Starting phenix.real_space_refine on Wed Mar 20 19:43:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/03_2024/5u76_8517.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/03_2024/5u76_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_8517/03_2024/5u76_8517.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/03_2024/5u76_8517.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/03_2024/5u76_8517.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u76_8517/03_2024/5u76_8517.pdb" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.176 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-dev-5265/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: 14.68, per 1000 atoms: 0.52 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: 11.22 Conformation dependent library (CDL) restraints added in 5.2 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: 3.64 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: 10.32 Time building geometry restraints manager: 12.15 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.090 Check model and map are aligned: 0.380 Set scattering table: 0.260 Process input model: 74.270 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.140 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.490 ------------------------------------------------------------------------------- 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 % Allowed : 4.09 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 222 HIS 0.004 0.001 HIS A 593 PHE 0.012 0.001 PHE B 931 TYR 0.015 0.001 TYR C 532 ARG 0.002 0.000 ARG B 993 *********************** 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 : 3.583 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 REVERT: A 159 GLN cc_start: 0.8324 (mt0) cc_final: 0.8075 (mm-40) REVERT: A 176 LEU cc_start: 0.7127 (mt) cc_final: 0.6446 (mt) REVERT: A 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7533 (p90) REVERT: A 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7778 (p90) REVERT: A 226 TYR cc_start: 0.7071 (t80) cc_final: 0.6675 (t80) REVERT: A 231 MET cc_start: 0.7544 (ttp) cc_final: 0.7307 (ttt) REVERT: A 309 LEU cc_start: 0.9416 (tp) cc_final: 0.9102 (tp) REVERT: A 326 GLU cc_start: 0.8478 (tt0) cc_final: 0.8078 (pp20) REVERT: A 358 SER cc_start: 0.8786 (t) cc_final: 0.8523 (p) REVERT: A 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8965 (t0) REVERT: A 371 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8141 (tp30) REVERT: A 375 HIS cc_start: 0.7388 (m90) cc_final: 0.6306 (m90) REVERT: A 382 TYR cc_start: 0.7872 (m-80) cc_final: 0.7587 (m-80) REVERT: A 383 VAL cc_start: 0.8033 (t) cc_final: 0.7780 (p) REVERT: A 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: A 470 ILE cc_start: 0.8140 (tp) cc_final: 0.7789 (tt) REVERT: A 489 GLU cc_start: 0.8376 (tt0) cc_final: 0.7928 (tp30) REVERT: A 538 ASN cc_start: 0.8429 (m110) cc_final: 0.7991 (m110) REVERT: A 572 VAL cc_start: 0.7606 (t) cc_final: 0.7369 (m) REVERT: A 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7514 (mmm) REVERT: A 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8944 (mt) REVERT: A 765 ASP cc_start: 0.7570 (m-30) cc_final: 0.6545 (p0) REVERT: A 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: A 903 MET cc_start: 0.8248 (tpt) cc_final: 0.7974 (tpp) REVERT: A 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: A 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8050 (m-80) REVERT: A 969 LEU cc_start: 0.9230 (mp) cc_final: 0.8847 (mp) REVERT: A 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7486 (mm) REVERT: A 1005 SER cc_start: 0.7690 (m) cc_final: 0.7421 (p) REVERT: A 1123 MET cc_start: 0.8326 (mtp) cc_final: 0.7893 (ttm) REVERT: A 1133 TYR cc_start: 0.8621 (t80) cc_final: 0.8390 (t80) REVERT: A 1137 ASN cc_start: 0.7578 (m-40) cc_final: 0.7371 (m110) REVERT: A 1157 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7576 (mp0) REVERT: A 1161 ILE cc_start: 0.7642 (mt) cc_final: 0.7405 (tp) REVERT: B 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8074 (mm-40) REVERT: B 176 LEU cc_start: 0.7125 (mt) cc_final: 0.6444 (mt) REVERT: B 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7534 (p90) REVERT: B 218 PHE cc_start: 0.8084 (p90) cc_final: 0.7777 (p90) REVERT: B 226 TYR cc_start: 0.7071 (t80) cc_final: 0.6676 (t80) REVERT: B 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7307 (ttt) REVERT: B 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8998 (tp) REVERT: B 326 GLU cc_start: 0.8480 (tt0) cc_final: 0.8079 (pp20) REVERT: B 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: B 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8966 (t0) REVERT: B 371 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8141 (tp30) REVERT: B 375 HIS cc_start: 0.7387 (m90) cc_final: 0.6307 (m90) REVERT: B 382 TYR cc_start: 0.7871 (m-80) cc_final: 0.7587 (m-80) REVERT: B 383 VAL cc_start: 0.8033 (t) cc_final: 0.7780 (p) REVERT: B 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: B 470 ILE cc_start: 0.8139 (tp) cc_final: 0.7787 (tt) REVERT: B 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7929 (tp30) REVERT: B 538 ASN cc_start: 0.8428 (m110) cc_final: 0.7991 (m110) REVERT: B 572 VAL cc_start: 0.7607 (t) cc_final: 0.7369 (m) REVERT: B 595 MET cc_start: 0.8211 (mmp) cc_final: 0.7512 (mmm) REVERT: B 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8945 (mt) REVERT: B 765 ASP cc_start: 0.7568 (m-30) cc_final: 0.6544 (p0) REVERT: B 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: B 903 MET cc_start: 0.8247 (tpt) cc_final: 0.7974 (tpp) REVERT: B 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: B 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8050 (m-80) REVERT: B 969 LEU cc_start: 0.9230 (mp) cc_final: 0.8847 (mp) REVERT: B 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7485 (mm) REVERT: B 1005 SER cc_start: 0.7689 (m) cc_final: 0.7420 (p) REVERT: B 1123 MET cc_start: 0.8327 (mtp) cc_final: 0.7893 (ttm) REVERT: B 1133 TYR cc_start: 0.8620 (t80) cc_final: 0.8391 (t80) REVERT: B 1137 ASN cc_start: 0.7580 (m-40) cc_final: 0.7374 (m110) REVERT: B 1157 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7576 (mp0) REVERT: B 1161 ILE cc_start: 0.7644 (mt) cc_final: 0.7406 (tp) REVERT: C 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: C 176 LEU cc_start: 0.7125 (mt) cc_final: 0.6446 (mt) REVERT: C 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7534 (p90) REVERT: C 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7778 (p90) REVERT: C 226 TYR cc_start: 0.7070 (t80) cc_final: 0.6676 (t80) REVERT: C 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7306 (ttt) REVERT: C 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8998 (tp) REVERT: C 326 GLU cc_start: 0.8481 (tt0) cc_final: 0.8080 (pp20) REVERT: C 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: C 367 ASP cc_start: 0.9362 (m-30) cc_final: 0.8966 (t0) REVERT: C 371 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8140 (tp30) REVERT: C 375 HIS cc_start: 0.7387 (m90) cc_final: 0.6306 (m90) REVERT: C 382 TYR cc_start: 0.7871 (m-80) cc_final: 0.7588 (m-80) REVERT: C 383 VAL cc_start: 0.8036 (t) cc_final: 0.7781 (p) REVERT: C 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: C 470 ILE cc_start: 0.8140 (tp) cc_final: 0.7789 (tt) REVERT: C 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7928 (tp30) REVERT: C 538 ASN cc_start: 0.8427 (m110) cc_final: 0.7990 (m110) REVERT: C 572 VAL cc_start: 0.7607 (t) cc_final: 0.7369 (m) REVERT: C 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7513 (mmm) REVERT: C 743 LEU cc_start: 0.9207 (mt) cc_final: 0.8944 (mt) REVERT: C 765 ASP cc_start: 0.7567 (m-30) cc_final: 0.6544 (p0) REVERT: C 837 ASP cc_start: 0.9361 (t70) cc_final: 0.8881 (m-30) REVERT: C 903 MET cc_start: 0.8246 (tpt) cc_final: 0.7973 (tpp) REVERT: C 912 SER cc_start: 0.9069 (m) cc_final: 0.8798 (p) REVERT: C 953 TYR cc_start: 0.9171 (m-10) cc_final: 0.8050 (m-80) REVERT: C 969 LEU cc_start: 0.9231 (mp) cc_final: 0.8847 (mp) REVERT: C 1002 LEU cc_start: 0.7938 (mt) cc_final: 0.7486 (mm) REVERT: C 1005 SER cc_start: 0.7690 (m) cc_final: 0.7421 (p) REVERT: C 1123 MET cc_start: 0.8325 (mtp) cc_final: 0.7892 (ttm) REVERT: C 1133 TYR cc_start: 0.8622 (t80) cc_final: 0.8392 (t80) REVERT: C 1137 ASN cc_start: 0.7582 (m-40) cc_final: 0.7375 (m110) REVERT: C 1157 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7577 (mp0) REVERT: C 1161 ILE cc_start: 0.7644 (mt) cc_final: 0.7407 (tp) REVERT: D 159 GLN cc_start: 0.8323 (mt0) cc_final: 0.8075 (mm-40) REVERT: D 176 LEU cc_start: 0.7126 (mt) cc_final: 0.6447 (mt) REVERT: D 183 TRP cc_start: 0.7870 (m-90) cc_final: 0.7533 (p90) REVERT: D 218 PHE cc_start: 0.8085 (p90) cc_final: 0.7778 (p90) REVERT: D 226 TYR cc_start: 0.7070 (t80) cc_final: 0.6676 (t80) REVERT: D 231 MET cc_start: 0.7543 (ttp) cc_final: 0.7306 (ttt) REVERT: D 309 LEU cc_start: 0.9416 (tp) cc_final: 0.8998 (tp) REVERT: D 326 GLU cc_start: 0.8479 (tt0) cc_final: 0.8078 (pp20) REVERT: D 358 SER cc_start: 0.8787 (t) cc_final: 0.8524 (p) REVERT: D 367 ASP cc_start: 0.9361 (m-30) cc_final: 0.8965 (t0) REVERT: D 371 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8140 (tp30) REVERT: D 375 HIS cc_start: 0.7386 (m90) cc_final: 0.6304 (m90) REVERT: D 382 TYR cc_start: 0.7870 (m-80) cc_final: 0.7587 (m-80) REVERT: D 383 VAL cc_start: 0.8035 (t) cc_final: 0.7781 (p) REVERT: D 406 GLN cc_start: 0.8438 (tt0) cc_final: 0.7986 (tt0) REVERT: D 470 ILE cc_start: 0.8139 (tp) cc_final: 0.7789 (tt) REVERT: D 489 GLU cc_start: 0.8377 (tt0) cc_final: 0.7929 (tp30) REVERT: D 538 ASN cc_start: 0.8429 (m110) cc_final: 0.7991 (m110) REVERT: D 572 VAL cc_start: 0.7605 (t) cc_final: 0.7368 (m) REVERT: D 595 MET cc_start: 0.8212 (mmp) cc_final: 0.7513 (mmm) REVERT: D 743 LEU cc_start: 0.9206 (mt) cc_final: 0.8943 (mt) REVERT: D 765 ASP cc_start: 0.7569 (m-30) cc_final: 0.6546 (p0) REVERT: D 837 ASP cc_start: 0.9362 (t70) cc_final: 0.8881 (m-30) REVERT: D 903 MET cc_start: 0.8249 (tpt) cc_final: 0.7975 (tpp) REVERT: D 912 SER cc_start: 0.9069 (m) cc_final: 0.8799 (p) REVERT: D 953 TYR cc_start: 0.9172 (m-10) cc_final: 0.8051 (m-80) REVERT: D 969 LEU cc_start: 0.9231 (mp) cc_final: 0.8847 (mp) REVERT: D 1002 LEU cc_start: 0.7937 (mt) cc_final: 0.7486 (mm) REVERT: D 1005 SER cc_start: 0.7689 (m) cc_final: 0.7420 (p) REVERT: D 1123 MET cc_start: 0.8326 (mtp) cc_final: 0.7893 (ttm) REVERT: D 1133 TYR cc_start: 0.8621 (t80) cc_final: 0.8392 (t80) REVERT: D 1137 ASN cc_start: 0.7580 (m-40) cc_final: 0.7373 (m110) REVERT: D 1157 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7577 (mp0) REVERT: D 1161 ILE cc_start: 0.7643 (mt) cc_final: 0.7405 (tp) outliers start: 16 outliers final: 0 residues processed: 1072 average time/residue: 0.4115 time to fit residues: 692.4532 Evaluate side-chains 687 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 3.267 ------------------------------------------------------------------------------- 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: 5.9990 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 272 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 316 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS B 499 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN B 904 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 HIS C 499 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 611 ASN C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 HIS ** 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 ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29024 Z= 0.226 Angle : 0.762 11.224 39320 Z= 0.368 Chirality : 0.044 0.201 4444 Planarity : 0.005 0.055 4924 Dihedral : 4.871 18.267 3836 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.94 % Favored : 95.95 % Rotamer: Outliers : 2.97 % Allowed : 14.85 % Favored : 82.18 % 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: -1.96 (0.14), residues: 3456 helix: -0.44 (0.12), residues: 1548 sheet: -2.07 (0.24), residues: 436 loop : -1.90 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 455 HIS 0.004 0.001 HIS B 567 PHE 0.027 0.002 PHE C 291 TYR 0.019 0.002 TYR D 798 ARG 0.006 0.000 ARG A 89 *********************** 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 832 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 739 time to evaluate : 3.381 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 revert: symmetry clash REVERT: A 285 TYR cc_start: 0.8984 (t80) cc_final: 0.8598 (t80) REVERT: A 291 PHE cc_start: 0.6383 (m-80) cc_final: 0.6138 (m-80) REVERT: A 371 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8188 (tp30) REVERT: A 375 HIS cc_start: 0.8252 (m90) cc_final: 0.5897 (m90) REVERT: A 378 LEU cc_start: 0.7592 (mt) cc_final: 0.6841 (tt) REVERT: A 382 TYR cc_start: 0.7917 (m-80) cc_final: 0.7680 (m-80) REVERT: A 406 GLN cc_start: 0.8470 (tt0) cc_final: 0.8086 (tt0) REVERT: A 470 ILE cc_start: 0.8344 (tp) cc_final: 0.7929 (tt) REVERT: A 489 GLU cc_start: 0.8652 (tt0) cc_final: 0.8123 (tp30) REVERT: A 595 MET cc_start: 0.7616 (mmp) cc_final: 0.6988 (mmm) REVERT: A 743 LEU cc_start: 0.9126 (mt) cc_final: 0.8886 (mp) REVERT: A 837 ASP cc_start: 0.9391 (t70) cc_final: 0.8836 (m-30) REVERT: A 869 MET cc_start: 0.9109 (ttm) cc_final: 0.8766 (ttm) REVERT: A 893 GLU cc_start: 0.7822 (pp20) cc_final: 0.6734 (tp30) REVERT: A 912 SER cc_start: 0.8936 (m) cc_final: 0.8735 (p) REVERT: A 953 TYR cc_start: 0.9130 (m-10) cc_final: 0.8391 (m-80) REVERT: A 1123 MET cc_start: 0.8438 (mtp) cc_final: 0.8136 (ttm) REVERT: A 1157 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7654 (mp0) REVERT: B 285 TYR cc_start: 0.8984 (t80) cc_final: 0.8597 (t80) REVERT: B 291 PHE cc_start: 0.6384 (m-80) cc_final: 0.6139 (m-80) REVERT: B 307 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8888 (mp10) REVERT: B 371 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8188 (tp30) REVERT: B 375 HIS cc_start: 0.8250 (m90) cc_final: 0.5893 (m90) REVERT: B 378 LEU cc_start: 0.7593 (mt) cc_final: 0.6841 (tt) REVERT: B 382 TYR cc_start: 0.7918 (m-80) cc_final: 0.7680 (m-80) REVERT: B 406 GLN cc_start: 0.8469 (tt0) cc_final: 0.8085 (tt0) REVERT: B 470 ILE cc_start: 0.8343 (tp) cc_final: 0.7928 (tt) REVERT: B 489 GLU cc_start: 0.8652 (tt0) cc_final: 0.8124 (tp30) REVERT: B 595 MET cc_start: 0.7614 (mmp) cc_final: 0.6986 (mmm) REVERT: B 743 LEU cc_start: 0.9125 (mt) cc_final: 0.8885 (mp) REVERT: B 837 ASP cc_start: 0.9391 (t70) cc_final: 0.8836 (m-30) REVERT: B 869 MET cc_start: 0.9109 (ttm) cc_final: 0.8765 (ttm) REVERT: B 893 GLU cc_start: 0.7822 (pp20) cc_final: 0.6733 (tp30) REVERT: B 912 SER cc_start: 0.8936 (m) cc_final: 0.8736 (p) REVERT: B 953 TYR cc_start: 0.9131 (m-10) cc_final: 0.8392 (m-80) REVERT: B 1123 MET cc_start: 0.8437 (mtp) cc_final: 0.8135 (ttm) REVERT: B 1157 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7653 (mp0) REVERT: C 285 TYR cc_start: 0.8985 (t80) cc_final: 0.8598 (t80) REVERT: C 291 PHE cc_start: 0.6376 (m-80) cc_final: 0.6129 (m-80) REVERT: C 307 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8888 (mp10) REVERT: C 371 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8187 (tp30) REVERT: C 375 HIS cc_start: 0.8247 (m90) cc_final: 0.5888 (m90) REVERT: C 378 LEU cc_start: 0.7592 (mt) cc_final: 0.6840 (tt) REVERT: C 382 TYR cc_start: 0.7916 (m-80) cc_final: 0.7680 (m-80) REVERT: C 406 GLN cc_start: 0.8469 (tt0) cc_final: 0.8085 (tt0) REVERT: C 470 ILE cc_start: 0.8343 (tp) cc_final: 0.7928 (tt) REVERT: C 489 GLU cc_start: 0.8653 (tt0) cc_final: 0.8124 (tp30) REVERT: C 595 MET cc_start: 0.7616 (mmp) cc_final: 0.6987 (mmm) REVERT: C 743 LEU cc_start: 0.9126 (mt) cc_final: 0.8886 (mp) REVERT: C 837 ASP cc_start: 0.9392 (t70) cc_final: 0.8837 (m-30) REVERT: C 869 MET cc_start: 0.9108 (ttm) cc_final: 0.8766 (ttm) REVERT: C 893 GLU cc_start: 0.7822 (pp20) cc_final: 0.6733 (tp30) REVERT: C 912 SER cc_start: 0.8936 (m) cc_final: 0.8736 (p) REVERT: C 953 TYR cc_start: 0.9131 (m-10) cc_final: 0.8392 (m-80) REVERT: C 1123 MET cc_start: 0.8438 (mtp) cc_final: 0.8136 (ttm) REVERT: C 1157 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7653 (mp0) REVERT: D 291 PHE cc_start: 0.6379 (m-80) cc_final: 0.6133 (m-80) REVERT: D 307 GLN cc_start: 0.9384 (mm-40) cc_final: 0.8888 (mp10) REVERT: D 371 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8188 (tp30) REVERT: D 375 HIS cc_start: 0.8250 (m90) cc_final: 0.5891 (m90) REVERT: D 378 LEU cc_start: 0.7592 (mt) cc_final: 0.6841 (tt) REVERT: D 382 TYR cc_start: 0.7918 (m-80) cc_final: 0.7681 (m-80) REVERT: D 406 GLN cc_start: 0.8469 (tt0) cc_final: 0.8086 (tt0) REVERT: D 470 ILE cc_start: 0.8343 (tp) cc_final: 0.7928 (tt) REVERT: D 489 GLU cc_start: 0.8652 (tt0) cc_final: 0.8123 (tp30) REVERT: D 595 MET cc_start: 0.7616 (mmp) cc_final: 0.6987 (mmm) REVERT: D 743 LEU cc_start: 0.9126 (mt) cc_final: 0.8886 (mp) REVERT: D 837 ASP cc_start: 0.9391 (t70) cc_final: 0.8836 (m-30) REVERT: D 869 MET cc_start: 0.9113 (ttm) cc_final: 0.8753 (ttm) REVERT: D 893 GLU cc_start: 0.7822 (pp20) cc_final: 0.6734 (tp30) REVERT: D 912 SER cc_start: 0.8936 (m) cc_final: 0.8736 (p) REVERT: D 953 TYR cc_start: 0.9130 (m-10) cc_final: 0.8391 (m-80) REVERT: D 1123 MET cc_start: 0.8438 (mtp) cc_final: 0.8135 (ttm) REVERT: D 1157 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7652 (mp0) outliers start: 93 outliers final: 52 residues processed: 775 average time/residue: 0.3504 time to fit residues: 443.4697 Evaluate side-chains 631 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 579 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 798 TYR Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 798 TYR Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 363 ASP Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 798 TYR Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain D residue 385 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 798 TYR Chi-restraints excluded: chain D residue 890 ILE Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 1008 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 10.0000 chunk 98 optimal weight: 20.0000 chunk 263 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 316 optimal weight: 0.5980 chunk 342 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 chunk 313 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 565 HIS B1137 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1137 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6145 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 29024 Z= 0.405 Angle : 0.776 9.133 39320 Z= 0.389 Chirality : 0.045 0.179 4444 Planarity : 0.005 0.044 4924 Dihedral : 4.974 17.976 3836 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.18 % Favored : 94.70 % Rotamer: Outliers : 3.93 % Allowed : 17.50 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.15), residues: 3456 helix: 0.17 (0.13), residues: 1556 sheet: -1.47 (0.25), residues: 472 loop : -1.59 (0.18), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 304 HIS 0.008 0.002 HIS D 567 PHE 0.024 0.003 PHE A 749 TYR 0.018 0.002 TYR A 798 ARG 0.009 0.001 ARG B 377 *********************** 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 739 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 616 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8216 (tp30) REVERT: A 375 HIS cc_start: 0.8237 (m90) cc_final: 0.6294 (m90) REVERT: A 378 LEU cc_start: 0.7652 (mt) cc_final: 0.6985 (tt) REVERT: A 391 MET cc_start: 0.7242 (mmm) cc_final: 0.6710 (tpp) REVERT: A 397 ARG cc_start: 0.8308 (mmt90) cc_final: 0.8003 (tpt170) REVERT: A 406 GLN cc_start: 0.8423 (tt0) cc_final: 0.7999 (tt0) REVERT: A 595 MET cc_start: 0.7460 (mmp) cc_final: 0.7126 (mmm) REVERT: A 738 THR cc_start: 0.8409 (m) cc_final: 0.8119 (p) REVERT: A 743 LEU cc_start: 0.9031 (mt) cc_final: 0.8786 (mt) REVERT: A 823 ILE cc_start: 0.9060 (tt) cc_final: 0.8851 (pt) REVERT: A 832 MET cc_start: 0.7337 (mmm) cc_final: 0.6686 (tpt) REVERT: A 837 ASP cc_start: 0.9373 (t70) cc_final: 0.9020 (m-30) REVERT: A 844 GLN cc_start: 0.9179 (mt0) cc_final: 0.8912 (tt0) REVERT: A 893 GLU cc_start: 0.8246 (pp20) cc_final: 0.7153 (tp30) REVERT: A 894 LEU cc_start: 0.8882 (mt) cc_final: 0.8386 (mm) REVERT: A 953 TYR cc_start: 0.9124 (m-10) cc_final: 0.8620 (m-80) REVERT: A 961 MET cc_start: 0.9397 (tpt) cc_final: 0.8491 (mtp) REVERT: A 1123 MET cc_start: 0.8523 (mtp) cc_final: 0.8173 (ttm) REVERT: A 1137 ASN cc_start: 0.7612 (m-40) cc_final: 0.7287 (m-40) REVERT: A 1157 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7665 (mp0) REVERT: B 371 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8215 (tp30) REVERT: B 375 HIS cc_start: 0.8235 (m90) cc_final: 0.6291 (m90) REVERT: B 378 LEU cc_start: 0.7653 (mt) cc_final: 0.6986 (tt) REVERT: B 391 MET cc_start: 0.7243 (mmm) cc_final: 0.6711 (tpp) REVERT: B 397 ARG cc_start: 0.8308 (mmt90) cc_final: 0.8003 (tpt170) REVERT: B 406 GLN cc_start: 0.8422 (tt0) cc_final: 0.7998 (tt0) REVERT: B 595 MET cc_start: 0.7461 (mmp) cc_final: 0.7126 (mmm) REVERT: B 738 THR cc_start: 0.8412 (m) cc_final: 0.8121 (p) REVERT: B 743 LEU cc_start: 0.9031 (mt) cc_final: 0.8786 (mt) REVERT: B 823 ILE cc_start: 0.9061 (tt) cc_final: 0.8852 (pt) REVERT: B 832 MET cc_start: 0.7338 (mmm) cc_final: 0.6688 (tpt) REVERT: B 837 ASP cc_start: 0.9373 (t70) cc_final: 0.9020 (m-30) REVERT: B 844 GLN cc_start: 0.9179 (mt0) cc_final: 0.8912 (tt0) REVERT: B 893 GLU cc_start: 0.8246 (pp20) cc_final: 0.7154 (tp30) REVERT: B 894 LEU cc_start: 0.8882 (mt) cc_final: 0.8386 (mm) REVERT: B 953 TYR cc_start: 0.9124 (m-10) cc_final: 0.8620 (m-80) REVERT: B 961 MET cc_start: 0.9397 (tpt) cc_final: 0.8491 (mtp) REVERT: B 1123 MET cc_start: 0.8524 (mtp) cc_final: 0.8174 (ttm) REVERT: B 1137 ASN cc_start: 0.7611 (m-40) cc_final: 0.7286 (m-40) REVERT: B 1157 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7665 (mp0) REVERT: C 371 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8215 (tp30) REVERT: C 375 HIS cc_start: 0.8234 (m90) cc_final: 0.6291 (m90) REVERT: C 378 LEU cc_start: 0.7653 (mt) cc_final: 0.6985 (tt) REVERT: C 391 MET cc_start: 0.7243 (mmm) cc_final: 0.6711 (tpp) REVERT: C 397 ARG cc_start: 0.8308 (mmt90) cc_final: 0.8003 (tpt170) REVERT: C 406 GLN cc_start: 0.8422 (tt0) cc_final: 0.7998 (tt0) REVERT: C 595 MET cc_start: 0.7460 (mmp) cc_final: 0.7125 (mmm) REVERT: C 738 THR cc_start: 0.8411 (m) cc_final: 0.8120 (p) REVERT: C 743 LEU cc_start: 0.9031 (mt) cc_final: 0.8787 (mt) REVERT: C 823 ILE cc_start: 0.9061 (tt) cc_final: 0.8851 (pt) REVERT: C 832 MET cc_start: 0.7337 (mmm) cc_final: 0.6686 (tpt) REVERT: C 837 ASP cc_start: 0.9373 (t70) cc_final: 0.9020 (m-30) REVERT: C 844 GLN cc_start: 0.9179 (mt0) cc_final: 0.8913 (tt0) REVERT: C 893 GLU cc_start: 0.8246 (pp20) cc_final: 0.7153 (tp30) REVERT: C 894 LEU cc_start: 0.8882 (mt) cc_final: 0.8386 (mm) REVERT: C 953 TYR cc_start: 0.9123 (m-10) cc_final: 0.8619 (m-80) REVERT: C 961 MET cc_start: 0.9397 (tpt) cc_final: 0.8491 (mtp) REVERT: C 1123 MET cc_start: 0.8525 (mtp) cc_final: 0.8174 (ttm) REVERT: C 1137 ASN cc_start: 0.7612 (m-40) cc_final: 0.7286 (m-40) REVERT: C 1157 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7664 (mp0) REVERT: D 371 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8215 (tp30) REVERT: D 375 HIS cc_start: 0.8235 (m90) cc_final: 0.6290 (m90) REVERT: D 378 LEU cc_start: 0.7651 (mt) cc_final: 0.6985 (tt) REVERT: D 391 MET cc_start: 0.7243 (mmm) cc_final: 0.6712 (tpp) REVERT: D 397 ARG cc_start: 0.8308 (mmt90) cc_final: 0.8003 (tpt170) REVERT: D 406 GLN cc_start: 0.8422 (tt0) cc_final: 0.7999 (tt0) REVERT: D 595 MET cc_start: 0.7461 (mmp) cc_final: 0.7126 (mmm) REVERT: D 738 THR cc_start: 0.8409 (m) cc_final: 0.8119 (p) REVERT: D 743 LEU cc_start: 0.9031 (mt) cc_final: 0.8787 (mt) REVERT: D 823 ILE cc_start: 0.9060 (tt) cc_final: 0.8850 (pt) REVERT: D 832 MET cc_start: 0.7337 (mmm) cc_final: 0.6687 (tpt) REVERT: D 837 ASP cc_start: 0.9372 (t70) cc_final: 0.9020 (m-30) REVERT: D 844 GLN cc_start: 0.9179 (mt0) cc_final: 0.8912 (tt0) REVERT: D 953 TYR cc_start: 0.9124 (m-10) cc_final: 0.8619 (m-80) REVERT: D 961 MET cc_start: 0.9397 (tpt) cc_final: 0.8490 (mtp) REVERT: D 1123 MET cc_start: 0.8523 (mtp) cc_final: 0.8174 (ttm) REVERT: D 1137 ASN cc_start: 0.7610 (m-40) cc_final: 0.7286 (m-40) REVERT: D 1157 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7665 (mp0) outliers start: 123 outliers final: 88 residues processed: 715 average time/residue: 0.3467 time to fit residues: 411.9154 Evaluate side-chains 622 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 534 time to evaluate : 3.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 408 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 890 ILE Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 392 ASP Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 890 ILE Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 392 ASP Chi-restraints excluded: chain C residue 408 VAL Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 890 ILE Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 392 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 890 ILE Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1011 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 6.9990 chunk 238 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 317 optimal weight: 6.9990 chunk 336 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 896 HIS ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 HIS ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 896 HIS ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 565 HIS ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.5047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 29024 Z= 0.311 Angle : 0.724 9.240 39320 Z= 0.354 Chirality : 0.044 0.215 4444 Planarity : 0.005 0.044 4924 Dihedral : 4.864 17.396 3836 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.63 % Favored : 95.25 % Rotamer: Outliers : 5.04 % Allowed : 19.73 % Favored : 75.22 % 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: -0.85 (0.15), residues: 3456 helix: 0.27 (0.13), residues: 1560 sheet: -1.10 (0.29), residues: 392 loop : -1.22 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 304 HIS 0.007 0.002 HIS A 567 PHE 0.033 0.002 PHE C 291 TYR 0.024 0.002 TYR D 285 ARG 0.006 0.001 ARG A 966 *********************** 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 713 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 555 time to evaluate : 3.131 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: A 213 LEU cc_start: 0.3514 (OUTLIER) cc_final: 0.3290 (mm) REVERT: A 296 TYR cc_start: 0.8271 (m-80) cc_final: 0.8034 (m-80) REVERT: A 315 CYS cc_start: 0.9422 (t) cc_final: 0.9217 (p) REVERT: A 371 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8232 (tp30) REVERT: A 375 HIS cc_start: 0.8257 (m90) cc_final: 0.6289 (m90) REVERT: A 379 GLN cc_start: 0.8951 (tt0) cc_final: 0.8610 (tm-30) REVERT: A 382 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7364 (t80) REVERT: A 391 MET cc_start: 0.7993 (mmm) cc_final: 0.7542 (tpp) REVERT: A 397 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7928 (tpt170) REVERT: A 561 TYR cc_start: 0.5040 (OUTLIER) cc_final: 0.4649 (t80) REVERT: A 595 MET cc_start: 0.7394 (mmp) cc_final: 0.7096 (mmm) REVERT: A 738 THR cc_start: 0.8509 (m) cc_final: 0.8230 (p) REVERT: A 743 LEU cc_start: 0.9103 (mt) cc_final: 0.8856 (mp) REVERT: A 828 MET cc_start: 0.7886 (mpp) cc_final: 0.7559 (mpp) REVERT: A 893 GLU cc_start: 0.8166 (pp20) cc_final: 0.7238 (tp30) REVERT: A 894 LEU cc_start: 0.8747 (mt) cc_final: 0.8429 (mm) REVERT: A 932 MET cc_start: 0.9037 (ptm) cc_final: 0.8566 (ppp) REVERT: A 953 TYR cc_start: 0.9114 (m-10) cc_final: 0.8628 (m-80) REVERT: A 961 MET cc_start: 0.9371 (tpt) cc_final: 0.8439 (mtp) REVERT: A 1098 TRP cc_start: 0.8066 (t-100) cc_final: 0.7584 (p-90) REVERT: A 1123 MET cc_start: 0.8542 (mtp) cc_final: 0.8142 (ttm) REVERT: B 296 TYR cc_start: 0.8261 (m-80) cc_final: 0.8028 (m-80) REVERT: B 315 CYS cc_start: 0.9424 (t) cc_final: 0.9218 (p) REVERT: B 371 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8232 (tp30) REVERT: B 375 HIS cc_start: 0.8256 (m90) cc_final: 0.6288 (m90) REVERT: B 379 GLN cc_start: 0.8951 (tt0) cc_final: 0.8611 (tm-30) REVERT: B 382 TYR cc_start: 0.7619 (OUTLIER) cc_final: 0.7363 (t80) REVERT: B 391 MET cc_start: 0.7992 (mmm) cc_final: 0.7543 (tpp) REVERT: B 397 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7928 (tpt170) REVERT: B 561 TYR cc_start: 0.5041 (OUTLIER) cc_final: 0.4649 (t80) REVERT: B 595 MET cc_start: 0.7392 (mmp) cc_final: 0.7094 (mmm) REVERT: B 738 THR cc_start: 0.8510 (m) cc_final: 0.8230 (p) REVERT: B 743 LEU cc_start: 0.9102 (mt) cc_final: 0.8855 (mp) REVERT: B 828 MET cc_start: 0.7885 (mpp) cc_final: 0.7558 (mpp) REVERT: B 893 GLU cc_start: 0.8165 (pp20) cc_final: 0.7237 (tp30) REVERT: B 894 LEU cc_start: 0.8744 (mt) cc_final: 0.8427 (mm) REVERT: B 932 MET cc_start: 0.9038 (ptm) cc_final: 0.8566 (ppp) REVERT: B 953 TYR cc_start: 0.9114 (m-10) cc_final: 0.8627 (m-80) REVERT: B 961 MET cc_start: 0.9370 (tpt) cc_final: 0.8437 (mtp) REVERT: B 1098 TRP cc_start: 0.8065 (t-100) cc_final: 0.7584 (p-90) REVERT: B 1123 MET cc_start: 0.8542 (mtp) cc_final: 0.8143 (ttm) REVERT: C 296 TYR cc_start: 0.8260 (m-80) cc_final: 0.8025 (m-80) REVERT: C 315 CYS cc_start: 0.9424 (t) cc_final: 0.9219 (p) REVERT: C 371 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8230 (tp30) REVERT: C 375 HIS cc_start: 0.8255 (m90) cc_final: 0.6285 (m90) REVERT: C 379 GLN cc_start: 0.8951 (tt0) cc_final: 0.8611 (tm-30) REVERT: C 382 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 391 MET cc_start: 0.7992 (mmm) cc_final: 0.7542 (tpp) REVERT: C 397 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7928 (tpt170) REVERT: C 561 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4681 (t80) REVERT: C 595 MET cc_start: 0.7384 (mmp) cc_final: 0.7089 (mmm) REVERT: C 738 THR cc_start: 0.8509 (m) cc_final: 0.8229 (p) REVERT: C 743 LEU cc_start: 0.9102 (mt) cc_final: 0.8855 (mp) REVERT: C 828 MET cc_start: 0.7885 (mpp) cc_final: 0.7557 (mpp) REVERT: C 893 GLU cc_start: 0.8166 (pp20) cc_final: 0.7238 (tp30) REVERT: C 894 LEU cc_start: 0.8745 (mt) cc_final: 0.8427 (mm) REVERT: C 932 MET cc_start: 0.9037 (ptm) cc_final: 0.8565 (ppp) REVERT: C 953 TYR cc_start: 0.9113 (m-10) cc_final: 0.8627 (m-80) REVERT: C 961 MET cc_start: 0.9370 (tpt) cc_final: 0.8437 (mtp) REVERT: C 1098 TRP cc_start: 0.8066 (t-100) cc_final: 0.7583 (p-90) REVERT: C 1123 MET cc_start: 0.8542 (mtp) cc_final: 0.8142 (ttm) REVERT: D 296 TYR cc_start: 0.8118 (m-80) cc_final: 0.7881 (m-80) REVERT: D 315 CYS cc_start: 0.9424 (t) cc_final: 0.9218 (p) REVERT: D 371 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8230 (tp30) REVERT: D 375 HIS cc_start: 0.8254 (m90) cc_final: 0.6285 (m90) REVERT: D 379 GLN cc_start: 0.8950 (tt0) cc_final: 0.8610 (tm-30) REVERT: D 382 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7365 (t80) REVERT: D 391 MET cc_start: 0.7992 (mmm) cc_final: 0.7543 (tpp) REVERT: D 397 ARG cc_start: 0.8211 (mmt90) cc_final: 0.7928 (tpt170) REVERT: D 561 TYR cc_start: 0.5049 (OUTLIER) cc_final: 0.4657 (t80) REVERT: D 595 MET cc_start: 0.7384 (mmp) cc_final: 0.7090 (mmm) REVERT: D 738 THR cc_start: 0.8509 (m) cc_final: 0.8230 (p) REVERT: D 743 LEU cc_start: 0.9102 (mt) cc_final: 0.8856 (mp) REVERT: D 828 MET cc_start: 0.7885 (mpp) cc_final: 0.7559 (mpp) REVERT: D 893 GLU cc_start: 0.8158 (pp20) cc_final: 0.7042 (tp30) REVERT: D 894 LEU cc_start: 0.8585 (mm) cc_final: 0.8021 (mm) REVERT: D 932 MET cc_start: 0.9036 (ptm) cc_final: 0.8565 (ppp) REVERT: D 953 TYR cc_start: 0.9114 (m-10) cc_final: 0.8627 (m-80) REVERT: D 961 MET cc_start: 0.9370 (tpt) cc_final: 0.8437 (mtp) REVERT: D 1098 TRP cc_start: 0.8066 (t-100) cc_final: 0.7584 (p-90) REVERT: D 1123 MET cc_start: 0.8544 (mtp) cc_final: 0.8142 (ttm) outliers start: 158 outliers final: 97 residues processed: 665 average time/residue: 0.3483 time to fit residues: 379.3614 Evaluate side-chains 619 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 513 time to evaluate : 3.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 382 TYR Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 531 MET Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 888 LEU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 382 TYR Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 531 MET Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 917 LYS Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 382 TYR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 611 ASN Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 888 LEU Chi-restraints excluded: chain C residue 917 LYS Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 382 TYR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 531 MET Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 611 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 888 LEU Chi-restraints excluded: chain D residue 917 LYS Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.0030 chunk 190 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 287 optimal weight: 3.9990 chunk 232 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** 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 538 ASN ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** 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 538 ASN ** 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: 0.6135 moved from start: 0.5431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29024 Z= 0.251 Angle : 0.694 8.924 39320 Z= 0.333 Chirality : 0.043 0.239 4444 Planarity : 0.004 0.043 4924 Dihedral : 4.693 17.277 3836 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.24 % Favored : 94.65 % Rotamer: Outliers : 4.95 % Allowed : 19.57 % Favored : 75.48 % 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: -0.56 (0.15), residues: 3456 helix: 0.40 (0.13), residues: 1556 sheet: -0.87 (0.29), residues: 392 loop : -0.97 (0.18), residues: 1508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 304 HIS 0.006 0.001 HIS B 567 PHE 0.032 0.002 PHE D 291 TYR 0.026 0.001 TYR D 285 ARG 0.007 0.001 ARG C 966 *********************** 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 687 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 532 time to evaluate : 3.144 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: A 201 PHE cc_start: 0.9156 (m-80) cc_final: 0.8695 (t80) REVERT: A 228 LEU cc_start: 0.9232 (mt) cc_final: 0.8984 (pp) REVERT: A 375 HIS cc_start: 0.8178 (m90) cc_final: 0.7657 (m90) REVERT: A 379 GLN cc_start: 0.9052 (tt0) cc_final: 0.8685 (tm-30) REVERT: A 561 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4629 (t80) REVERT: A 595 MET cc_start: 0.7841 (mmp) cc_final: 0.7463 (mmp) REVERT: A 610 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8270 (tm-30) REVERT: A 738 THR cc_start: 0.8546 (m) cc_final: 0.8335 (p) REVERT: A 743 LEU cc_start: 0.9144 (mt) cc_final: 0.8906 (mp) REVERT: A 781 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: A 828 MET cc_start: 0.8114 (mpp) cc_final: 0.7713 (mpp) REVERT: A 932 MET cc_start: 0.9040 (ptm) cc_final: 0.8647 (ppp) REVERT: A 953 TYR cc_start: 0.9006 (m-10) cc_final: 0.8580 (m-80) REVERT: A 961 MET cc_start: 0.9220 (tpt) cc_final: 0.8058 (mtp) REVERT: A 1123 MET cc_start: 0.8606 (mtp) cc_final: 0.8280 (ttm) REVERT: B 201 PHE cc_start: 0.9155 (m-80) cc_final: 0.8686 (t80) REVERT: B 375 HIS cc_start: 0.8177 (m90) cc_final: 0.7656 (m90) REVERT: B 379 GLN cc_start: 0.9052 (tt0) cc_final: 0.8685 (tm-30) REVERT: B 561 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4628 (t80) REVERT: B 595 MET cc_start: 0.7844 (mmp) cc_final: 0.7464 (mmp) REVERT: B 610 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8270 (tm-30) REVERT: B 738 THR cc_start: 0.8545 (m) cc_final: 0.8334 (p) REVERT: B 743 LEU cc_start: 0.9144 (mt) cc_final: 0.8906 (mp) REVERT: B 781 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: B 828 MET cc_start: 0.8115 (mpp) cc_final: 0.7713 (mpp) REVERT: B 932 MET cc_start: 0.9040 (ptm) cc_final: 0.8647 (ppp) REVERT: B 953 TYR cc_start: 0.9006 (m-10) cc_final: 0.8581 (m-80) REVERT: B 961 MET cc_start: 0.9220 (tpt) cc_final: 0.8059 (mtp) REVERT: B 1123 MET cc_start: 0.8607 (mtp) cc_final: 0.8280 (ttm) REVERT: C 201 PHE cc_start: 0.9155 (m-80) cc_final: 0.8686 (t80) REVERT: C 375 HIS cc_start: 0.8176 (m90) cc_final: 0.7656 (m90) REVERT: C 379 GLN cc_start: 0.9052 (tt0) cc_final: 0.8685 (tm-30) REVERT: C 561 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4690 (t80) REVERT: C 595 MET cc_start: 0.7835 (mmp) cc_final: 0.7457 (mmp) REVERT: C 610 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8270 (tm-30) REVERT: C 738 THR cc_start: 0.8546 (m) cc_final: 0.8335 (p) REVERT: C 743 LEU cc_start: 0.9143 (mt) cc_final: 0.8905 (mp) REVERT: C 781 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: C 828 MET cc_start: 0.8115 (mpp) cc_final: 0.7713 (mpp) REVERT: C 932 MET cc_start: 0.9040 (ptm) cc_final: 0.8646 (ppp) REVERT: C 953 TYR cc_start: 0.9005 (m-10) cc_final: 0.8579 (m-80) REVERT: C 961 MET cc_start: 0.9220 (tpt) cc_final: 0.8058 (mtp) REVERT: C 1123 MET cc_start: 0.8607 (mtp) cc_final: 0.8280 (ttm) REVERT: D 201 PHE cc_start: 0.9155 (m-80) cc_final: 0.8686 (t80) REVERT: D 375 HIS cc_start: 0.8178 (m90) cc_final: 0.7656 (m90) REVERT: D 379 GLN cc_start: 0.9052 (tt0) cc_final: 0.8686 (tm-30) REVERT: D 561 TYR cc_start: 0.5037 (OUTLIER) cc_final: 0.4655 (t80) REVERT: D 595 MET cc_start: 0.7844 (mmp) cc_final: 0.7466 (mmp) REVERT: D 610 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8270 (tm-30) REVERT: D 738 THR cc_start: 0.8545 (m) cc_final: 0.8334 (p) REVERT: D 743 LEU cc_start: 0.9144 (mt) cc_final: 0.8906 (mp) REVERT: D 781 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: D 828 MET cc_start: 0.8114 (mpp) cc_final: 0.7711 (mpp) REVERT: D 893 GLU cc_start: 0.8132 (pp20) cc_final: 0.7182 (tp30) REVERT: D 894 LEU cc_start: 0.8345 (mm) cc_final: 0.7887 (mm) REVERT: D 932 MET cc_start: 0.9040 (ptm) cc_final: 0.8646 (ppp) REVERT: D 953 TYR cc_start: 0.9005 (m-10) cc_final: 0.8579 (m-80) REVERT: D 961 MET cc_start: 0.9220 (tpt) cc_final: 0.8059 (mtp) REVERT: D 1123 MET cc_start: 0.8605 (mtp) cc_final: 0.8278 (ttm) outliers start: 155 outliers final: 97 residues processed: 647 average time/residue: 0.3444 time to fit residues: 368.7878 Evaluate side-chains 590 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 485 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 356 CYS Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1011 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1011 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 356 CYS Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1011 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1011 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 0.9980 chunk 302 optimal weight: 0.0770 chunk 66 optimal weight: 0.9980 chunk 197 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 279 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.8142 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 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: 0.6120 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 29024 Z= 0.215 Angle : 0.692 9.199 39320 Z= 0.330 Chirality : 0.043 0.234 4444 Planarity : 0.004 0.044 4924 Dihedral : 4.591 15.708 3836 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.92 % Favored : 94.97 % Rotamer: Outliers : 4.28 % Allowed : 21.68 % Favored : 74.04 % 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: -0.54 (0.15), residues: 3456 helix: 0.43 (0.13), residues: 1560 sheet: -0.88 (0.27), residues: 408 loop : -0.95 (0.18), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 304 HIS 0.007 0.001 HIS C 345 PHE 0.032 0.002 PHE D 291 TYR 0.035 0.001 TYR A 285 ARG 0.005 0.000 ARG C 966 *********************** 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 694 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 560 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.9135 (m-80) cc_final: 0.8900 (m-80) REVERT: A 213 LEU cc_start: 0.3867 (OUTLIER) cc_final: 0.3615 (mm) REVERT: A 272 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8395 (tp30) REVERT: A 361 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7554 (mttt) REVERT: A 375 HIS cc_start: 0.8262 (m90) cc_final: 0.7837 (m90) REVERT: A 513 VAL cc_start: 0.8531 (m) cc_final: 0.8313 (m) REVERT: A 561 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4846 (t80) REVERT: A 595 MET cc_start: 0.7889 (mmp) cc_final: 0.7553 (mmp) REVERT: A 610 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8317 (tm-30) REVERT: A 743 LEU cc_start: 0.9143 (mt) cc_final: 0.8910 (mp) REVERT: A 781 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: A 798 TYR cc_start: 0.9196 (p90) cc_final: 0.8432 (p90) REVERT: A 828 MET cc_start: 0.7829 (mpp) cc_final: 0.7519 (mpp) REVERT: A 893 GLU cc_start: 0.8104 (pp20) cc_final: 0.6925 (tp30) REVERT: A 932 MET cc_start: 0.9050 (ptm) cc_final: 0.8699 (ppp) REVERT: A 953 TYR cc_start: 0.8966 (m-10) cc_final: 0.8479 (m-80) REVERT: A 1123 MET cc_start: 0.8564 (mtp) cc_final: 0.8226 (ttm) REVERT: B 201 PHE cc_start: 0.9124 (m-80) cc_final: 0.8898 (m-80) REVERT: B 228 LEU cc_start: 0.9275 (mt) cc_final: 0.9020 (pp) REVERT: B 272 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8443 (tp30) REVERT: B 361 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7556 (mttt) REVERT: B 375 HIS cc_start: 0.8263 (m90) cc_final: 0.7839 (m90) REVERT: B 513 VAL cc_start: 0.8531 (m) cc_final: 0.8314 (m) REVERT: B 561 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4845 (t80) REVERT: B 595 MET cc_start: 0.7890 (mmp) cc_final: 0.7555 (mmp) REVERT: B 610 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8316 (tm-30) REVERT: B 743 LEU cc_start: 0.9143 (mt) cc_final: 0.8910 (mp) REVERT: B 781 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: B 798 TYR cc_start: 0.9195 (p90) cc_final: 0.8433 (p90) REVERT: B 828 MET cc_start: 0.7831 (mpp) cc_final: 0.7520 (mpp) REVERT: B 893 GLU cc_start: 0.8105 (pp20) cc_final: 0.6924 (tp30) REVERT: B 932 MET cc_start: 0.9051 (ptm) cc_final: 0.8700 (ppp) REVERT: B 953 TYR cc_start: 0.8966 (m-10) cc_final: 0.8479 (m-80) REVERT: B 1123 MET cc_start: 0.8565 (mtp) cc_final: 0.8227 (ttm) REVERT: C 201 PHE cc_start: 0.9124 (m-80) cc_final: 0.8897 (m-80) REVERT: C 228 LEU cc_start: 0.9275 (mt) cc_final: 0.9020 (pp) REVERT: C 272 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8445 (tp30) REVERT: C 361 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7554 (mttt) REVERT: C 375 HIS cc_start: 0.8261 (m90) cc_final: 0.7838 (m90) REVERT: C 513 VAL cc_start: 0.8530 (m) cc_final: 0.8313 (m) REVERT: C 561 TYR cc_start: 0.5275 (OUTLIER) cc_final: 0.4890 (t80) REVERT: C 595 MET cc_start: 0.7878 (mmp) cc_final: 0.7543 (mmp) REVERT: C 610 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8316 (tm-30) REVERT: C 743 LEU cc_start: 0.9143 (mt) cc_final: 0.8909 (mp) REVERT: C 781 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: C 798 TYR cc_start: 0.9195 (p90) cc_final: 0.8433 (p90) REVERT: C 828 MET cc_start: 0.7830 (mpp) cc_final: 0.7519 (mpp) REVERT: C 893 GLU cc_start: 0.8105 (pp20) cc_final: 0.6924 (tp30) REVERT: C 932 MET cc_start: 0.9049 (ptm) cc_final: 0.8699 (ppp) REVERT: C 953 TYR cc_start: 0.8965 (m-10) cc_final: 0.8478 (m-80) REVERT: C 1123 MET cc_start: 0.8565 (mtp) cc_final: 0.8227 (ttm) REVERT: D 201 PHE cc_start: 0.9123 (m-80) cc_final: 0.8896 (m-80) REVERT: D 228 LEU cc_start: 0.9275 (mt) cc_final: 0.9019 (pp) REVERT: D 272 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8445 (tp30) REVERT: D 361 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7556 (mttt) REVERT: D 375 HIS cc_start: 0.8262 (m90) cc_final: 0.7838 (m90) REVERT: D 513 VAL cc_start: 0.8531 (m) cc_final: 0.8316 (m) REVERT: D 561 TYR cc_start: 0.5228 (OUTLIER) cc_final: 0.4851 (t80) REVERT: D 595 MET cc_start: 0.7887 (mmp) cc_final: 0.7552 (mmp) REVERT: D 610 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8317 (tm-30) REVERT: D 743 LEU cc_start: 0.9143 (mt) cc_final: 0.8910 (mp) REVERT: D 781 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: D 798 TYR cc_start: 0.9196 (p90) cc_final: 0.8432 (p90) REVERT: D 828 MET cc_start: 0.7829 (mpp) cc_final: 0.7518 (mpp) REVERT: D 893 GLU cc_start: 0.8027 (pp20) cc_final: 0.6865 (tp30) REVERT: D 894 LEU cc_start: 0.8159 (mm) cc_final: 0.7494 (mm) REVERT: D 932 MET cc_start: 0.9049 (ptm) cc_final: 0.8700 (ppp) REVERT: D 953 TYR cc_start: 0.8965 (m-10) cc_final: 0.8477 (m-80) REVERT: D 1123 MET cc_start: 0.8563 (mtp) cc_final: 0.8223 (ttm) outliers start: 134 outliers final: 83 residues processed: 658 average time/residue: 0.3406 time to fit residues: 376.4327 Evaluate side-chains 591 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 499 time to evaluate : 3.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 794 LEU Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 303 ILE Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 245 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 283 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 335 optimal weight: 0.0670 chunk 209 optimal weight: 0.9990 chunk 204 optimal weight: 1.9990 chunk 154 optimal weight: 0.3980 overall best weight: 1.4924 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 904 GLN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 341 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29024 Z= 0.216 Angle : 0.749 11.729 39320 Z= 0.352 Chirality : 0.045 0.264 4444 Planarity : 0.004 0.048 4924 Dihedral : 4.586 15.908 3836 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 4.37 % Allowed : 23.63 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3456 helix: 0.38 (0.13), residues: 1564 sheet: -0.69 (0.27), residues: 408 loop : -0.98 (0.18), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 304 HIS 0.004 0.001 HIS B1139 PHE 0.034 0.002 PHE D 291 TYR 0.033 0.001 TYR C 285 ARG 0.005 0.000 ARG D 966 *********************** 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 645 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 508 time to evaluate : 3.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.3870 (OUTLIER) cc_final: 0.3627 (mm) REVERT: A 272 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8415 (tp30) REVERT: A 375 HIS cc_start: 0.8325 (m90) cc_final: 0.7850 (m90) REVERT: A 561 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4841 (t80) REVERT: A 595 MET cc_start: 0.7758 (mmp) cc_final: 0.7392 (mmp) REVERT: A 610 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8331 (tm-30) REVERT: A 743 LEU cc_start: 0.9128 (mt) cc_final: 0.8901 (mp) REVERT: A 781 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: A 798 TYR cc_start: 0.9189 (p90) cc_final: 0.8403 (p90) REVERT: A 828 MET cc_start: 0.7827 (mpp) cc_final: 0.7517 (mpp) REVERT: A 832 MET cc_start: 0.6231 (tpp) cc_final: 0.5763 (tpp) REVERT: A 842 LEU cc_start: 0.8768 (mp) cc_final: 0.8506 (mp) REVERT: A 893 GLU cc_start: 0.8199 (pp20) cc_final: 0.7034 (tp30) REVERT: A 932 MET cc_start: 0.9063 (ptm) cc_final: 0.8726 (ppp) REVERT: A 953 TYR cc_start: 0.8939 (m-10) cc_final: 0.8401 (m-80) REVERT: A 1123 MET cc_start: 0.8567 (mtp) cc_final: 0.8226 (ttm) REVERT: B 272 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8410 (tp30) REVERT: B 375 HIS cc_start: 0.8326 (m90) cc_final: 0.7851 (m90) REVERT: B 561 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4841 (t80) REVERT: B 595 MET cc_start: 0.7758 (mmp) cc_final: 0.7392 (mmp) REVERT: B 610 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8331 (tm-30) REVERT: B 743 LEU cc_start: 0.9128 (mt) cc_final: 0.8901 (mp) REVERT: B 781 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: B 798 TYR cc_start: 0.9190 (p90) cc_final: 0.8404 (p90) REVERT: B 828 MET cc_start: 0.7828 (mpp) cc_final: 0.7518 (mpp) REVERT: B 832 MET cc_start: 0.6230 (tpp) cc_final: 0.5762 (tpp) REVERT: B 842 LEU cc_start: 0.8768 (mp) cc_final: 0.8506 (mp) REVERT: B 893 GLU cc_start: 0.8200 (pp20) cc_final: 0.7035 (tp30) REVERT: B 932 MET cc_start: 0.9064 (ptm) cc_final: 0.8727 (ppp) REVERT: B 953 TYR cc_start: 0.8939 (m-10) cc_final: 0.8441 (m-80) REVERT: B 1123 MET cc_start: 0.8568 (mtp) cc_final: 0.8225 (ttm) REVERT: C 272 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8409 (tp30) REVERT: C 375 HIS cc_start: 0.8325 (m90) cc_final: 0.7850 (m90) REVERT: C 561 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.4886 (t80) REVERT: C 595 MET cc_start: 0.7747 (mmp) cc_final: 0.7381 (mmp) REVERT: C 610 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8331 (tm-30) REVERT: C 743 LEU cc_start: 0.9128 (mt) cc_final: 0.8900 (mp) REVERT: C 781 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: C 798 TYR cc_start: 0.9190 (p90) cc_final: 0.8405 (p90) REVERT: C 828 MET cc_start: 0.7828 (mpp) cc_final: 0.7518 (mpp) REVERT: C 832 MET cc_start: 0.6229 (tpp) cc_final: 0.5762 (tpp) REVERT: C 842 LEU cc_start: 0.8768 (mp) cc_final: 0.8507 (mp) REVERT: C 893 GLU cc_start: 0.8200 (pp20) cc_final: 0.7035 (tp30) REVERT: C 932 MET cc_start: 0.9063 (ptm) cc_final: 0.8726 (ppp) REVERT: C 953 TYR cc_start: 0.8938 (m-10) cc_final: 0.8440 (m-80) REVERT: C 1123 MET cc_start: 0.8567 (mtp) cc_final: 0.8225 (ttm) REVERT: D 272 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8408 (tp30) REVERT: D 375 HIS cc_start: 0.8326 (m90) cc_final: 0.7851 (m90) REVERT: D 561 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4845 (t80) REVERT: D 595 MET cc_start: 0.7756 (mmp) cc_final: 0.7391 (mmp) REVERT: D 610 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8331 (tm-30) REVERT: D 743 LEU cc_start: 0.9128 (mt) cc_final: 0.8901 (mp) REVERT: D 781 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: D 798 TYR cc_start: 0.9190 (p90) cc_final: 0.8403 (p90) REVERT: D 828 MET cc_start: 0.7826 (mpp) cc_final: 0.7516 (mpp) REVERT: D 832 MET cc_start: 0.6230 (tpp) cc_final: 0.5762 (tpp) REVERT: D 893 GLU cc_start: 0.8090 (pp20) cc_final: 0.6919 (tp30) REVERT: D 894 LEU cc_start: 0.8092 (mm) cc_final: 0.7379 (mm) REVERT: D 932 MET cc_start: 0.9064 (ptm) cc_final: 0.8727 (ppp) REVERT: D 943 PHE cc_start: 0.7415 (p90) cc_final: 0.6330 (p90) REVERT: D 953 TYR cc_start: 0.8938 (m-10) cc_final: 0.8401 (m-80) REVERT: D 1123 MET cc_start: 0.8555 (mtp) cc_final: 0.8211 (ttm) outliers start: 137 outliers final: 109 residues processed: 609 average time/residue: 0.3345 time to fit residues: 344.2342 Evaluate side-chains 597 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 479 time to evaluate : 3.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 505 THR Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 843 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ASN Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 843 LEU Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 899 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 582 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 843 LEU Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 899 ASN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 200 optimal weight: 0.0020 chunk 101 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 228 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 ASN A 341 ASN A 499 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN ** A1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN ** B 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 ASN ** B1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 ASN ** C 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 789 ASN C 904 GLN ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 ASN ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.6078 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= 0.195 Angle : 0.775 16.617 39320 Z= 0.352 Chirality : 0.046 0.266 4444 Planarity : 0.004 0.048 4924 Dihedral : 4.505 18.209 3836 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.43 % Favored : 95.46 % Rotamer: Outliers : 3.74 % Allowed : 24.46 % Favored : 71.81 % 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: -0.62 (0.15), residues: 3456 helix: 0.21 (0.13), residues: 1600 sheet: -0.59 (0.28), residues: 368 loop : -0.95 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 304 HIS 0.003 0.001 HIS C1139 PHE 0.034 0.002 PHE C 291 TYR 0.020 0.001 TYR C 285 ARG 0.004 0.000 ARG A 966 *********************** 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 624 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 507 time to evaluate : 3.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8522 (mmm) cc_final: 0.8036 (ttm) REVERT: A 213 LEU cc_start: 0.3724 (OUTLIER) cc_final: 0.3492 (mm) REVERT: A 272 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8399 (tp30) REVERT: A 361 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7975 (mttt) REVERT: A 375 HIS cc_start: 0.8314 (m90) cc_final: 0.7837 (m90) REVERT: A 489 GLU cc_start: 0.8709 (tt0) cc_final: 0.8195 (tp30) REVERT: A 561 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4784 (t80) REVERT: A 595 MET cc_start: 0.7761 (mmp) cc_final: 0.7430 (mmp) REVERT: A 610 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8374 (tm-30) REVERT: A 743 LEU cc_start: 0.9160 (mt) cc_final: 0.8936 (mp) REVERT: A 781 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: A 798 TYR cc_start: 0.9071 (p90) cc_final: 0.8806 (p90) REVERT: A 828 MET cc_start: 0.7903 (mpp) cc_final: 0.7692 (mpp) REVERT: A 881 MET cc_start: 0.9231 (mmm) cc_final: 0.9016 (mmm) REVERT: A 893 GLU cc_start: 0.8038 (pp20) cc_final: 0.6873 (tp30) REVERT: A 932 MET cc_start: 0.9021 (ptm) cc_final: 0.8786 (ppp) REVERT: A 953 TYR cc_start: 0.8864 (m-10) cc_final: 0.8344 (m-80) REVERT: A 1123 MET cc_start: 0.8537 (mtp) cc_final: 0.8222 (ttm) REVERT: B 195 MET cc_start: 0.8549 (mmm) cc_final: 0.8049 (ttm) REVERT: B 201 PHE cc_start: 0.8835 (m-80) cc_final: 0.8474 (t80) REVERT: B 361 LYS cc_start: 0.8273 (mmmt) cc_final: 0.7969 (mttt) REVERT: B 375 HIS cc_start: 0.8315 (m90) cc_final: 0.7838 (m90) REVERT: B 489 GLU cc_start: 0.8707 (tt0) cc_final: 0.8194 (tp30) REVERT: B 561 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4784 (t80) REVERT: B 595 MET cc_start: 0.7761 (mmp) cc_final: 0.7431 (mmp) REVERT: B 610 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8374 (tm-30) REVERT: B 743 LEU cc_start: 0.9160 (mt) cc_final: 0.8935 (mp) REVERT: B 781 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: B 798 TYR cc_start: 0.9070 (p90) cc_final: 0.8806 (p90) REVERT: B 828 MET cc_start: 0.7903 (mpp) cc_final: 0.7692 (mpp) REVERT: B 881 MET cc_start: 0.9233 (mmm) cc_final: 0.9018 (mmm) REVERT: B 893 GLU cc_start: 0.8037 (pp20) cc_final: 0.6873 (tp30) REVERT: B 932 MET cc_start: 0.9022 (ptm) cc_final: 0.8788 (ppp) REVERT: B 953 TYR cc_start: 0.8869 (m-10) cc_final: 0.8348 (m-80) REVERT: B 1123 MET cc_start: 0.8537 (mtp) cc_final: 0.8222 (ttm) REVERT: C 195 MET cc_start: 0.8548 (mmm) cc_final: 0.8049 (ttm) REVERT: C 201 PHE cc_start: 0.8835 (m-80) cc_final: 0.8474 (t80) REVERT: C 361 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7968 (mttt) REVERT: C 375 HIS cc_start: 0.8317 (m90) cc_final: 0.7838 (m90) REVERT: C 489 GLU cc_start: 0.8708 (tt0) cc_final: 0.8211 (tp30) REVERT: C 561 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.4792 (t80) REVERT: C 595 MET cc_start: 0.7750 (mmp) cc_final: 0.7420 (mmp) REVERT: C 610 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8373 (tm-30) REVERT: C 743 LEU cc_start: 0.9159 (mt) cc_final: 0.8934 (mp) REVERT: C 781 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: C 798 TYR cc_start: 0.9070 (p90) cc_final: 0.8806 (p90) REVERT: C 828 MET cc_start: 0.7903 (mpp) cc_final: 0.7693 (mpp) REVERT: C 881 MET cc_start: 0.9233 (mmm) cc_final: 0.9018 (mmm) REVERT: C 893 GLU cc_start: 0.8039 (pp20) cc_final: 0.6874 (tp30) REVERT: C 932 MET cc_start: 0.9021 (ptm) cc_final: 0.8787 (ppp) REVERT: C 953 TYR cc_start: 0.8867 (m-10) cc_final: 0.8346 (m-80) REVERT: C 1123 MET cc_start: 0.8537 (mtp) cc_final: 0.8223 (ttm) REVERT: D 195 MET cc_start: 0.8548 (mmm) cc_final: 0.8048 (ttm) REVERT: D 201 PHE cc_start: 0.8836 (m-80) cc_final: 0.8474 (t80) REVERT: D 361 LYS cc_start: 0.8262 (mmmt) cc_final: 0.7967 (mttt) REVERT: D 375 HIS cc_start: 0.8315 (m90) cc_final: 0.7837 (m90) REVERT: D 489 GLU cc_start: 0.8705 (tt0) cc_final: 0.8203 (tp30) REVERT: D 561 TYR cc_start: 0.5057 (OUTLIER) cc_final: 0.4697 (t80) REVERT: D 595 MET cc_start: 0.7762 (mmp) cc_final: 0.7432 (mmp) REVERT: D 610 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8373 (tm-30) REVERT: D 743 LEU cc_start: 0.9160 (mt) cc_final: 0.8935 (mp) REVERT: D 781 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: D 798 TYR cc_start: 0.9071 (p90) cc_final: 0.8805 (p90) REVERT: D 828 MET cc_start: 0.7902 (mpp) cc_final: 0.7691 (mpp) REVERT: D 881 MET cc_start: 0.9232 (mmm) cc_final: 0.9016 (mmm) REVERT: D 893 GLU cc_start: 0.7941 (pp20) cc_final: 0.6747 (tp30) REVERT: D 894 LEU cc_start: 0.8095 (mm) cc_final: 0.7395 (mm) REVERT: D 932 MET cc_start: 0.9023 (ptm) cc_final: 0.8787 (ppp) REVERT: D 953 TYR cc_start: 0.8869 (m-10) cc_final: 0.8359 (m-80) REVERT: D 1123 MET cc_start: 0.8532 (mtp) cc_final: 0.8220 (ttm) outliers start: 117 outliers final: 100 residues processed: 593 average time/residue: 0.3309 time to fit residues: 332.2582 Evaluate side-chains 585 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 476 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 414 SER Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 582 ASN Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 899 ASN Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1008 GLU Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 357 VAL Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 414 SER Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 582 ASN Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 899 ASN Chi-restraints excluded: chain B residue 951 LEU Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1008 GLU Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 414 SER Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 470 ILE Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 582 ASN Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 899 ASN Chi-restraints excluded: chain C residue 951 LEU Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1008 GLU Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 308 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 386 LEU Chi-restraints excluded: chain D residue 436 SER Chi-restraints excluded: chain D residue 470 ILE Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 582 ASN Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 867 ASP Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 899 ASN Chi-restraints excluded: chain D residue 951 LEU Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 5.9990 chunk 321 optimal weight: 0.9980 chunk 293 optimal weight: 7.9990 chunk 312 optimal weight: 1.9990 chunk 188 optimal weight: 0.0070 chunk 136 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 95 optimal weight: 0.0000 chunk 282 optimal weight: 0.6980 chunk 295 optimal weight: 5.9990 chunk 311 optimal weight: 0.1980 overall best weight: 0.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 904 GLN ** 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 538 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29024 Z= 0.189 Angle : 0.789 16.585 39320 Z= 0.354 Chirality : 0.046 0.281 4444 Planarity : 0.004 0.048 4924 Dihedral : 4.424 17.571 3836 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.10 % Allowed : 25.38 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3456 helix: 0.22 (0.13), residues: 1584 sheet: -0.50 (0.28), residues: 368 loop : -0.90 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 528 HIS 0.003 0.001 HIS A 345 PHE 0.036 0.001 PHE B 291 TYR 0.014 0.001 TYR C 285 ARG 0.005 0.000 ARG A 966 *********************** 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 617 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 520 time to evaluate : 3.228 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: A 195 MET cc_start: 0.8458 (mmm) cc_final: 0.8005 (ttm) REVERT: A 201 PHE cc_start: 0.8761 (m-80) cc_final: 0.8390 (t80) REVERT: A 213 LEU cc_start: 0.3590 (OUTLIER) cc_final: 0.3358 (mm) REVERT: A 272 GLU cc_start: 0.8641 (mm-30) cc_final: 0.8405 (tp30) REVERT: A 361 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7962 (mttt) REVERT: A 489 GLU cc_start: 0.8683 (tt0) cc_final: 0.8228 (tp30) REVERT: A 490 GLU cc_start: 0.9010 (tt0) cc_final: 0.8627 (tp30) REVERT: A 561 TYR cc_start: 0.5216 (OUTLIER) cc_final: 0.4851 (t80) REVERT: A 595 MET cc_start: 0.8106 (mmp) cc_final: 0.7861 (mmp) REVERT: A 610 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8368 (tm-30) REVERT: A 743 LEU cc_start: 0.9160 (mt) cc_final: 0.8929 (mp) REVERT: A 781 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: A 798 TYR cc_start: 0.9052 (p90) cc_final: 0.8781 (p90) REVERT: A 828 MET cc_start: 0.7906 (mpp) cc_final: 0.7696 (mpp) REVERT: A 881 MET cc_start: 0.9264 (mmm) cc_final: 0.9050 (mmm) REVERT: A 893 GLU cc_start: 0.7875 (pp20) cc_final: 0.7515 (pm20) REVERT: A 953 TYR cc_start: 0.8799 (m-10) cc_final: 0.8428 (m-80) REVERT: A 1123 MET cc_start: 0.8514 (mtp) cc_final: 0.8193 (ttm) REVERT: B 195 MET cc_start: 0.8496 (mmm) cc_final: 0.8023 (ttm) REVERT: B 201 PHE cc_start: 0.8827 (m-80) cc_final: 0.8507 (t80) REVERT: B 361 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7953 (mttt) REVERT: B 489 GLU cc_start: 0.8706 (tt0) cc_final: 0.8226 (tp30) REVERT: B 561 TYR cc_start: 0.5216 (OUTLIER) cc_final: 0.4851 (t80) REVERT: B 595 MET cc_start: 0.8107 (mmp) cc_final: 0.7862 (mmp) REVERT: B 610 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8368 (tm-30) REVERT: B 743 LEU cc_start: 0.9160 (mt) cc_final: 0.8929 (mp) REVERT: B 781 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: B 798 TYR cc_start: 0.9051 (p90) cc_final: 0.8781 (p90) REVERT: B 828 MET cc_start: 0.7906 (mpp) cc_final: 0.7696 (mpp) REVERT: B 881 MET cc_start: 0.9266 (mmm) cc_final: 0.9052 (mmm) REVERT: B 893 GLU cc_start: 0.7875 (pp20) cc_final: 0.7514 (pm20) REVERT: B 953 TYR cc_start: 0.8791 (m-10) cc_final: 0.8421 (m-80) REVERT: B 1123 MET cc_start: 0.8515 (mtp) cc_final: 0.8194 (ttm) REVERT: C 195 MET cc_start: 0.8496 (mmm) cc_final: 0.8023 (ttm) REVERT: C 201 PHE cc_start: 0.8828 (m-80) cc_final: 0.8508 (t80) REVERT: C 361 LYS cc_start: 0.8305 (mmmt) cc_final: 0.7952 (mttt) REVERT: C 489 GLU cc_start: 0.8725 (tt0) cc_final: 0.8247 (tp30) REVERT: C 490 GLU cc_start: 0.9001 (tt0) cc_final: 0.8614 (tp30) REVERT: C 561 TYR cc_start: 0.5272 (OUTLIER) cc_final: 0.4899 (t80) REVERT: C 595 MET cc_start: 0.8097 (mmp) cc_final: 0.7854 (mmp) REVERT: C 610 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8368 (tm-30) REVERT: C 743 LEU cc_start: 0.9159 (mt) cc_final: 0.8929 (mp) REVERT: C 781 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: C 798 TYR cc_start: 0.9053 (p90) cc_final: 0.8782 (p90) REVERT: C 828 MET cc_start: 0.7906 (mpp) cc_final: 0.7696 (mpp) REVERT: C 881 MET cc_start: 0.9264 (mmm) cc_final: 0.9050 (mmm) REVERT: C 893 GLU cc_start: 0.7873 (pp20) cc_final: 0.7514 (pm20) REVERT: C 953 TYR cc_start: 0.8789 (m-10) cc_final: 0.8420 (m-80) REVERT: C 1123 MET cc_start: 0.8517 (mtp) cc_final: 0.8195 (ttm) REVERT: D 195 MET cc_start: 0.8495 (mmm) cc_final: 0.8021 (ttm) REVERT: D 201 PHE cc_start: 0.8827 (m-80) cc_final: 0.8507 (t80) REVERT: D 361 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7958 (mttt) REVERT: D 489 GLU cc_start: 0.8712 (tt0) cc_final: 0.8231 (tp30) REVERT: D 561 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4852 (t80) REVERT: D 595 MET cc_start: 0.8105 (mmp) cc_final: 0.7861 (mmp) REVERT: D 610 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8368 (tm-30) REVERT: D 743 LEU cc_start: 0.9159 (mt) cc_final: 0.8928 (mp) REVERT: D 781 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 798 TYR cc_start: 0.9052 (p90) cc_final: 0.8783 (p90) REVERT: D 828 MET cc_start: 0.7907 (mpp) cc_final: 0.7696 (mpp) REVERT: D 881 MET cc_start: 0.9266 (mmm) cc_final: 0.9052 (mmm) REVERT: D 893 GLU cc_start: 0.7690 (pp20) cc_final: 0.7407 (pm20) REVERT: D 953 TYR cc_start: 0.8799 (m-10) cc_final: 0.8302 (m-80) REVERT: D 1123 MET cc_start: 0.8510 (mtp) cc_final: 0.8197 (ttm) outliers start: 97 outliers final: 73 residues processed: 591 average time/residue: 0.3368 time to fit residues: 331.9571 Evaluate side-chains 541 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 459 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 262 PHE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 262 PHE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 884 LEU Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1008 GLU Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1115 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.9990 chunk 330 optimal weight: 0.0980 chunk 201 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 346 optimal weight: 5.9990 chunk 319 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 28 optimal weight: 0.0970 chunk 213 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 789 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6092 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 29024 Z= 0.191 Angle : 0.830 14.312 39320 Z= 0.369 Chirality : 0.047 0.346 4444 Planarity : 0.004 0.048 4924 Dihedral : 4.443 17.416 3836 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.91 % Allowed : 26.47 % Favored : 70.63 % 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: -0.64 (0.15), residues: 3456 helix: 0.21 (0.13), residues: 1584 sheet: -0.54 (0.26), residues: 408 loop : -0.98 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 455 HIS 0.003 0.001 HIS C 345 PHE 0.036 0.002 PHE B 291 TYR 0.019 0.001 TYR D 532 ARG 0.004 0.000 ARG D 966 ********************** 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 595 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 504 time to evaluate : 4.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 MET cc_start: 0.8485 (mmm) cc_final: 0.8006 (ttm) REVERT: A 201 PHE cc_start: 0.8779 (m-80) cc_final: 0.8441 (t80) REVERT: A 213 LEU cc_start: 0.2897 (OUTLIER) cc_final: 0.2665 (mm) REVERT: A 272 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8391 (tp30) REVERT: A 361 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7977 (mttt) REVERT: A 489 GLU cc_start: 0.8713 (tt0) cc_final: 0.8265 (tp30) REVERT: A 561 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.5010 (t80) REVERT: A 595 MET cc_start: 0.8077 (mmp) cc_final: 0.7567 (mmp) REVERT: A 610 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8368 (tm-30) REVERT: A 743 LEU cc_start: 0.9182 (mt) cc_final: 0.8967 (mp) REVERT: A 781 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8049 (mp0) REVERT: A 798 TYR cc_start: 0.9083 (p90) cc_final: 0.8289 (p90) REVERT: A 828 MET cc_start: 0.7921 (mpp) cc_final: 0.7709 (mpp) REVERT: A 881 MET cc_start: 0.9258 (mmm) cc_final: 0.9052 (mmm) REVERT: A 893 GLU cc_start: 0.7985 (pp20) cc_final: 0.7533 (pm20) REVERT: A 933 PHE cc_start: 0.9037 (m-80) cc_final: 0.8672 (m-10) REVERT: A 953 TYR cc_start: 0.8878 (m-10) cc_final: 0.8444 (m-80) REVERT: A 1123 MET cc_start: 0.8499 (mtp) cc_final: 0.8180 (ttm) REVERT: B 195 MET cc_start: 0.8497 (mmm) cc_final: 0.8069 (ttm) REVERT: B 201 PHE cc_start: 0.8814 (m-80) cc_final: 0.8503 (t80) REVERT: B 361 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8012 (mttt) REVERT: B 489 GLU cc_start: 0.8766 (tt0) cc_final: 0.8318 (tp30) REVERT: B 490 GLU cc_start: 0.8881 (tt0) cc_final: 0.8467 (tp30) REVERT: B 561 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.5009 (t80) REVERT: B 595 MET cc_start: 0.8077 (mmp) cc_final: 0.7566 (mmp) REVERT: B 610 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8368 (tm-30) REVERT: B 743 LEU cc_start: 0.9183 (mt) cc_final: 0.8968 (mp) REVERT: B 781 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: B 798 TYR cc_start: 0.9080 (p90) cc_final: 0.8793 (p90) REVERT: B 828 MET cc_start: 0.7920 (mpp) cc_final: 0.7708 (mpp) REVERT: B 881 MET cc_start: 0.9262 (mmm) cc_final: 0.9050 (mmm) REVERT: B 893 GLU cc_start: 0.7990 (pp20) cc_final: 0.7537 (pm20) REVERT: B 933 PHE cc_start: 0.9037 (m-80) cc_final: 0.8672 (m-10) REVERT: B 953 TYR cc_start: 0.8864 (m-10) cc_final: 0.8430 (m-80) REVERT: B 1123 MET cc_start: 0.8499 (mtp) cc_final: 0.8181 (ttm) REVERT: C 195 MET cc_start: 0.8497 (mmm) cc_final: 0.8068 (ttm) REVERT: C 201 PHE cc_start: 0.8813 (m-80) cc_final: 0.8502 (t80) REVERT: C 361 LYS cc_start: 0.8329 (mmmt) cc_final: 0.8011 (mttt) REVERT: C 489 GLU cc_start: 0.8747 (tt0) cc_final: 0.8295 (tp30) REVERT: C 561 TYR cc_start: 0.5436 (OUTLIER) cc_final: 0.5078 (t80) REVERT: C 595 MET cc_start: 0.8061 (mmp) cc_final: 0.7559 (mmp) REVERT: C 610 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8368 (tm-30) REVERT: C 743 LEU cc_start: 0.9182 (mt) cc_final: 0.8966 (mp) REVERT: C 781 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8059 (mp0) REVERT: C 798 TYR cc_start: 0.9082 (p90) cc_final: 0.8796 (p90) REVERT: C 828 MET cc_start: 0.7921 (mpp) cc_final: 0.7710 (mpp) REVERT: C 881 MET cc_start: 0.9258 (mmm) cc_final: 0.9053 (mmm) REVERT: C 893 GLU cc_start: 0.7988 (pp20) cc_final: 0.7537 (pm20) REVERT: C 933 PHE cc_start: 0.9037 (m-80) cc_final: 0.8672 (m-10) REVERT: C 953 TYR cc_start: 0.8862 (m-10) cc_final: 0.8428 (m-80) REVERT: C 1123 MET cc_start: 0.8500 (mtp) cc_final: 0.8181 (ttm) REVERT: D 195 MET cc_start: 0.8497 (mmm) cc_final: 0.8068 (ttm) REVERT: D 201 PHE cc_start: 0.8813 (m-80) cc_final: 0.8502 (t80) REVERT: D 361 LYS cc_start: 0.8322 (mmmt) cc_final: 0.7987 (mttt) REVERT: D 489 GLU cc_start: 0.8759 (tt0) cc_final: 0.8312 (tp30) REVERT: D 561 TYR cc_start: 0.5380 (OUTLIER) cc_final: 0.5029 (t80) REVERT: D 595 MET cc_start: 0.8075 (mmp) cc_final: 0.7562 (mmp) REVERT: D 610 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8368 (tm-30) REVERT: D 743 LEU cc_start: 0.9182 (mt) cc_final: 0.8967 (mp) REVERT: D 781 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: D 798 TYR cc_start: 0.9072 (p90) cc_final: 0.8791 (p90) REVERT: D 828 MET cc_start: 0.7921 (mpp) cc_final: 0.7708 (mpp) REVERT: D 893 GLU cc_start: 0.7850 (pp20) cc_final: 0.7498 (pm20) REVERT: D 933 PHE cc_start: 0.9037 (m-80) cc_final: 0.8672 (m-10) REVERT: D 953 TYR cc_start: 0.8735 (m-10) cc_final: 0.8278 (m-80) REVERT: D 1123 MET cc_start: 0.8490 (mtp) cc_final: 0.8165 (ttm) outliers start: 91 outliers final: 74 residues processed: 574 average time/residue: 0.3414 time to fit residues: 331.4447 Evaluate side-chains 556 residues out of total 3192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 473 time to evaluate : 3.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 483 ASP Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 561 TYR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 776 ILE Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 818 HIS Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 963 THR Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 988 ASP Chi-restraints excluded: chain A residue 1009 ILE Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 483 ASP Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 561 TYR Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 776 ILE Chi-restraints excluded: chain B residue 781 GLU Chi-restraints excluded: chain B residue 818 HIS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 891 ILE Chi-restraints excluded: chain B residue 963 THR Chi-restraints excluded: chain B residue 968 LEU Chi-restraints excluded: chain B residue 988 ASP Chi-restraints excluded: chain B residue 1009 ILE Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 561 TYR Chi-restraints excluded: chain C residue 574 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 776 ILE Chi-restraints excluded: chain C residue 781 GLU Chi-restraints excluded: chain C residue 818 HIS Chi-restraints excluded: chain C residue 867 ASP Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 963 THR Chi-restraints excluded: chain C residue 968 LEU Chi-restraints excluded: chain C residue 988 ASP Chi-restraints excluded: chain C residue 1009 ILE Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 280 LEU Chi-restraints excluded: chain D residue 323 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 483 ASP Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 561 TYR Chi-restraints excluded: chain D residue 574 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 776 ILE Chi-restraints excluded: chain D residue 781 GLU Chi-restraints excluded: chain D residue 818 HIS Chi-restraints excluded: chain D residue 891 ILE Chi-restraints excluded: chain D residue 963 THR Chi-restraints excluded: chain D residue 968 LEU Chi-restraints excluded: chain D residue 988 ASP Chi-restraints excluded: chain D residue 1009 ILE Chi-restraints excluded: chain D residue 1115 LEU 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: 6.9990 chunk 84 optimal weight: 10.0000 chunk 254 optimal weight: 0.0980 chunk 40 optimal weight: 9.9990 chunk 76 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 115 optimal weight: 0.0070 chunk 283 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 overall best weight: 3.4204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 904 GLN ** 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 538 ASN ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN ** 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 = 0.3590 r_free = 0.3590 target = 0.082217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065561 restraints weight = 105988.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067986 restraints weight = 53586.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.069638 restraints weight = 33009.281| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29024 Z= 0.293 Angle : 0.819 13.554 39320 Z= 0.386 Chirality : 0.046 0.388 4444 Planarity : 0.004 0.050 4924 Dihedral : 4.556 17.764 3836 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.45 % Allowed : 26.25 % Favored : 70.31 % 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: -0.49 (0.15), residues: 3456 helix: 0.32 (0.13), residues: 1576 sheet: -0.51 (0.28), residues: 376 loop : -0.86 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 332 HIS 0.006 0.002 HIS C1139 PHE 0.032 0.002 PHE B 291 TYR 0.014 0.002 TYR D 285 ARG 0.005 0.001 ARG C1103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6822.58 seconds wall clock time: 124 minutes 22.85 seconds (7462.85 seconds total)