdb=" N ILE C 205 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE C 206 " --> pdb=" O ILE C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 230 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN C 233 " --> pdb=" O GLU C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE C 252 " --> pdb=" O ASN C 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 293 Processing helix chain 'C' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU C 308 " --> pdb=" O TRP C 304 " (cutoff:3.500A) Proline residue: C 322 - end of helix removed outlier: 3.587A pdb=" N LEU C 331 " --> pdb=" O GLU C 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU C 334 " --> pdb=" O TYR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR C 349 " --> pdb=" O HIS C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP C 367 " --> pdb=" O ASP C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG C 397 " --> pdb=" O ILE C 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL C 398 " --> pdb=" O GLN C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN C 406 " --> pdb=" O PRO C 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA C 424 " --> pdb=" O ASP C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA C 446 " --> pdb=" O ASP C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU C 512 " --> pdb=" O LEU C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG C 530 " --> pdb=" O GLU C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS C 565 " --> pdb=" O TYR C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS C 617 " --> pdb=" O ALA C 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 618 " --> pdb=" O PHE C 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 613 through 618' Processing helix chain 'C' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU C 752 " --> pdb=" O PRO C 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG C 753 " --> pdb=" O PHE C 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 748 through 753' Processing helix chain 'C' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR C 769 " --> pdb=" O ASP C 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 765 through 770' Processing helix chain 'C' and resid 785 through 795 Proline residue: C 793 - end of helix Processing helix chain 'C' and resid 800 through 804 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU C 842 " --> pdb=" O ASN C 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS C 845 " --> pdb=" O SER C 841 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 870 Processing helix chain 'C' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE C 875 " --> pdb=" O ASP C 871 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN C 899 " --> pdb=" O HIS C 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET C 900 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG C 901 " --> pdb=" O SER C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 896 through 901' Processing helix chain 'C' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU C 913 " --> pdb=" O ASP C 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 916 " --> pdb=" O SER C 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS C 917 " --> pdb=" O LEU C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE C 933 " --> pdb=" O ALA C 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 930 through 933' Processing helix chain 'C' and resid 934 through 939 Processing helix chain 'C' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 957 No H-bonds generated for 'chain 'C' and resid 956 through 957' Processing helix chain 'C' and resid 958 through 959 No H-bonds generated for 'chain 'C' and resid 958 through 959' Processing helix chain 'C' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU C 969 " --> pdb=" O THR C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU C 990 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP C 991 " --> pdb=" O ASP C 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 992 " --> pdb=" O ASP C 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 987 through 992' Processing helix chain 'C' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS C1001 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C1004 " --> pdb=" O GLN C1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C1006 " --> pdb=" O LEU C1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C1007 " --> pdb=" O CYS C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER C1105 " --> pdb=" O GLN C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1127 Processing helix chain 'C' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY C1132 " --> pdb=" O PRO C1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C1133 " --> pdb=" O THR C1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1129 through 1133' Processing helix chain 'D' and resid 78 through 85 removed outlier: 3.979A pdb=" N LEU D 82 " --> pdb=" O GLU D 78 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 117 removed outlier: 3.521A pdb=" N ARG D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS D 106 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN D 117 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 177 removed outlier: 3.723A pdb=" N VAL D 158 " --> pdb=" O PRO D 154 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D 159 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR D 175 " --> pdb=" O MET D 171 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 176 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 207 removed outlier: 3.784A pdb=" N LEU D 193 " --> pdb=" O ILE D 189 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU D 194 " --> pdb=" O SER D 190 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL D 199 " --> pdb=" O MET D 195 " (cutoff:3.500A) Proline residue: D 200 - end of helix removed outlier: 3.672A pdb=" N ILE D 205 " --> pdb=" O PHE D 201 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE D 206 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 218 No H-bonds generated for 'chain 'D' and resid 216 through 218' Processing helix chain 'D' and resid 219 through 233 removed outlier: 3.587A pdb=" N LEU D 223 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN D 233 " --> pdb=" O GLU D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 272 removed outlier: 3.544A pdb=" N ILE D 252 " --> pdb=" O ASN D 248 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 303 through 334 removed outlier: 3.586A pdb=" N LEU D 308 " --> pdb=" O TRP D 304 " (cutoff:3.500A) Proline residue: D 322 - end of helix removed outlier: 3.587A pdb=" N LEU D 331 " --> pdb=" O GLU D 327 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU D 334 " --> pdb=" O TYR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.566A pdb=" N THR D 349 " --> pdb=" O HIS D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 374 removed outlier: 3.563A pdb=" N ASP D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 400 removed outlier: 3.618A pdb=" N ARG D 397 " --> pdb=" O ILE D 393 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL D 398 " --> pdb=" O GLN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 407 removed outlier: 3.791A pdb=" N GLN D 406 " --> pdb=" O PRO D 402 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 425 removed outlier: 3.527A pdb=" N ALA D 424 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 461 removed outlier: 3.518A pdb=" N ALA D 446 " --> pdb=" O ASP D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 488 through 502 removed outlier: 3.754A pdb=" N CYS D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 501 " --> pdb=" O ALA D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.733A pdb=" N LEU D 512 " --> pdb=" O LEU D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 526 through 535 removed outlier: 3.557A pdb=" N ARG D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 removed outlier: 3.656A pdb=" N HIS D 565 " --> pdb=" O TYR D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 618 removed outlier: 3.741A pdb=" N LYS D 617 " --> pdb=" O ALA D 613 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN D 618 " --> pdb=" O PHE D 614 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 613 through 618' Processing helix chain 'D' and resid 748 through 753 removed outlier: 3.547A pdb=" N LEU D 752 " --> pdb=" O PRO D 748 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG D 753 " --> pdb=" O PHE D 749 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 748 through 753' Processing helix chain 'D' and resid 765 through 770 removed outlier: 4.101A pdb=" N TYR D 769 " --> pdb=" O ASP D 765 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY D 770 " --> pdb=" O ALA D 766 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 765 through 770' Processing helix chain 'D' and resid 785 through 795 Proline residue: D 793 - end of helix Processing helix chain 'D' and resid 800 through 804 Processing helix chain 'D' and resid 816 through 824 Processing helix chain 'D' and resid 838 through 846 removed outlier: 3.737A pdb=" N LEU D 842 " --> pdb=" O ASN D 838 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N CYS D 845 " --> pdb=" O SER D 841 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 870 Processing helix chain 'D' and resid 871 through 885 removed outlier: 3.803A pdb=" N ILE D 875 " --> pdb=" O ASP D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 901 removed outlier: 3.791A pdb=" N ASN D 899 " --> pdb=" O HIS D 896 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET D 900 " --> pdb=" O PRO D 897 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG D 901 " --> pdb=" O SER D 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 896 through 901' Processing helix chain 'D' and resid 909 through 926 removed outlier: 3.609A pdb=" N LEU D 913 " --> pdb=" O ASP D 909 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER D 916 " --> pdb=" O SER D 912 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 917 " --> pdb=" O LEU D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 930 through 933 removed outlier: 3.787A pdb=" N PHE D 933 " --> pdb=" O ALA D 930 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 930 through 933' Processing helix chain 'D' and resid 934 through 939 Processing helix chain 'D' and resid 945 through 955 removed outlier: 3.580A pdb=" N LEU D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 957 No H-bonds generated for 'chain 'D' and resid 956 through 957' Processing helix chain 'D' and resid 958 through 959 No H-bonds generated for 'chain 'D' and resid 958 through 959' Processing helix chain 'D' and resid 960 through 970 removed outlier: 3.860A pdb=" N LEU D 969 " --> pdb=" O THR D 965 " (cutoff:3.500A) Processing helix chain 'D' and resid 987 through 992 removed outlier: 3.786A pdb=" N LEU D 990 " --> pdb=" O GLU D 987 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP D 991 " --> pdb=" O ASP D 988 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE D 992 " --> pdb=" O ASP D 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 987 through 992' Processing helix chain 'D' and resid 997 through 1007 removed outlier: 3.979A pdb=" N LYS D1001 " --> pdb=" O ARG D 997 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D1004 " --> pdb=" O GLN D1000 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D1006 " --> pdb=" O LEU D1002 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D1007 " --> pdb=" O CYS D1003 " (cutoff:3.500A) Processing helix chain 'D' and resid 1098 through 1100 No H-bonds generated for 'chain 'D' and resid 1098 through 1100' Processing helix chain 'D' and resid 1101 through 1108 removed outlier: 3.640A pdb=" N SER D1105 " --> pdb=" O GLN D1101 " (cutoff:3.500A) Processing helix chain 'D' and resid 1110 through 1127 Processing helix chain 'D' and resid 1129 through 1133 removed outlier: 3.815A pdb=" N GLY D1132 " --> pdb=" O PRO D1129 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR D1133 " --> pdb=" O THR D1130 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1129 through 1133' Processing sheet with id= 1, first strand: chain 'A' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL A 353 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU A 386 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU A 355 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS A 432 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN A 469 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 434 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 484 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL A 486 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE A 602 " --> pdb=" O ILE A 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 573 " --> pdb=" O ILE A 604 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 723 through 725 Processing sheet with id= 4, first strand: chain 'A' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU A 775 " --> pdb=" O ASN A 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL A 854 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE A 777 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR A 892 " --> pdb=" O PHE A 943 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'A' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP A1160 " --> pdb=" O ILE A 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A1012 " --> pdb=" O TYR A1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A1165 " --> pdb=" O PRO A1010 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL B 353 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU B 386 " --> pdb=" O VAL B 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 355 " --> pdb=" O LEU B 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS B 432 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN B 469 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 434 " --> pdb=" O GLN B 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS B 484 " --> pdb=" O LEU B 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 486 " --> pdb=" O VAL B 468 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE B 602 " --> pdb=" O ILE B 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS B 573 " --> pdb=" O ILE B 604 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 723 through 725 Processing sheet with id= 10, first strand: chain 'B' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU B 775 " --> pdb=" O ASN B 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL B 854 " --> pdb=" O LEU B 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE B 777 " --> pdb=" O VAL B 854 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR B 892 " --> pdb=" O PHE B 943 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'B' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP B1160 " --> pdb=" O ILE B 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B1012 " --> pdb=" O TYR B1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B1165 " --> pdb=" O PRO B1010 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL C 353 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU C 386 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU C 355 " --> pdb=" O LEU C 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS C 432 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN C 469 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 434 " --> pdb=" O GLN C 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 484 " --> pdb=" O LEU C 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C 486 " --> pdb=" O VAL C 468 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE C 602 " --> pdb=" O ILE C 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS C 573 " --> pdb=" O ILE C 604 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 723 through 725 Processing sheet with id= 16, first strand: chain 'C' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU C 775 " --> pdb=" O ASN C 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL C 854 " --> pdb=" O LEU C 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE C 777 " --> pdb=" O VAL C 854 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'C' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR C 892 " --> pdb=" O PHE C 943 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'C' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP C1160 " --> pdb=" O ILE C 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY C1012 " --> pdb=" O TYR C1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE C1165 " --> pdb=" O PRO C1010 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'D' and resid 408 through 412 removed outlier: 6.750A pdb=" N VAL D 353 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N LEU D 386 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU D 355 " --> pdb=" O LEU D 386 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N CYS D 432 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N GLN D 469 " --> pdb=" O CYS D 432 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 434 " --> pdb=" O GLN D 469 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS D 484 " --> pdb=" O LEU D 466 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 486 " --> pdb=" O VAL D 468 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 539 through 544 removed outlier: 6.461A pdb=" N PHE D 602 " --> pdb=" O ILE D 575 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS D 573 " --> pdb=" O ILE D 604 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 723 through 725 Processing sheet with id= 22, first strand: chain 'D' and resid 829 through 831 removed outlier: 6.593A pdb=" N LEU D 775 " --> pdb=" O ASN D 852 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N VAL D 854 " --> pdb=" O LEU D 775 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ILE D 777 " --> pdb=" O VAL D 854 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 892 through 893 removed outlier: 6.871A pdb=" N THR D 892 " --> pdb=" O PHE D 943 " (cutoff:3.500A) No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'D' and resid 980 through 985 removed outlier: 3.949A pdb=" N ASP D1160 " --> pdb=" O ILE D 985 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY D1012 " --> pdb=" O TYR D1163 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D1165 " --> pdb=" O PRO D1010 " (cutoff:3.500A) 1128 hydrogen bonds defined for protein. 3276 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: 9.97 Time building geometry restraints manager: 11.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 8808 1.34 - 1.46: 3656 1.46 - 1.58: 16228 1.58 - 1.69: 0 1.69 - 1.81: 332 Bond restraints: 29024 Sorted by residual: bond pdb=" CA PRO D1151 " pdb=" C PRO D1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO A1151 " pdb=" C PRO A1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO C1151 " pdb=" C PRO C1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO B1151 " pdb=" C PRO B1151 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.70e+01 bond pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 1.517 1.550 -0.033 9.30e-03 1.16e+04 1.24e+01 ... (remaining 29019 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.73: 804 106.73 - 113.59: 15300 113.59 - 120.46: 11956 120.46 - 127.32: 10972 127.32 - 134.19: 288 Bond angle restraints: 39320 Sorted by residual: angle pdb=" N PRO C 208 " pdb=" CA PRO C 208 " pdb=" C PRO C 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO D 208 " pdb=" CA PRO D 208 " pdb=" C PRO D 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO B 208 " pdb=" CA PRO B 208 " pdb=" C PRO B 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N PRO A 208 " pdb=" CA PRO A 208 " pdb=" C PRO A 208 " ideal model delta sigma weight residual 110.70 118.45 -7.75 1.22e+00 6.72e-01 4.03e+01 angle pdb=" N TYR B 960 " pdb=" CA TYR B 960 " pdb=" C TYR B 960 " ideal model delta sigma weight residual 111.75 117.69 -5.94 1.28e+00 6.10e-01 2.15e+01 ... (remaining 39315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 15604 15.03 - 30.07: 1348 30.07 - 45.10: 388 45.10 - 60.13: 80 60.13 - 75.17: 28 Dihedral angle restraints: 17448 sinusoidal: 7048 harmonic: 10400 Sorted by residual: dihedral pdb=" CA ARG B 438 " pdb=" C ARG B 438 " pdb=" N ASN B 439 " pdb=" CA ASN B 439 " ideal model delta harmonic sigma weight residual 180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG C 438 " pdb=" C ARG C 438 " pdb=" N ASN C 439 " pdb=" CA ASN C 439 " ideal model delta harmonic sigma weight residual -180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA ARG A 438 " pdb=" C ARG A 438 " pdb=" N ASN A 439 " pdb=" CA ASN A 439 " ideal model delta harmonic sigma weight residual 180.00 -162.46 -17.54 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 17445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2664 0.044 - 0.088: 1204 0.088 - 0.131: 388 0.131 - 0.175: 132 0.175 - 0.219: 56 Chirality restraints: 4444 Sorted by residual: chirality pdb=" CA VAL B 299 " pdb=" N VAL B 299 " pdb=" C VAL B 299 " pdb=" CB VAL B 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL C 299 " pdb=" N VAL C 299 " pdb=" C VAL C 299 " pdb=" CB VAL C 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA VAL D 299 " pdb=" N VAL D 299 " pdb=" C VAL D 299 " pdb=" CB VAL D 299 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4441 not shown) Planarity restraints: 4924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 199 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO D 200 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 200 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 200 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 199 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO A 200 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 200 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 200 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 199 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO B 200 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 200 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 200 " -0.030 5.00e-02 4.00e+02 ... (remaining 4921 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.11: 12 2.11 - 2.81: 4832 2.81 - 3.50: 38334 3.50 - 4.20: 62862 4.20 - 4.90: 114106 Nonbonded interactions: 220146 Sorted by model distance: nonbonded pdb=" OE2 GLU B 866 " pdb=" CB PRO C 388 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU C 866 " pdb=" CB PRO D 388 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU A 866 " pdb=" CB PRO B 388 " model vdw 1.410 3.440 nonbonded pdb=" CB PRO A 388 " pdb=" OE2 GLU D 866 " model vdw 1.410 3.440 nonbonded pdb=" OE2 GLU A 866 " pdb=" CG PRO B 388 " model vdw 1.839 3.440 ... (remaining 220141 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 6.200 Check model and map are aligned: 0.520 Set scattering table: 0.260 Process input model: 69.460 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 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 : 0.007 0.037 29024 Z= 0.481 Angle : 1.045 7.745 39320 Z= 0.705 Chirality : 0.060 0.219 4444 Planarity : 0.004 0.054 4924 Dihedral : 13.034 75.167 10696 Min Nonbonded Distance : 1.410 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.45 % Favored : 91.32 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.12), residues: 3456 helix: -2.17 (0.10), residues: 1504 sheet: -2.92 (0.23), residues: 316 loop : -2.56 (0.14), residues: 1636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1076 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 1060 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 0 residues processed: 1072 average time/residue: 0.4099 time to fit residues: 686.2815 Evaluate side-chains 625 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 3.516 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 9.9990 chunk 263 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 272 optimal weight: 0.0570 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 overall best weight: 1.7702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 HIS A 499 ASN A 611 ASN A 904 GLN A1137 ASN B 478 HIS B 499 ASN B 611 ASN B 904 GLN B1137 ASN C 478 HIS C 499 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN C 904 GLN C1137 ASN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS D 499 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN D 904 GLN D1137 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6058 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 29024 Z= 0.238 Angle : 0.781 11.395 39320 Z= 0.381 Chirality : 0.045 0.214 4444 Planarity : 0.005 0.054 4924 Dihedral : 4.927 18.395 3836 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.05 % Favored : 95.83 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3456 helix: -0.41 (0.12), residues: 1544 sheet: -2.03 (0.24), residues: 444 loop : -1.90 (0.16), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 700 time to evaluate : 3.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 97 outliers final: 56 residues processed: 744 average time/residue: 0.3779 time to fit residues: 457.6649 Evaluate side-chains 609 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 553 time to evaluate : 3.671 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.2858 time to fit residues: 33.6021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 263 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 316 optimal weight: 5.9990 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 107 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 230 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 HIS A1137 ASN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 230 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS B1137 ASN ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 ASN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN D 230 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.114 29024 Z= 0.413 Angle : 0.808 14.366 39320 Z= 0.404 Chirality : 0.046 0.188 4444 Planarity : 0.005 0.046 4924 Dihedral : 5.021 18.132 3836 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.21 % Favored : 94.68 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.14), residues: 3456 helix: -0.02 (0.12), residues: 1564 sheet: -1.43 (0.25), residues: 472 loop : -1.61 (0.18), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 585 time to evaluate : 3.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 52 residues processed: 676 average time/residue: 0.3784 time to fit residues: 425.2543 Evaluate side-chains 558 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 506 time to evaluate : 3.516 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2527 time to fit residues: 30.0181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 chunk 336 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 301 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 HIS ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 375 HIS ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 HIS ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 HIS ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 896 HIS D 904 GLN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29024 Z= 0.227 Angle : 0.735 12.484 39320 Z= 0.347 Chirality : 0.044 0.256 4444 Planarity : 0.005 0.059 4924 Dihedral : 4.776 16.655 3836 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.37 % Favored : 95.52 % Rotamer Outliers : 3.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.15), residues: 3456 helix: 0.21 (0.13), residues: 1532 sheet: -0.98 (0.27), residues: 432 loop : -1.24 (0.17), residues: 1492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 560 time to evaluate : 3.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 33 residues processed: 618 average time/residue: 0.3722 time to fit residues: 387.3796 Evaluate side-chains 515 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 482 time to evaluate : 3.842 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2672 time to fit residues: 21.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 4.9990 chunk 190 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 250 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 287 optimal weight: 0.0020 chunk 232 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 overall best weight: 2.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 904 GLN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.5613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.060 29024 Z= 0.248 Angle : 0.740 12.313 39320 Z= 0.351 Chirality : 0.045 0.165 4444 Planarity : 0.004 0.046 4924 Dihedral : 4.739 15.986 3836 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.01 % Favored : 94.88 % Rotamer Outliers : 2.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3456 helix: 0.10 (0.13), residues: 1584 sheet: -0.77 (0.26), residues: 472 loop : -1.31 (0.18), residues: 1400 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 571 time to evaluate : 3.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 52 residues processed: 634 average time/residue: 0.3360 time to fit residues: 357.9101 Evaluate side-chains 555 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 503 time to evaluate : 3.183 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.2526 time to fit residues: 29.7214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 6.9990 chunk 302 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 197 optimal weight: 10.0000 chunk 83 optimal weight: 0.0040 chunk 336 optimal weight: 0.1980 chunk 279 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN ** A1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29024 Z= 0.201 Angle : 0.734 11.389 39320 Z= 0.346 Chirality : 0.045 0.229 4444 Planarity : 0.004 0.050 4924 Dihedral : 4.625 15.895 3836 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.73 % Favored : 96.15 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3456 helix: 0.10 (0.13), residues: 1580 sheet: -0.59 (0.27), residues: 408 loop : -1.22 (0.17), residues: 1468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 561 time to evaluate : 3.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 601 average time/residue: 0.3476 time to fit residues: 352.4898 Evaluate side-chains 515 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 486 time to evaluate : 3.564 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2609 time to fit residues: 18.9870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 188 optimal weight: 7.9990 chunk 335 optimal weight: 2.9990 chunk 209 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1137 ASN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 439 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1137 ASN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN C 439 ASN ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1137 ASN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN D 439 ASN ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.6342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 29024 Z= 0.299 Angle : 0.763 10.505 39320 Z= 0.369 Chirality : 0.045 0.199 4444 Planarity : 0.005 0.058 4924 Dihedral : 4.891 17.442 3836 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.03 % Favored : 94.85 % Rotamer Outliers : 1.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3456 helix: 0.07 (0.13), residues: 1572 sheet: -0.39 (0.26), residues: 428 loop : -1.07 (0.17), residues: 1456 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 485 time to evaluate : 3.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 35 residues processed: 509 average time/residue: 0.3492 time to fit residues: 303.3338 Evaluate side-chains 505 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 470 time to evaluate : 3.600 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.2482 time to fit residues: 21.6057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 6.9990 chunk 133 optimal weight: 0.2980 chunk 200 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 263 optimal weight: 4.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 439 ASN A 499 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 499 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 499 ASN ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN D 499 ASN ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6141 moved from start: 0.6475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 29024 Z= 0.273 Angle : 0.777 12.479 39320 Z= 0.369 Chirality : 0.046 0.340 4444 Planarity : 0.004 0.062 4924 Dihedral : 4.862 18.008 3836 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3456 helix: 0.05 (0.13), residues: 1568 sheet: -0.56 (0.25), residues: 468 loop : -1.12 (0.17), residues: 1420 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 479 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 500 average time/residue: 0.3524 time to fit residues: 300.3288 Evaluate side-chains 463 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 447 time to evaluate : 3.517 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2728 time to fit residues: 13.4157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 3.9990 chunk 321 optimal weight: 0.7980 chunk 293 optimal weight: 0.9980 chunk 312 optimal weight: 4.9990 chunk 188 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 282 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 311 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 439 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 439 ASN ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6102 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 29024 Z= 0.205 Angle : 0.805 12.918 39320 Z= 0.371 Chirality : 0.047 0.376 4444 Planarity : 0.004 0.057 4924 Dihedral : 4.796 18.652 3836 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3456 helix: 0.11 (0.13), residues: 1528 sheet: -0.31 (0.26), residues: 420 loop : -0.94 (0.17), residues: 1508 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 503 time to evaluate : 3.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 7 residues processed: 517 average time/residue: 0.3327 time to fit residues: 292.7024 Evaluate side-chains 466 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 459 time to evaluate : 3.338 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2468 time to fit residues: 7.8383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.7980 chunk 330 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 229 optimal weight: 2.9990 chunk 346 optimal weight: 0.9990 chunk 319 optimal weight: 0.8980 chunk 276 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 213 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 475 ASN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 475 ASN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN D 904 GLN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.6673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 29024 Z= 0.222 Angle : 0.849 18.841 39320 Z= 0.386 Chirality : 0.047 0.297 4444 Planarity : 0.004 0.055 4924 Dihedral : 4.720 20.698 3836 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3456 helix: 0.11 (0.13), residues: 1576 sheet: -0.08 (0.28), residues: 380 loop : -1.01 (0.17), residues: 1500 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 485 time to evaluate : 3.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 489 average time/residue: 0.3427 time to fit residues: 286.8505 Evaluate side-chains 468 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 465 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2792 time to fit residues: 6.4739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 254 optimal weight: 0.0970 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 276 optimal weight: 7.9990 chunk 115 optimal weight: 0.0370 chunk 283 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 overall best weight: 2.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN ** C 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.083224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066299 restraints weight = 106495.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.068750 restraints weight = 53153.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.070418 restraints weight = 32765.772| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 29024 Z= 0.279 Angle : 0.842 14.398 39320 Z= 0.390 Chirality : 0.046 0.263 4444 Planarity : 0.005 0.057 4924 Dihedral : 4.828 24.172 3836 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3456 helix: 0.17 (0.13), residues: 1556 sheet: -0.02 (0.27), residues: 400 loop : -1.09 (0.17), residues: 1500 =============================================================================== Job complete usr+sys time: 6544.54 seconds wall clock time: 119 minutes 34.51 seconds (7174.51 seconds total)