Starting phenix.real_space_refine on Sun Jun 29 21:19:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.map" model { file = "/net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwb_29500/06_2025/8fwb_29500.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.042 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 168 5.16 5 C 22320 2.51 5 N 6048 2.21 5 O 6720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 368 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 35256 Number of models: 1 Model: "" Number of chains: 12 Chain: "U" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "V" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "W" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "X" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "Y" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "Z" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "a" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "b" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "c" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "d" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "e" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Chain: "f" Number of atoms: 2938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2938 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 21, 'TRANS': 359} Chain breaks: 1 Time building chain proxies: 20.84, per 1000 atoms: 0.59 Number of scatterers: 35256 At special positions: 0 Unit cell: (165.24, 165.24, 112.32, 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 168 16.00 O 6720 8.00 N 6048 7.00 C 22320 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.84 Conformation dependent library (CDL) restraints added in 4.9 seconds 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8400 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 60 sheets defined 46.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'U' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE U 27 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG U 28 " --> pdb=" O LYS U 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 23 through 28' Processing helix chain 'U' and resid 41 through 51 Processing helix chain 'U' and resid 54 through 70 Processing helix chain 'U' and resid 92 through 103 Processing helix chain 'U' and resid 109 through 125 Processing helix chain 'U' and resid 212 through 216 Processing helix chain 'U' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP U 236 " --> pdb=" O ILE U 232 " (cutoff:3.500A) Processing helix chain 'U' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN U 255 " --> pdb=" O LEU U 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA U 256 " --> pdb=" O ASP U 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS U 257 " --> pdb=" O ASP U 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU U 258 " --> pdb=" O GLY U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP U 304 " --> pdb=" O VAL U 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN U 305 " --> pdb=" O PRO U 301 " (cutoff:3.500A) Processing helix chain 'U' and resid 316 through 320 Processing helix chain 'U' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR U 345 " --> pdb=" O PHE U 341 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR U 352 " --> pdb=" O PRO U 348 " (cutoff:3.500A) Proline residue: U 353 - end of helix removed outlier: 3.547A pdb=" N PHE U 361 " --> pdb=" O GLY U 357 " (cutoff:3.500A) Processing helix chain 'U' and resid 373 through 378 Proline residue: U 377 - end of helix Processing helix chain 'U' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL U 393 " --> pdb=" O THR U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 397 through 404 Processing helix chain 'V' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE V 27 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG V 28 " --> pdb=" O LYS V 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 23 through 28' Processing helix chain 'V' and resid 41 through 51 Processing helix chain 'V' and resid 54 through 70 Processing helix chain 'V' and resid 92 through 103 Processing helix chain 'V' and resid 109 through 125 Processing helix chain 'V' and resid 212 through 216 Processing helix chain 'V' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP V 236 " --> pdb=" O ILE V 232 " (cutoff:3.500A) Processing helix chain 'V' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN V 255 " --> pdb=" O LEU V 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA V 256 " --> pdb=" O ASP V 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS V 257 " --> pdb=" O ASP V 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU V 258 " --> pdb=" O GLY V 254 " (cutoff:3.500A) Processing helix chain 'V' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP V 304 " --> pdb=" O VAL V 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN V 305 " --> pdb=" O PRO V 301 " (cutoff:3.500A) Processing helix chain 'V' and resid 316 through 320 Processing helix chain 'V' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR V 345 " --> pdb=" O PHE V 341 " (cutoff:3.500A) Processing helix chain 'V' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR V 352 " --> pdb=" O PRO V 348 " (cutoff:3.500A) Proline residue: V 353 - end of helix removed outlier: 3.547A pdb=" N PHE V 361 " --> pdb=" O GLY V 357 " (cutoff:3.500A) Processing helix chain 'V' and resid 373 through 378 Proline residue: V 377 - end of helix Processing helix chain 'V' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL V 393 " --> pdb=" O THR V 389 " (cutoff:3.500A) Processing helix chain 'V' and resid 397 through 404 Processing helix chain 'W' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE W 27 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG W 28 " --> pdb=" O LYS W 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 23 through 28' Processing helix chain 'W' and resid 41 through 51 Processing helix chain 'W' and resid 54 through 70 Processing helix chain 'W' and resid 92 through 103 Processing helix chain 'W' and resid 109 through 125 Processing helix chain 'W' and resid 212 through 216 Processing helix chain 'W' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP W 236 " --> pdb=" O ILE W 232 " (cutoff:3.500A) Processing helix chain 'W' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN W 255 " --> pdb=" O LEU W 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA W 256 " --> pdb=" O ASP W 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS W 257 " --> pdb=" O ASP W 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU W 258 " --> pdb=" O GLY W 254 " (cutoff:3.500A) Processing helix chain 'W' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP W 304 " --> pdb=" O VAL W 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN W 305 " --> pdb=" O PRO W 301 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 320 Processing helix chain 'W' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR W 345 " --> pdb=" O PHE W 341 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR W 352 " --> pdb=" O PRO W 348 " (cutoff:3.500A) Proline residue: W 353 - end of helix removed outlier: 3.548A pdb=" N PHE W 361 " --> pdb=" O GLY W 357 " (cutoff:3.500A) Processing helix chain 'W' and resid 373 through 378 Proline residue: W 377 - end of helix Processing helix chain 'W' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL W 393 " --> pdb=" O THR W 389 " (cutoff:3.500A) Processing helix chain 'W' and resid 397 through 404 Processing helix chain 'X' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG X 28 " --> pdb=" O LYS X 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 23 through 28' Processing helix chain 'X' and resid 41 through 51 Processing helix chain 'X' and resid 54 through 70 Processing helix chain 'X' and resid 92 through 103 Processing helix chain 'X' and resid 109 through 125 Processing helix chain 'X' and resid 212 through 216 Processing helix chain 'X' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP X 236 " --> pdb=" O ILE X 232 " (cutoff:3.500A) Processing helix chain 'X' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN X 255 " --> pdb=" O LEU X 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA X 256 " --> pdb=" O ASP X 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS X 257 " --> pdb=" O ASP X 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU X 258 " --> pdb=" O GLY X 254 " (cutoff:3.500A) Processing helix chain 'X' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP X 304 " --> pdb=" O VAL X 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN X 305 " --> pdb=" O PRO X 301 " (cutoff:3.500A) Processing helix chain 'X' and resid 316 through 320 Processing helix chain 'X' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR X 345 " --> pdb=" O PHE X 341 " (cutoff:3.500A) Processing helix chain 'X' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR X 352 " --> pdb=" O PRO X 348 " (cutoff:3.500A) Proline residue: X 353 - end of helix removed outlier: 3.547A pdb=" N PHE X 361 " --> pdb=" O GLY X 357 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 378 Proline residue: X 377 - end of helix Processing helix chain 'X' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL X 393 " --> pdb=" O THR X 389 " (cutoff:3.500A) Processing helix chain 'X' and resid 397 through 404 Processing helix chain 'Y' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE Y 27 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG Y 28 " --> pdb=" O LYS Y 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 23 through 28' Processing helix chain 'Y' and resid 41 through 51 Processing helix chain 'Y' and resid 54 through 70 Processing helix chain 'Y' and resid 92 through 103 Processing helix chain 'Y' and resid 109 through 125 Processing helix chain 'Y' and resid 212 through 216 Processing helix chain 'Y' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP Y 236 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) Processing helix chain 'Y' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN Y 255 " --> pdb=" O LEU Y 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Y 256 " --> pdb=" O ASP Y 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS Y 257 " --> pdb=" O ASP Y 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU Y 258 " --> pdb=" O GLY Y 254 " (cutoff:3.500A) Processing helix chain 'Y' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP Y 304 " --> pdb=" O VAL Y 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Y 305 " --> pdb=" O PRO Y 301 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 320 Processing helix chain 'Y' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR Y 345 " --> pdb=" O PHE Y 341 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR Y 352 " --> pdb=" O PRO Y 348 " (cutoff:3.500A) Proline residue: Y 353 - end of helix removed outlier: 3.547A pdb=" N PHE Y 361 " --> pdb=" O GLY Y 357 " (cutoff:3.500A) Processing helix chain 'Y' and resid 373 through 378 Proline residue: Y 377 - end of helix Processing helix chain 'Y' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL Y 393 " --> pdb=" O THR Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 397 through 404 Processing helix chain 'Z' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE Z 27 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG Z 28 " --> pdb=" O LYS Z 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 23 through 28' Processing helix chain 'Z' and resid 41 through 51 Processing helix chain 'Z' and resid 54 through 70 Processing helix chain 'Z' and resid 92 through 103 Processing helix chain 'Z' and resid 109 through 125 Processing helix chain 'Z' and resid 212 through 216 Processing helix chain 'Z' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP Z 236 " --> pdb=" O ILE Z 232 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN Z 255 " --> pdb=" O LEU Z 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA Z 256 " --> pdb=" O ASP Z 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS Z 257 " --> pdb=" O ASP Z 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU Z 258 " --> pdb=" O GLY Z 254 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP Z 304 " --> pdb=" O VAL Z 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN Z 305 " --> pdb=" O PRO Z 301 " (cutoff:3.500A) Processing helix chain 'Z' and resid 316 through 320 Processing helix chain 'Z' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR Z 345 " --> pdb=" O PHE Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR Z 352 " --> pdb=" O PRO Z 348 " (cutoff:3.500A) Proline residue: Z 353 - end of helix removed outlier: 3.548A pdb=" N PHE Z 361 " --> pdb=" O GLY Z 357 " (cutoff:3.500A) Processing helix chain 'Z' and resid 373 through 378 Proline residue: Z 377 - end of helix Processing helix chain 'Z' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL Z 393 " --> pdb=" O THR Z 389 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 404 Processing helix chain 'a' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE a 27 " --> pdb=" O ALA a 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG a 28 " --> pdb=" O LYS a 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 23 through 28' Processing helix chain 'a' and resid 41 through 51 Processing helix chain 'a' and resid 54 through 70 Processing helix chain 'a' and resid 92 through 103 Processing helix chain 'a' and resid 109 through 125 Processing helix chain 'a' and resid 212 through 216 Processing helix chain 'a' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP a 236 " --> pdb=" O ILE a 232 " (cutoff:3.500A) Processing helix chain 'a' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN a 255 " --> pdb=" O LEU a 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA a 256 " --> pdb=" O ASP a 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS a 257 " --> pdb=" O ASP a 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU a 258 " --> pdb=" O GLY a 254 " (cutoff:3.500A) Processing helix chain 'a' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP a 304 " --> pdb=" O VAL a 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN a 305 " --> pdb=" O PRO a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 316 through 320 Processing helix chain 'a' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR a 345 " --> pdb=" O PHE a 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR a 352 " --> pdb=" O PRO a 348 " (cutoff:3.500A) Proline residue: a 353 - end of helix removed outlier: 3.547A pdb=" N PHE a 361 " --> pdb=" O GLY a 357 " (cutoff:3.500A) Processing helix chain 'a' and resid 373 through 378 Proline residue: a 377 - end of helix Processing helix chain 'a' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL a 393 " --> pdb=" O THR a 389 " (cutoff:3.500A) Processing helix chain 'a' and resid 397 through 404 Processing helix chain 'b' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE b 27 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG b 28 " --> pdb=" O LYS b 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 23 through 28' Processing helix chain 'b' and resid 41 through 51 Processing helix chain 'b' and resid 54 through 70 Processing helix chain 'b' and resid 92 through 103 Processing helix chain 'b' and resid 109 through 125 Processing helix chain 'b' and resid 212 through 216 Processing helix chain 'b' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP b 236 " --> pdb=" O ILE b 232 " (cutoff:3.500A) Processing helix chain 'b' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN b 255 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA b 256 " --> pdb=" O ASP b 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS b 257 " --> pdb=" O ASP b 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU b 258 " --> pdb=" O GLY b 254 " (cutoff:3.500A) Processing helix chain 'b' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP b 304 " --> pdb=" O VAL b 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN b 305 " --> pdb=" O PRO b 301 " (cutoff:3.500A) Processing helix chain 'b' and resid 316 through 320 Processing helix chain 'b' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR b 345 " --> pdb=" O PHE b 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR b 352 " --> pdb=" O PRO b 348 " (cutoff:3.500A) Proline residue: b 353 - end of helix removed outlier: 3.547A pdb=" N PHE b 361 " --> pdb=" O GLY b 357 " (cutoff:3.500A) Processing helix chain 'b' and resid 373 through 378 Proline residue: b 377 - end of helix Processing helix chain 'b' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL b 393 " --> pdb=" O THR b 389 " (cutoff:3.500A) Processing helix chain 'b' and resid 397 through 404 Processing helix chain 'c' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE c 27 " --> pdb=" O ALA c 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG c 28 " --> pdb=" O LYS c 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 23 through 28' Processing helix chain 'c' and resid 41 through 51 Processing helix chain 'c' and resid 54 through 70 Processing helix chain 'c' and resid 92 through 103 Processing helix chain 'c' and resid 109 through 125 Processing helix chain 'c' and resid 212 through 216 Processing helix chain 'c' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP c 236 " --> pdb=" O ILE c 232 " (cutoff:3.500A) Processing helix chain 'c' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN c 255 " --> pdb=" O LEU c 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA c 256 " --> pdb=" O ASP c 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS c 257 " --> pdb=" O ASP c 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU c 258 " --> pdb=" O GLY c 254 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP c 304 " --> pdb=" O VAL c 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN c 305 " --> pdb=" O PRO c 301 " (cutoff:3.500A) Processing helix chain 'c' and resid 316 through 320 Processing helix chain 'c' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR c 345 " --> pdb=" O PHE c 341 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR c 352 " --> pdb=" O PRO c 348 " (cutoff:3.500A) Proline residue: c 353 - end of helix removed outlier: 3.548A pdb=" N PHE c 361 " --> pdb=" O GLY c 357 " (cutoff:3.500A) Processing helix chain 'c' and resid 373 through 378 Proline residue: c 377 - end of helix Processing helix chain 'c' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL c 393 " --> pdb=" O THR c 389 " (cutoff:3.500A) Processing helix chain 'c' and resid 397 through 404 Processing helix chain 'd' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE d 27 " --> pdb=" O ALA d 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG d 28 " --> pdb=" O LYS d 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 23 through 28' Processing helix chain 'd' and resid 41 through 51 Processing helix chain 'd' and resid 54 through 70 Processing helix chain 'd' and resid 92 through 103 Processing helix chain 'd' and resid 109 through 125 Processing helix chain 'd' and resid 212 through 216 Processing helix chain 'd' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP d 236 " --> pdb=" O ILE d 232 " (cutoff:3.500A) Processing helix chain 'd' and resid 251 through 265 removed outlier: 4.264A pdb=" N GLN d 255 " --> pdb=" O LEU d 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA d 256 " --> pdb=" O ASP d 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS d 257 " --> pdb=" O ASP d 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU d 258 " --> pdb=" O GLY d 254 " (cutoff:3.500A) Processing helix chain 'd' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP d 304 " --> pdb=" O VAL d 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN d 305 " --> pdb=" O PRO d 301 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 320 Processing helix chain 'd' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR d 345 " --> pdb=" O PHE d 341 " (cutoff:3.500A) Processing helix chain 'd' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR d 352 " --> pdb=" O PRO d 348 " (cutoff:3.500A) Proline residue: d 353 - end of helix removed outlier: 3.547A pdb=" N PHE d 361 " --> pdb=" O GLY d 357 " (cutoff:3.500A) Processing helix chain 'd' and resid 373 through 378 Proline residue: d 377 - end of helix Processing helix chain 'd' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL d 393 " --> pdb=" O THR d 389 " (cutoff:3.500A) Processing helix chain 'd' and resid 397 through 404 Processing helix chain 'e' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE e 27 " --> pdb=" O ALA e 23 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG e 28 " --> pdb=" O LYS e 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 23 through 28' Processing helix chain 'e' and resid 41 through 51 Processing helix chain 'e' and resid 54 through 70 Processing helix chain 'e' and resid 92 through 103 Processing helix chain 'e' and resid 109 through 125 Processing helix chain 'e' and resid 212 through 216 Processing helix chain 'e' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP e 236 " --> pdb=" O ILE e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN e 255 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA e 256 " --> pdb=" O ASP e 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS e 257 " --> pdb=" O ASP e 253 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU e 258 " --> pdb=" O GLY e 254 " (cutoff:3.500A) Processing helix chain 'e' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP e 304 " --> pdb=" O VAL e 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN e 305 " --> pdb=" O PRO e 301 " (cutoff:3.500A) Processing helix chain 'e' and resid 316 through 320 Processing helix chain 'e' and resid 335 through 345 removed outlier: 3.749A pdb=" N THR e 345 " --> pdb=" O PHE e 341 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 361 removed outlier: 6.136A pdb=" N THR e 352 " --> pdb=" O PRO e 348 " (cutoff:3.500A) Proline residue: e 353 - end of helix removed outlier: 3.547A pdb=" N PHE e 361 " --> pdb=" O GLY e 357 " (cutoff:3.500A) Processing helix chain 'e' and resid 373 through 378 Proline residue: e 377 - end of helix Processing helix chain 'e' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL e 393 " --> pdb=" O THR e 389 " (cutoff:3.500A) Processing helix chain 'e' and resid 397 through 404 Processing helix chain 'f' and resid 23 through 28 removed outlier: 4.505A pdb=" N ILE f 27 " --> pdb=" O ALA f 23 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG f 28 " --> pdb=" O LYS f 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 23 through 28' Processing helix chain 'f' and resid 41 through 51 Processing helix chain 'f' and resid 54 through 70 Processing helix chain 'f' and resid 92 through 103 Processing helix chain 'f' and resid 109 through 125 Processing helix chain 'f' and resid 212 through 216 Processing helix chain 'f' and resid 217 through 236 removed outlier: 3.612A pdb=" N ASP f 236 " --> pdb=" O ILE f 232 " (cutoff:3.500A) Processing helix chain 'f' and resid 251 through 265 removed outlier: 4.265A pdb=" N GLN f 255 " --> pdb=" O LEU f 251 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA f 256 " --> pdb=" O ASP f 252 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS f 257 " --> pdb=" O ASP f 253 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU f 258 " --> pdb=" O GLY f 254 " (cutoff:3.500A) Processing helix chain 'f' and resid 299 through 312 removed outlier: 3.667A pdb=" N ASP f 304 " --> pdb=" O VAL f 300 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLN f 305 " --> pdb=" O PRO f 301 " (cutoff:3.500A) Processing helix chain 'f' and resid 316 through 320 Processing helix chain 'f' and resid 335 through 345 removed outlier: 3.750A pdb=" N THR f 345 " --> pdb=" O PHE f 341 " (cutoff:3.500A) Processing helix chain 'f' and resid 346 through 361 removed outlier: 6.135A pdb=" N THR f 352 " --> pdb=" O PRO f 348 " (cutoff:3.500A) Proline residue: f 353 - end of helix removed outlier: 3.548A pdb=" N PHE f 361 " --> pdb=" O GLY f 357 " (cutoff:3.500A) Processing helix chain 'f' and resid 373 through 378 Proline residue: f 377 - end of helix Processing helix chain 'f' and resid 379 through 393 removed outlier: 3.642A pdb=" N VAL f 393 " --> pdb=" O THR f 389 " (cutoff:3.500A) Processing helix chain 'f' and resid 397 through 404 Processing sheet with id=AA1, first strand: chain 'U' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER U 162 " --> pdb=" O LYS U 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 73 through 77 Processing sheet with id=AA3, first strand: chain 'U' and resid 126 through 127 Processing sheet with id=AA4, first strand: chain 'U' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR U 192 " --> pdb=" O VAL U 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'U' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN U 287 " --> pdb=" O LEU U 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE V 277 " --> pdb=" O VAL U 245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'U' and resid 277 through 279 removed outlier: 5.713A pdb=" N ILE U 277 " --> pdb=" O VAL f 245 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN f 287 " --> pdb=" O LEU f 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER V 162 " --> pdb=" O LYS V 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 73 through 77 Processing sheet with id=AA9, first strand: chain 'V' and resid 126 through 127 Processing sheet with id=AB1, first strand: chain 'V' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR V 192 " --> pdb=" O VAL V 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'V' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN V 287 " --> pdb=" O LEU V 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE W 277 " --> pdb=" O VAL V 245 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER W 162 " --> pdb=" O LYS W 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AB5, first strand: chain 'W' and resid 126 through 127 Processing sheet with id=AB6, first strand: chain 'W' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR W 192 " --> pdb=" O VAL W 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'W' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN W 287 " --> pdb=" O LEU W 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE X 277 " --> pdb=" O VAL W 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER X 162 " --> pdb=" O LYS X 153 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'X' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'X' and resid 126 through 127 Processing sheet with id=AC2, first strand: chain 'X' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR X 192 " --> pdb=" O VAL X 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN X 287 " --> pdb=" O LEU X 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Y 277 " --> pdb=" O VAL X 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER Y 162 " --> pdb=" O LYS Y 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 73 through 77 Processing sheet with id=AC6, first strand: chain 'Y' and resid 126 through 127 Processing sheet with id=AC7, first strand: chain 'Y' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR Y 192 " --> pdb=" O VAL Y 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN Y 287 " --> pdb=" O LEU Y 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE Z 277 " --> pdb=" O VAL Y 245 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER Z 162 " --> pdb=" O LYS Z 153 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 73 through 77 Processing sheet with id=AD2, first strand: chain 'Z' and resid 126 through 127 Processing sheet with id=AD3, first strand: chain 'Z' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR Z 192 " --> pdb=" O VAL Z 131 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN Z 287 " --> pdb=" O LEU Z 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE a 277 " --> pdb=" O VAL Z 245 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'a' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER a 162 " --> pdb=" O LYS a 153 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 73 through 77 Processing sheet with id=AD7, first strand: chain 'a' and resid 126 through 127 Processing sheet with id=AD8, first strand: chain 'a' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR a 192 " --> pdb=" O VAL a 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'a' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN a 287 " --> pdb=" O LEU a 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE b 277 " --> pdb=" O VAL a 245 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'b' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER b 162 " --> pdb=" O LYS b 153 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'b' and resid 73 through 77 Processing sheet with id=AE3, first strand: chain 'b' and resid 126 through 127 Processing sheet with id=AE4, first strand: chain 'b' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR b 192 " --> pdb=" O VAL b 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'b' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN b 287 " --> pdb=" O LEU b 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE c 277 " --> pdb=" O VAL b 245 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER c 162 " --> pdb=" O LYS c 153 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 73 through 77 Processing sheet with id=AE8, first strand: chain 'c' and resid 126 through 127 Processing sheet with id=AE9, first strand: chain 'c' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR c 192 " --> pdb=" O VAL c 131 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN c 287 " --> pdb=" O LEU c 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE d 277 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER d 162 " --> pdb=" O LYS d 153 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 73 through 77 Processing sheet with id=AF4, first strand: chain 'd' and resid 126 through 127 Processing sheet with id=AF5, first strand: chain 'd' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR d 192 " --> pdb=" O VAL d 131 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'd' and resid 285 through 287 removed outlier: 3.502A pdb=" N GLN d 287 " --> pdb=" O LEU d 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE e 277 " --> pdb=" O VAL d 245 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'e' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER e 162 " --> pdb=" O LYS e 153 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'e' and resid 73 through 77 Processing sheet with id=AF9, first strand: chain 'e' and resid 126 through 127 Processing sheet with id=AG1, first strand: chain 'e' and resid 142 through 144 removed outlier: 3.708A pdb=" N TYR e 192 " --> pdb=" O VAL e 131 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'e' and resid 285 through 287 removed outlier: 3.501A pdb=" N GLN e 287 " --> pdb=" O LEU e 244 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE f 277 " --> pdb=" O VAL e 245 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'f' and resid 37 through 38 removed outlier: 3.633A pdb=" N SER f 162 " --> pdb=" O LYS f 153 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 73 through 77 Processing sheet with id=AG5, first strand: chain 'f' and resid 126 through 127 Processing sheet with id=AG6, first strand: chain 'f' and resid 142 through 144 removed outlier: 3.707A pdb=" N TYR f 192 " --> pdb=" O VAL f 131 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4068 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: 15.46 Time building geometry restraints manager: 11.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11736 1.34 - 1.46: 7968 1.46 - 1.59: 15996 1.59 - 1.71: 0 1.71 - 1.83: 300 Bond restraints: 36000 Sorted by residual: bond pdb=" C GLY V 349 " pdb=" N TYR V 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY Y 349 " pdb=" N TYR Y 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY b 349 " pdb=" N TYR b 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY e 349 " pdb=" N TYR e 350 " ideal model delta sigma weight residual 1.332 1.306 0.026 1.40e-02 5.10e+03 3.55e+00 bond pdb=" C GLY d 349 " pdb=" N TYR d 350 " ideal model delta sigma weight residual 1.332 1.307 0.026 1.40e-02 5.10e+03 3.38e+00 ... (remaining 35995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 47474 2.29 - 4.58: 1006 4.58 - 6.87: 144 6.87 - 9.16: 24 9.16 - 11.45: 24 Bond angle restraints: 48672 Sorted by residual: angle pdb=" C ASP f 167 " pdb=" N GLU f 168 " pdb=" CA GLU f 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP W 167 " pdb=" N GLU W 168 " pdb=" CA GLU W 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP Z 167 " pdb=" N GLU Z 168 " pdb=" CA GLU Z 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP c 167 " pdb=" N GLU c 168 " pdb=" CA GLU c 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ASP U 167 " pdb=" N GLU U 168 " pdb=" CA GLU U 168 " ideal model delta sigma weight residual 121.54 114.05 7.49 1.91e+00 2.74e-01 1.54e+01 ... (remaining 48667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 19436 17.85 - 35.69: 1864 35.69 - 53.54: 408 53.54 - 71.39: 36 71.39 - 89.23: 60 Dihedral angle restraints: 21804 sinusoidal: 8736 harmonic: 13068 Sorted by residual: dihedral pdb=" CA PHE X 361 " pdb=" C PHE X 361 " pdb=" N LEU X 362 " pdb=" CA LEU X 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE a 361 " pdb=" C PHE a 361 " pdb=" N LEU a 362 " pdb=" CA LEU a 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA PHE d 361 " pdb=" C PHE d 361 " pdb=" N LEU d 362 " pdb=" CA LEU d 362 " ideal model delta harmonic sigma weight residual 180.00 153.65 26.35 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 21801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2779 0.030 - 0.060: 1349 0.060 - 0.090: 738 0.090 - 0.119: 298 0.119 - 0.149: 104 Chirality restraints: 5268 Sorted by residual: chirality pdb=" CA ASP f 208 " pdb=" N ASP f 208 " pdb=" C ASP f 208 " pdb=" CB ASP f 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASP W 208 " pdb=" N ASP W 208 " pdb=" C ASP W 208 " pdb=" CB ASP W 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ASP c 208 " pdb=" N ASP c 208 " pdb=" C ASP c 208 " pdb=" CB ASP c 208 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 ... (remaining 5265 not shown) Planarity restraints: 6420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL Z 133 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL Z 133 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL Z 133 " 0.009 2.00e-02 2.50e+03 pdb=" N MET Z 134 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL W 133 " 0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL W 133 " -0.025 2.00e-02 2.50e+03 pdb=" O VAL W 133 " 0.009 2.00e-02 2.50e+03 pdb=" N MET W 134 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL c 133 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C VAL c 133 " 0.025 2.00e-02 2.50e+03 pdb=" O VAL c 133 " -0.009 2.00e-02 2.50e+03 pdb=" N MET c 134 " -0.008 2.00e-02 2.50e+03 ... (remaining 6417 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7576 2.77 - 3.30: 35256 3.30 - 3.83: 57400 3.83 - 4.37: 67052 4.37 - 4.90: 114906 Nonbonded interactions: 282190 Sorted by model distance: nonbonded pdb=" N ASN f 183 " pdb=" O ARG f 187 " model vdw 2.237 3.120 nonbonded pdb=" N ASN c 183 " pdb=" O ARG c 187 " model vdw 2.237 3.120 nonbonded pdb=" N ASN W 183 " pdb=" O ARG W 187 " model vdw 2.237 3.120 nonbonded pdb=" N ASN Z 183 " pdb=" O ARG Z 187 " model vdw 2.237 3.120 nonbonded pdb=" N ASN d 183 " pdb=" O ARG d 187 " model vdw 2.237 3.120 ... (remaining 282185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.31 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'f' selection = chain 'U' selection = chain 'W' selection = chain 'V' selection = chain 'Y' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.440 Check model and map are aligned: 0.250 Set scattering table: 0.310 Process input model: 83.930 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.290 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 36000 Z= 0.235 Angle : 0.827 11.446 48672 Z= 0.438 Chirality : 0.048 0.149 5268 Planarity : 0.005 0.035 6420 Dihedral : 14.996 89.231 13404 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.82 % Favored : 87.18 % Rotamer: Outliers : 2.57 % Allowed : 9.00 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.11), residues: 4524 helix: -1.10 (0.10), residues: 1968 sheet: -1.79 (0.24), residues: 504 loop : -3.78 (0.11), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 143 HIS 0.014 0.005 HIS e 297 PHE 0.021 0.002 PHE Z 361 TYR 0.012 0.001 TYR c 192 ARG 0.005 0.001 ARG X 373 Details of bonding type rmsd hydrogen bonds : bond 0.13449 ( 1464) hydrogen bonds : angle 6.52893 ( 4068) covalent geometry : bond 0.00540 (36000) covalent geometry : angle 0.82688 (48672) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 992 time to evaluate : 4.018 Fit side-chains REVERT: U 49 GLN cc_start: 0.8821 (tp40) cc_final: 0.8447 (tp40) REVERT: U 153 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8302 (ttmt) REVERT: U 201 ILE cc_start: 0.8213 (mt) cc_final: 0.7981 (tp) REVERT: U 249 ARG cc_start: 0.5831 (tpt170) cc_final: 0.4484 (ttt90) REVERT: U 285 LYS cc_start: 0.8762 (ttpp) cc_final: 0.8492 (tttp) REVERT: U 386 ILE cc_start: 0.9048 (mm) cc_final: 0.8809 (mt) REVERT: V 37 LYS cc_start: 0.8598 (tttt) cc_final: 0.8335 (tttt) REVERT: V 49 GLN cc_start: 0.8803 (tp40) cc_final: 0.8592 (mm-40) REVERT: V 201 ILE cc_start: 0.8196 (mt) cc_final: 0.7955 (tp) REVERT: V 209 VAL cc_start: 0.8957 (t) cc_final: 0.8741 (m) REVERT: V 249 ARG cc_start: 0.6309 (tpt170) cc_final: 0.4988 (ttt90) REVERT: W 49 GLN cc_start: 0.8782 (tp40) cc_final: 0.8427 (mm-40) REVERT: W 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8708 (mm-40) REVERT: W 164 GLN cc_start: 0.8175 (tt0) cc_final: 0.7960 (tt0) REVERT: W 183 ASN cc_start: 0.6904 (m-40) cc_final: 0.6629 (m-40) REVERT: W 209 VAL cc_start: 0.8925 (t) cc_final: 0.8611 (t) REVERT: W 249 ARG cc_start: 0.5983 (tpt170) cc_final: 0.4562 (ttt90) REVERT: W 285 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8467 (tttp) REVERT: W 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8429 (tptp) REVERT: X 49 GLN cc_start: 0.8821 (tp40) cc_final: 0.8445 (tp40) REVERT: X 153 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8301 (ttmt) REVERT: X 201 ILE cc_start: 0.8211 (mt) cc_final: 0.7978 (tp) REVERT: X 249 ARG cc_start: 0.5830 (tpt170) cc_final: 0.4485 (ttt90) REVERT: X 285 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8493 (tttp) REVERT: X 386 ILE cc_start: 0.9042 (mm) cc_final: 0.8802 (mt) REVERT: Y 37 LYS cc_start: 0.8596 (tttt) cc_final: 0.8335 (tttt) REVERT: Y 49 GLN cc_start: 0.8801 (tp40) cc_final: 0.8590 (mm-40) REVERT: Y 201 ILE cc_start: 0.8194 (mt) cc_final: 0.7950 (tp) REVERT: Y 209 VAL cc_start: 0.8960 (t) cc_final: 0.8743 (m) REVERT: Y 249 ARG cc_start: 0.6316 (tpt170) cc_final: 0.4992 (ttt90) REVERT: Z 49 GLN cc_start: 0.8775 (tp40) cc_final: 0.8421 (mm-40) REVERT: Z 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8709 (mm-40) REVERT: Z 164 GLN cc_start: 0.8173 (tt0) cc_final: 0.7959 (tt0) REVERT: Z 183 ASN cc_start: 0.6902 (m-40) cc_final: 0.6632 (m-40) REVERT: Z 209 VAL cc_start: 0.8932 (t) cc_final: 0.8620 (t) REVERT: Z 249 ARG cc_start: 0.5981 (tpt170) cc_final: 0.4567 (ttt90) REVERT: Z 285 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8465 (tttp) REVERT: Z 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8428 (tptp) REVERT: a 49 GLN cc_start: 0.8819 (tp40) cc_final: 0.8447 (tp40) REVERT: a 153 LYS cc_start: 0.8603 (ttmt) cc_final: 0.8303 (ttmt) REVERT: a 201 ILE cc_start: 0.8213 (mt) cc_final: 0.7987 (tp) REVERT: a 249 ARG cc_start: 0.5830 (tpt170) cc_final: 0.4481 (ttt90) REVERT: a 285 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8492 (tttp) REVERT: a 386 ILE cc_start: 0.9040 (mm) cc_final: 0.8802 (mt) REVERT: b 37 LYS cc_start: 0.8598 (tttt) cc_final: 0.8336 (tttt) REVERT: b 49 GLN cc_start: 0.8799 (tp40) cc_final: 0.8591 (mm-40) REVERT: b 201 ILE cc_start: 0.8191 (mt) cc_final: 0.7946 (tp) REVERT: b 209 VAL cc_start: 0.8963 (t) cc_final: 0.8748 (m) REVERT: b 249 ARG cc_start: 0.6319 (tpt170) cc_final: 0.4994 (ttt90) REVERT: c 49 GLN cc_start: 0.8774 (tp40) cc_final: 0.8419 (mm-40) REVERT: c 99 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8709 (mm-40) REVERT: c 164 GLN cc_start: 0.8171 (tt0) cc_final: 0.7957 (tt0) REVERT: c 183 ASN cc_start: 0.6900 (m-40) cc_final: 0.6633 (m-40) REVERT: c 209 VAL cc_start: 0.8928 (t) cc_final: 0.8614 (t) REVERT: c 249 ARG cc_start: 0.5982 (tpt170) cc_final: 0.4569 (ttt90) REVERT: c 285 LYS cc_start: 0.8778 (ttpp) cc_final: 0.8466 (tttp) REVERT: c 290 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8429 (tptp) REVERT: d 49 GLN cc_start: 0.8820 (tp40) cc_final: 0.8448 (tp40) REVERT: d 153 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8303 (ttmt) REVERT: d 201 ILE cc_start: 0.8215 (mt) cc_final: 0.7990 (tp) REVERT: d 249 ARG cc_start: 0.5828 (tpt170) cc_final: 0.4478 (ttt90) REVERT: d 285 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8493 (tttp) REVERT: d 386 ILE cc_start: 0.9046 (mm) cc_final: 0.8807 (mt) REVERT: e 37 LYS cc_start: 0.8599 (tttt) cc_final: 0.8338 (tttt) REVERT: e 49 GLN cc_start: 0.8801 (tp40) cc_final: 0.8592 (mm-40) REVERT: e 201 ILE cc_start: 0.8196 (mt) cc_final: 0.7954 (tp) REVERT: e 209 VAL cc_start: 0.8965 (t) cc_final: 0.8748 (m) REVERT: e 249 ARG cc_start: 0.6311 (tpt170) cc_final: 0.4988 (ttt90) REVERT: f 49 GLN cc_start: 0.8780 (tp40) cc_final: 0.8423 (mm-40) REVERT: f 99 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8708 (mm-40) REVERT: f 164 GLN cc_start: 0.8171 (tt0) cc_final: 0.7959 (tt0) REVERT: f 183 ASN cc_start: 0.6903 (m-40) cc_final: 0.6628 (m-40) REVERT: f 209 VAL cc_start: 0.8925 (t) cc_final: 0.8613 (t) REVERT: f 249 ARG cc_start: 0.5979 (tpt170) cc_final: 0.4561 (ttt90) REVERT: f 285 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8468 (tttp) REVERT: f 290 LYS cc_start: 0.8736 (mmmt) cc_final: 0.8429 (tptp) outliers start: 96 outliers final: 28 residues processed: 1064 average time/residue: 0.5671 time to fit residues: 914.7419 Evaluate side-chains 684 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 656 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 41 SER Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain W residue 41 SER Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 41 SER Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain Y residue 41 SER Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Z residue 41 SER Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 41 SER Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain b residue 41 SER Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain c residue 41 SER Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 41 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain e residue 41 SER Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain f residue 41 SER Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 1.9990 chunk 345 optimal weight: 8.9990 chunk 191 optimal weight: 0.8980 chunk 118 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 184 optimal weight: 4.9990 chunk 357 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 414 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 164 GLN U 191 ASN U 202 ASN U 291 ASN U 305 GLN V 80 GLN V 191 ASN V 202 ASN V 291 ASN V 305 GLN W 80 GLN ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 191 ASN W 202 ASN W 215 GLN W 291 ASN W 305 GLN X 164 GLN X 191 ASN X 202 ASN X 291 ASN X 305 GLN Y 80 GLN Y 191 ASN Y 202 ASN Y 291 ASN Y 305 GLN Z 80 GLN ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 191 ASN Z 202 ASN Z 215 GLN Z 291 ASN Z 305 GLN a 164 GLN a 191 ASN a 202 ASN a 291 ASN a 305 GLN b 80 GLN b 191 ASN b 202 ASN b 291 ASN b 305 GLN c 80 GLN ** c 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 191 ASN c 202 ASN c 215 GLN c 291 ASN c 305 GLN d 164 GLN d 191 ASN d 202 ASN d 291 ASN e 80 GLN e 191 ASN e 202 ASN e 291 ASN e 305 GLN ** f 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 191 ASN f 202 ASN f 215 GLN f 291 ASN f 305 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099102 restraints weight = 55092.893| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.00 r_work: 0.3026 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 36000 Z= 0.192 Angle : 0.706 8.007 48672 Z= 0.365 Chirality : 0.047 0.164 5268 Planarity : 0.005 0.032 6420 Dihedral : 6.236 54.747 4952 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.33 % Favored : 87.67 % Rotamer: Outliers : 3.32 % Allowed : 16.08 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4524 helix: 0.19 (0.12), residues: 1956 sheet: -0.81 (0.31), residues: 360 loop : -3.30 (0.12), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 143 HIS 0.012 0.004 HIS e 297 PHE 0.013 0.001 PHE Y 26 TYR 0.010 0.001 TYR c 367 ARG 0.004 0.001 ARG f 383 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1464) hydrogen bonds : angle 4.83975 ( 4068) covalent geometry : bond 0.00462 (36000) covalent geometry : angle 0.70639 (48672) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 721 time to evaluate : 3.879 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: U 49 GLN cc_start: 0.9014 (tp40) cc_final: 0.8653 (tp40) REVERT: U 153 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8427 (ttmt) REVERT: U 205 MET cc_start: 0.7914 (mtm) cc_final: 0.7576 (mtt) REVERT: U 249 ARG cc_start: 0.6335 (tpt170) cc_final: 0.4644 (ttt90) REVERT: U 265 GLU cc_start: 0.8781 (tp30) cc_final: 0.8132 (tt0) REVERT: U 272 ASN cc_start: 0.8944 (p0) cc_final: 0.8676 (p0) REVERT: U 285 LYS cc_start: 0.8403 (ttpp) cc_final: 0.7861 (tttp) REVERT: U 405 THR cc_start: 0.8690 (OUTLIER) cc_final: 0.8448 (p) REVERT: V 99 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8408 (mp10) REVERT: V 153 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8273 (ttmt) REVERT: V 183 ASN cc_start: 0.7488 (m-40) cc_final: 0.7233 (m-40) REVERT: V 205 MET cc_start: 0.8033 (mtt) cc_final: 0.7783 (mmm) REVERT: V 215 GLN cc_start: 0.8696 (mt0) cc_final: 0.8469 (mt0) REVERT: V 249 ARG cc_start: 0.6316 (tpt170) cc_final: 0.4853 (ttt90) REVERT: V 355 GLU cc_start: 0.7996 (pt0) cc_final: 0.7771 (pt0) REVERT: V 405 THR cc_start: 0.8683 (OUTLIER) cc_final: 0.8398 (p) REVERT: W 66 LEU cc_start: 0.9038 (mt) cc_final: 0.8687 (mt) REVERT: W 89 MET cc_start: 0.5801 (mmm) cc_final: 0.5575 (mmm) REVERT: W 153 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8516 (ttmt) REVERT: W 249 ARG cc_start: 0.6459 (tpt170) cc_final: 0.4592 (ttt90) REVERT: W 285 LYS cc_start: 0.8434 (ttpp) cc_final: 0.8071 (tttp) REVERT: W 290 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8644 (tptp) REVERT: W 405 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (p) REVERT: X 49 GLN cc_start: 0.9007 (tp40) cc_final: 0.8644 (tp40) REVERT: X 153 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8425 (ttmt) REVERT: X 205 MET cc_start: 0.7921 (mtm) cc_final: 0.7653 (mtt) REVERT: X 249 ARG cc_start: 0.6359 (tpt170) cc_final: 0.4649 (ttt90) REVERT: X 265 GLU cc_start: 0.8768 (tp30) cc_final: 0.8121 (tt0) REVERT: X 272 ASN cc_start: 0.8941 (p0) cc_final: 0.8671 (p0) REVERT: X 285 LYS cc_start: 0.8388 (ttpp) cc_final: 0.7848 (tttp) REVERT: X 405 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8449 (p) REVERT: Y 99 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8409 (mp10) REVERT: Y 153 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8280 (ttmt) REVERT: Y 183 ASN cc_start: 0.7474 (m-40) cc_final: 0.7220 (m-40) REVERT: Y 205 MET cc_start: 0.8031 (mtt) cc_final: 0.7783 (mmm) REVERT: Y 215 GLN cc_start: 0.8693 (mt0) cc_final: 0.8467 (mt0) REVERT: Y 249 ARG cc_start: 0.6324 (tpt170) cc_final: 0.4855 (ttt90) REVERT: Y 355 GLU cc_start: 0.7995 (pt0) cc_final: 0.7770 (pt0) REVERT: Y 405 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8410 (p) REVERT: Z 66 LEU cc_start: 0.9039 (mt) cc_final: 0.8688 (mt) REVERT: Z 89 MET cc_start: 0.5793 (mmm) cc_final: 0.5567 (mmm) REVERT: Z 153 LYS cc_start: 0.8848 (ttmt) cc_final: 0.8514 (ttmt) REVERT: Z 249 ARG cc_start: 0.6493 (tpt170) cc_final: 0.4603 (ttt90) REVERT: Z 285 LYS cc_start: 0.8430 (ttpp) cc_final: 0.8066 (tttp) REVERT: Z 290 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8633 (tptp) REVERT: Z 405 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8372 (p) REVERT: a 49 GLN cc_start: 0.9006 (tp40) cc_final: 0.8641 (tp40) REVERT: a 153 LYS cc_start: 0.8735 (ttmt) cc_final: 0.8430 (ttmt) REVERT: a 205 MET cc_start: 0.7920 (mtm) cc_final: 0.7653 (mtt) REVERT: a 249 ARG cc_start: 0.6356 (tpt170) cc_final: 0.4653 (ttt90) REVERT: a 265 GLU cc_start: 0.8784 (tp30) cc_final: 0.8128 (tt0) REVERT: a 272 ASN cc_start: 0.8944 (p0) cc_final: 0.8674 (p0) REVERT: a 285 LYS cc_start: 0.8384 (ttpp) cc_final: 0.7842 (tttp) REVERT: a 405 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8449 (p) REVERT: b 99 GLN cc_start: 0.8920 (mm-40) cc_final: 0.8413 (mp10) REVERT: b 153 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8269 (ttmt) REVERT: b 183 ASN cc_start: 0.7488 (m-40) cc_final: 0.7234 (m-40) REVERT: b 205 MET cc_start: 0.8035 (mtt) cc_final: 0.7780 (mmm) REVERT: b 215 GLN cc_start: 0.8695 (mt0) cc_final: 0.8467 (mt0) REVERT: b 249 ARG cc_start: 0.6327 (tpt170) cc_final: 0.4860 (ttt90) REVERT: b 355 GLU cc_start: 0.7991 (pt0) cc_final: 0.7766 (pt0) REVERT: b 405 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8405 (p) REVERT: c 66 LEU cc_start: 0.9024 (mt) cc_final: 0.8673 (mt) REVERT: c 89 MET cc_start: 0.5805 (mmm) cc_final: 0.5579 (mmm) REVERT: c 153 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8518 (ttmt) REVERT: c 249 ARG cc_start: 0.6505 (tpt170) cc_final: 0.4607 (ttt90) REVERT: c 285 LYS cc_start: 0.8429 (ttpp) cc_final: 0.8068 (tttp) REVERT: c 290 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8631 (tptp) REVERT: c 405 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8375 (p) REVERT: d 49 GLN cc_start: 0.9006 (tp40) cc_final: 0.8640 (tp40) REVERT: d 153 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8428 (ttmt) REVERT: d 205 MET cc_start: 0.7920 (mtm) cc_final: 0.7653 (mtt) REVERT: d 249 ARG cc_start: 0.6354 (tpt170) cc_final: 0.4651 (ttt90) REVERT: d 265 GLU cc_start: 0.8781 (tp30) cc_final: 0.8131 (tt0) REVERT: d 272 ASN cc_start: 0.8943 (p0) cc_final: 0.8674 (p0) REVERT: d 285 LYS cc_start: 0.8393 (ttpp) cc_final: 0.7848 (tttp) REVERT: d 405 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8449 (p) REVERT: e 99 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8412 (mp10) REVERT: e 153 LYS cc_start: 0.8622 (ttmt) cc_final: 0.8277 (ttmt) REVERT: e 183 ASN cc_start: 0.7487 (m-40) cc_final: 0.7234 (m-40) REVERT: e 205 MET cc_start: 0.8035 (mtt) cc_final: 0.7784 (mmm) REVERT: e 215 GLN cc_start: 0.8696 (mt0) cc_final: 0.8467 (mt0) REVERT: e 249 ARG cc_start: 0.6321 (tpt170) cc_final: 0.4860 (ttt90) REVERT: e 355 GLU cc_start: 0.7988 (pt0) cc_final: 0.7764 (pt0) REVERT: e 405 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8402 (p) REVERT: f 66 LEU cc_start: 0.9036 (mt) cc_final: 0.8685 (mt) REVERT: f 89 MET cc_start: 0.5808 (mmm) cc_final: 0.5583 (mmm) REVERT: f 153 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8521 (ttmt) REVERT: f 249 ARG cc_start: 0.6472 (tpt170) cc_final: 0.4590 (ttt90) REVERT: f 285 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8077 (tttp) REVERT: f 290 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8638 (tptp) REVERT: f 405 THR cc_start: 0.8607 (OUTLIER) cc_final: 0.8369 (p) outliers start: 124 outliers final: 96 residues processed: 813 average time/residue: 0.5010 time to fit residues: 651.2706 Evaluate side-chains 738 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 630 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 74 ASP Chi-restraints excluded: chain U residue 120 SER Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 236 ASP Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 405 THR Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 93 GLN Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 405 THR Chi-restraints excluded: chain W residue 93 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 74 ASP Chi-restraints excluded: chain X residue 120 SER Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 236 ASP Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 405 THR Chi-restraints excluded: chain Y residue 74 ASP Chi-restraints excluded: chain Y residue 93 GLN Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 405 THR Chi-restraints excluded: chain Z residue 93 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain a residue 74 ASP Chi-restraints excluded: chain a residue 120 SER Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 236 ASP Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain b residue 74 ASP Chi-restraints excluded: chain b residue 93 GLN Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 74 ASP Chi-restraints excluded: chain d residue 120 SER Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 236 ASP Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 405 THR Chi-restraints excluded: chain e residue 74 ASP Chi-restraints excluded: chain e residue 93 GLN Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain f residue 93 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 405 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 266 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 243 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 297 optimal weight: 0.8980 chunk 386 optimal weight: 0.6980 chunk 229 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 370 optimal weight: 0.9990 chunk 353 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 GLN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 215 GLN ** c 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 215 GLN d 305 GLN ** f 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.139765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100403 restraints weight = 54771.850| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.99 r_work: 0.3054 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36000 Z= 0.141 Angle : 0.637 7.227 48672 Z= 0.330 Chirality : 0.044 0.196 5268 Planarity : 0.004 0.033 6420 Dihedral : 5.993 59.931 4940 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.20 % Favored : 87.80 % Rotamer: Outliers : 4.07 % Allowed : 19.08 % Favored : 76.85 % 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: -1.71 (0.13), residues: 4524 helix: 0.64 (0.12), residues: 1968 sheet: -0.42 (0.32), residues: 360 loop : -3.11 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 143 HIS 0.008 0.002 HIS Y 297 PHE 0.010 0.001 PHE b 26 TYR 0.013 0.001 TYR Z 367 ARG 0.005 0.000 ARG V 50 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 1464) hydrogen bonds : angle 4.57660 ( 4068) covalent geometry : bond 0.00331 (36000) covalent geometry : angle 0.63748 (48672) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 672 time to evaluate : 4.029 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: U 49 GLN cc_start: 0.9001 (tp40) cc_final: 0.8786 (tp40) REVERT: U 89 MET cc_start: 0.6083 (mmm) cc_final: 0.5786 (mmm) REVERT: U 249 ARG cc_start: 0.6417 (tpt170) cc_final: 0.3991 (ttm-80) REVERT: U 265 GLU cc_start: 0.8744 (tp30) cc_final: 0.8091 (tt0) REVERT: U 285 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8063 (tttt) REVERT: U 350 TYR cc_start: 0.9413 (m-80) cc_final: 0.8900 (m-80) REVERT: V 99 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8466 (mp10) REVERT: V 153 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8361 (ttmm) REVERT: V 215 GLN cc_start: 0.8669 (mt0) cc_final: 0.8406 (mt0) REVERT: V 249 ARG cc_start: 0.6204 (tpt170) cc_final: 0.4543 (ttt90) REVERT: V 290 LYS cc_start: 0.8991 (mmmt) cc_final: 0.8690 (tptp) REVERT: V 355 GLU cc_start: 0.8020 (pt0) cc_final: 0.7739 (pt0) REVERT: W 153 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8517 (ttmt) REVERT: W 205 MET cc_start: 0.7839 (mtm) cc_final: 0.7510 (mtt) REVERT: W 212 THR cc_start: 0.8777 (t) cc_final: 0.8533 (t) REVERT: W 249 ARG cc_start: 0.6511 (tpt170) cc_final: 0.4531 (ttt90) REVERT: W 285 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7992 (tttp) REVERT: W 290 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8645 (tptp) REVERT: X 49 GLN cc_start: 0.9000 (tp40) cc_final: 0.8786 (tp40) REVERT: X 89 MET cc_start: 0.6081 (mmm) cc_final: 0.5784 (mmm) REVERT: X 205 MET cc_start: 0.7851 (mtm) cc_final: 0.7616 (mtt) REVERT: X 249 ARG cc_start: 0.6438 (tpt170) cc_final: 0.3985 (ttm-80) REVERT: X 265 GLU cc_start: 0.8742 (tp30) cc_final: 0.8087 (tt0) REVERT: X 350 TYR cc_start: 0.9409 (m-80) cc_final: 0.8899 (m-80) REVERT: Y 99 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8466 (mp10) REVERT: Y 153 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8361 (ttmm) REVERT: Y 215 GLN cc_start: 0.8671 (mt0) cc_final: 0.8410 (mt0) REVERT: Y 249 ARG cc_start: 0.6205 (tpt170) cc_final: 0.4534 (ttt90) REVERT: Y 290 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8688 (tptp) REVERT: Y 355 GLU cc_start: 0.8018 (pt0) cc_final: 0.7736 (pt0) REVERT: Z 153 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8519 (ttmt) REVERT: Z 205 MET cc_start: 0.7836 (mtm) cc_final: 0.7503 (mtt) REVERT: Z 212 THR cc_start: 0.8781 (t) cc_final: 0.8537 (t) REVERT: Z 249 ARG cc_start: 0.6527 (tpt170) cc_final: 0.4543 (ttt90) REVERT: Z 285 LYS cc_start: 0.8480 (ttpp) cc_final: 0.7993 (tttp) REVERT: Z 290 LYS cc_start: 0.8992 (mmmt) cc_final: 0.8646 (tptp) REVERT: a 49 GLN cc_start: 0.8998 (tp40) cc_final: 0.8784 (tp40) REVERT: a 89 MET cc_start: 0.6075 (mmm) cc_final: 0.5779 (mmm) REVERT: a 205 MET cc_start: 0.7853 (mtm) cc_final: 0.7620 (mtt) REVERT: a 249 ARG cc_start: 0.6457 (tpt170) cc_final: 0.3985 (ttm-80) REVERT: a 265 GLU cc_start: 0.8742 (tp30) cc_final: 0.8091 (tt0) REVERT: a 350 TYR cc_start: 0.9407 (m-80) cc_final: 0.8895 (m-80) REVERT: b 99 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8464 (mp10) REVERT: b 153 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8360 (ttmm) REVERT: b 215 GLN cc_start: 0.8671 (mt0) cc_final: 0.8408 (mt0) REVERT: b 249 ARG cc_start: 0.6203 (tpt170) cc_final: 0.4535 (ttt90) REVERT: b 290 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8687 (tptp) REVERT: b 355 GLU cc_start: 0.8012 (pt0) cc_final: 0.7732 (pt0) REVERT: c 153 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8517 (ttmt) REVERT: c 205 MET cc_start: 0.7834 (mtm) cc_final: 0.7504 (mtt) REVERT: c 212 THR cc_start: 0.8787 (t) cc_final: 0.8543 (t) REVERT: c 249 ARG cc_start: 0.6540 (tpt170) cc_final: 0.4546 (ttt90) REVERT: c 285 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7993 (tttp) REVERT: c 290 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8653 (tptp) REVERT: d 49 GLN cc_start: 0.9000 (tp40) cc_final: 0.8786 (tp40) REVERT: d 89 MET cc_start: 0.6073 (mmm) cc_final: 0.5777 (mmm) REVERT: d 205 MET cc_start: 0.7849 (mtm) cc_final: 0.7617 (mtt) REVERT: d 249 ARG cc_start: 0.6439 (tpt170) cc_final: 0.3993 (ttm-80) REVERT: d 265 GLU cc_start: 0.8744 (tp30) cc_final: 0.8090 (tt0) REVERT: d 350 TYR cc_start: 0.9410 (m-80) cc_final: 0.8896 (m-80) REVERT: e 99 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8465 (mp10) REVERT: e 153 LYS cc_start: 0.8663 (ttmt) cc_final: 0.8362 (ttmm) REVERT: e 215 GLN cc_start: 0.8670 (mt0) cc_final: 0.8406 (mt0) REVERT: e 249 ARG cc_start: 0.6203 (tpt170) cc_final: 0.4543 (ttt90) REVERT: e 290 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8686 (tptp) REVERT: e 355 GLU cc_start: 0.8018 (pt0) cc_final: 0.7737 (pt0) REVERT: f 153 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8521 (ttmt) REVERT: f 212 THR cc_start: 0.8782 (t) cc_final: 0.8539 (t) REVERT: f 249 ARG cc_start: 0.6506 (tpt170) cc_final: 0.4529 (ttt90) REVERT: f 285 LYS cc_start: 0.8477 (ttpp) cc_final: 0.7990 (tttp) REVERT: f 290 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8655 (tptp) outliers start: 152 outliers final: 104 residues processed: 773 average time/residue: 0.4926 time to fit residues: 611.5722 Evaluate side-chains 765 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 661 time to evaluate : 4.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 75 VAL Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 75 VAL Chi-restraints excluded: chain W residue 93 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 252 ASP Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 252 ASP Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 75 VAL Chi-restraints excluded: chain Z residue 93 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 252 ASP Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 252 ASP Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 75 VAL Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 93 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 252 ASP Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 252 ASP Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 75 VAL Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 75 VAL Chi-restraints excluded: chain f residue 93 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 210 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 196 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 381 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 69 GLN ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 69 GLN W 105 ASN Y 69 GLN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN b 69 GLN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN c 105 ASN e 69 GLN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 69 GLN f 105 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101138 restraints weight = 54549.624| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.96 r_work: 0.3057 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36000 Z= 0.128 Angle : 0.616 7.251 48672 Z= 0.316 Chirality : 0.044 0.202 5268 Planarity : 0.004 0.032 6420 Dihedral : 5.802 59.648 4940 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 4.93 % Allowed : 19.48 % Favored : 75.59 % 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: -1.52 (0.13), residues: 4524 helix: 0.87 (0.12), residues: 1968 sheet: -0.53 (0.28), residues: 480 loop : -3.18 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 143 HIS 0.007 0.002 HIS b 297 PHE 0.013 0.001 PHE f 30 TYR 0.015 0.001 TYR Y 367 ARG 0.002 0.000 ARG V 103 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 1464) hydrogen bonds : angle 4.43327 ( 4068) covalent geometry : bond 0.00300 (36000) covalent geometry : angle 0.61644 (48672) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 715 time to evaluate : 4.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 MET cc_start: 0.5946 (mmm) cc_final: 0.5709 (mmm) REVERT: U 149 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.6849 (p90) REVERT: U 249 ARG cc_start: 0.6371 (tpt170) cc_final: 0.4738 (ttt90) REVERT: U 265 GLU cc_start: 0.8715 (tp30) cc_final: 0.8013 (tt0) REVERT: U 350 TYR cc_start: 0.9378 (m-80) cc_final: 0.8718 (m-80) REVERT: V 149 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.6653 (p90) REVERT: V 153 LYS cc_start: 0.8677 (ttmt) cc_final: 0.8357 (ttmm) REVERT: V 205 MET cc_start: 0.8585 (mmm) cc_final: 0.7870 (mmt) REVERT: V 249 ARG cc_start: 0.6443 (tpt170) cc_final: 0.4686 (ttt90) REVERT: V 290 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8668 (tptp) REVERT: V 367 TYR cc_start: 0.8261 (m-80) cc_final: 0.7949 (m-80) REVERT: W 153 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8496 (ttmt) REVERT: W 249 ARG cc_start: 0.6462 (tpt170) cc_final: 0.3324 (ttm170) REVERT: W 265 GLU cc_start: 0.8656 (tp30) cc_final: 0.7984 (tt0) REVERT: W 285 LYS cc_start: 0.8461 (ttpp) cc_final: 0.8121 (tttp) REVERT: W 290 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8665 (tptp) REVERT: W 391 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8635 (t70) REVERT: W 405 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8503 (p) REVERT: X 89 MET cc_start: 0.5938 (mmm) cc_final: 0.5703 (mmm) REVERT: X 149 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6842 (p90) REVERT: X 205 MET cc_start: 0.7826 (mtm) cc_final: 0.7571 (mtt) REVERT: X 249 ARG cc_start: 0.6375 (tpt170) cc_final: 0.4740 (ttt90) REVERT: X 265 GLU cc_start: 0.8707 (tp30) cc_final: 0.8012 (tt0) REVERT: X 350 TYR cc_start: 0.9407 (m-80) cc_final: 0.8741 (m-80) REVERT: Y 149 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.6661 (p90) REVERT: Y 153 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8359 (ttmm) REVERT: Y 205 MET cc_start: 0.8583 (mmm) cc_final: 0.7865 (mmt) REVERT: Y 249 ARG cc_start: 0.6448 (tpt170) cc_final: 0.4679 (ttt90) REVERT: Y 290 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8671 (tptp) REVERT: Y 367 TYR cc_start: 0.8268 (m-80) cc_final: 0.7958 (m-80) REVERT: Z 153 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8498 (ttmt) REVERT: Z 249 ARG cc_start: 0.6451 (tpt170) cc_final: 0.3323 (ttm170) REVERT: Z 265 GLU cc_start: 0.8649 (tp30) cc_final: 0.7983 (tt0) REVERT: Z 285 LYS cc_start: 0.8450 (ttpp) cc_final: 0.8108 (tttp) REVERT: Z 290 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8664 (tptp) REVERT: Z 391 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8632 (t70) REVERT: Z 405 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8506 (p) REVERT: a 89 MET cc_start: 0.5932 (mmm) cc_final: 0.5698 (mmm) REVERT: a 149 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6845 (p90) REVERT: a 205 MET cc_start: 0.7827 (mtm) cc_final: 0.7572 (mtt) REVERT: a 249 ARG cc_start: 0.6397 (tpt170) cc_final: 0.4741 (ttt90) REVERT: a 265 GLU cc_start: 0.8708 (tp30) cc_final: 0.8014 (tt0) REVERT: a 350 TYR cc_start: 0.9408 (m-80) cc_final: 0.8742 (m-80) REVERT: b 149 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.6670 (p90) REVERT: b 153 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8361 (ttmm) REVERT: b 205 MET cc_start: 0.8580 (mmm) cc_final: 0.7869 (mmt) REVERT: b 249 ARG cc_start: 0.6432 (tpt170) cc_final: 0.4669 (ttt90) REVERT: b 290 LYS cc_start: 0.8953 (mmmt) cc_final: 0.8665 (tptp) REVERT: b 367 TYR cc_start: 0.8259 (m-80) cc_final: 0.7950 (m-80) REVERT: c 153 LYS cc_start: 0.8847 (ttmt) cc_final: 0.8495 (ttmt) REVERT: c 249 ARG cc_start: 0.6466 (tpt170) cc_final: 0.3322 (ttm170) REVERT: c 265 GLU cc_start: 0.8652 (tp30) cc_final: 0.7984 (tt0) REVERT: c 285 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8120 (tttp) REVERT: c 290 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8666 (tptp) REVERT: c 391 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8631 (t70) REVERT: c 405 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8502 (p) REVERT: d 89 MET cc_start: 0.5928 (mmm) cc_final: 0.5698 (mmm) REVERT: d 149 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.6850 (p90) REVERT: d 205 MET cc_start: 0.7827 (mtm) cc_final: 0.7575 (mtt) REVERT: d 249 ARG cc_start: 0.6389 (tpt170) cc_final: 0.4741 (ttt90) REVERT: d 265 GLU cc_start: 0.8716 (tp30) cc_final: 0.8013 (tt0) REVERT: d 350 TYR cc_start: 0.9414 (m-80) cc_final: 0.8749 (m-80) REVERT: e 149 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.6663 (p90) REVERT: e 153 LYS cc_start: 0.8683 (ttmt) cc_final: 0.8364 (ttmm) REVERT: e 205 MET cc_start: 0.8581 (mmm) cc_final: 0.7874 (mmt) REVERT: e 249 ARG cc_start: 0.6449 (tpt170) cc_final: 0.4682 (ttt90) REVERT: e 290 LYS cc_start: 0.8950 (mmmt) cc_final: 0.8659 (tptp) REVERT: e 367 TYR cc_start: 0.8263 (m-80) cc_final: 0.7955 (m-80) REVERT: f 153 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8503 (ttmt) REVERT: f 157 TYR cc_start: 0.7682 (m-80) cc_final: 0.7123 (m-80) REVERT: f 249 ARG cc_start: 0.6460 (tpt170) cc_final: 0.3310 (ttm170) REVERT: f 265 GLU cc_start: 0.8664 (tp30) cc_final: 0.7991 (tt0) REVERT: f 285 LYS cc_start: 0.8462 (ttpp) cc_final: 0.8123 (tttp) REVERT: f 290 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8665 (tptp) REVERT: f 391 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8635 (t70) REVERT: f 405 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8502 (p) outliers start: 184 outliers final: 84 residues processed: 842 average time/residue: 0.4849 time to fit residues: 661.3586 Evaluate side-chains 739 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 639 time to evaluate : 4.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 168 GLU Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 168 GLU Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 236 ASP Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 168 GLU Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 236 ASP Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 168 GLU Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 236 ASP Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 405 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 24 optimal weight: 0.0980 chunk 432 optimal weight: 10.0000 chunk 259 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 333 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 262 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 ASN W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 69 GLN Z 105 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.100277 restraints weight = 54638.501| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.95 r_work: 0.3049 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36000 Z= 0.143 Angle : 0.628 7.272 48672 Z= 0.320 Chirality : 0.044 0.202 5268 Planarity : 0.004 0.032 6420 Dihedral : 5.652 55.896 4940 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 4.61 % Allowed : 21.33 % Favored : 74.06 % 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: -1.37 (0.13), residues: 4524 helix: 0.98 (0.12), residues: 1968 sheet: -0.40 (0.28), residues: 480 loop : -3.09 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Z 143 HIS 0.003 0.001 HIS e 297 PHE 0.012 0.001 PHE U 371 TYR 0.012 0.001 TYR Y 367 ARG 0.006 0.000 ARG U 103 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 1464) hydrogen bonds : angle 4.41921 ( 4068) covalent geometry : bond 0.00341 (36000) covalent geometry : angle 0.62835 (48672) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 671 time to evaluate : 3.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 149 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.6876 (p90) REVERT: U 249 ARG cc_start: 0.6361 (tpt170) cc_final: 0.3438 (ttm170) REVERT: U 265 GLU cc_start: 0.8718 (tp30) cc_final: 0.7975 (tt0) REVERT: U 350 TYR cc_start: 0.9436 (m-80) cc_final: 0.8758 (m-80) REVERT: V 149 PHE cc_start: 0.8444 (OUTLIER) cc_final: 0.6715 (p90) REVERT: V 153 LYS cc_start: 0.8715 (ttmt) cc_final: 0.8370 (ttmm) REVERT: V 205 MET cc_start: 0.8767 (mmm) cc_final: 0.8161 (mmt) REVERT: V 249 ARG cc_start: 0.6174 (tpt170) cc_final: 0.3295 (ttm170) REVERT: V 285 LYS cc_start: 0.8312 (tttt) cc_final: 0.8032 (tttp) REVERT: V 367 TYR cc_start: 0.8272 (m-80) cc_final: 0.7968 (m-80) REVERT: W 99 GLN cc_start: 0.8925 (mm-40) cc_final: 0.8513 (mp10) REVERT: W 149 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7860 (p90) REVERT: W 153 LYS cc_start: 0.8851 (ttmt) cc_final: 0.8479 (ttmt) REVERT: W 249 ARG cc_start: 0.6396 (tpt170) cc_final: 0.3255 (ttm170) REVERT: W 290 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8713 (tptp) REVERT: W 391 ASP cc_start: 0.8983 (OUTLIER) cc_final: 0.8640 (t70) REVERT: W 405 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8511 (p) REVERT: X 149 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6874 (p90) REVERT: X 205 MET cc_start: 0.7831 (mtm) cc_final: 0.7605 (mtt) REVERT: X 249 ARG cc_start: 0.6389 (tpt170) cc_final: 0.3446 (ttm170) REVERT: X 265 GLU cc_start: 0.8710 (tp30) cc_final: 0.7976 (tt0) REVERT: X 350 TYR cc_start: 0.9431 (m-80) cc_final: 0.8758 (m-80) REVERT: Y 149 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.6727 (p90) REVERT: Y 153 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8374 (ttmm) REVERT: Y 205 MET cc_start: 0.8767 (mmm) cc_final: 0.8164 (mmt) REVERT: Y 249 ARG cc_start: 0.6174 (tpt170) cc_final: 0.3304 (ttm170) REVERT: Y 285 LYS cc_start: 0.8317 (tttt) cc_final: 0.8036 (tttp) REVERT: Y 367 TYR cc_start: 0.8271 (m-80) cc_final: 0.7967 (m-80) REVERT: Z 99 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8515 (mp10) REVERT: Z 149 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7870 (p90) REVERT: Z 153 LYS cc_start: 0.8862 (ttmt) cc_final: 0.8491 (ttmt) REVERT: Z 249 ARG cc_start: 0.6408 (tpt170) cc_final: 0.3258 (ttm170) REVERT: Z 290 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8709 (tptp) REVERT: Z 391 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8636 (t70) REVERT: Z 405 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8505 (p) REVERT: a 149 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.6881 (p90) REVERT: a 205 MET cc_start: 0.7833 (mtm) cc_final: 0.7604 (mtt) REVERT: a 249 ARG cc_start: 0.6405 (tpt170) cc_final: 0.3451 (ttm170) REVERT: a 265 GLU cc_start: 0.8713 (tp30) cc_final: 0.7979 (tt0) REVERT: a 350 TYR cc_start: 0.9433 (m-80) cc_final: 0.8757 (m-80) REVERT: b 149 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.6728 (p90) REVERT: b 153 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8370 (ttmm) REVERT: b 205 MET cc_start: 0.8767 (mmm) cc_final: 0.8163 (mmt) REVERT: b 249 ARG cc_start: 0.6171 (tpt170) cc_final: 0.3302 (ttm170) REVERT: b 285 LYS cc_start: 0.8306 (tttt) cc_final: 0.8025 (tttp) REVERT: b 367 TYR cc_start: 0.8262 (m-80) cc_final: 0.7959 (m-80) REVERT: c 99 GLN cc_start: 0.8922 (mm-40) cc_final: 0.8510 (mp10) REVERT: c 149 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.7874 (p90) REVERT: c 153 LYS cc_start: 0.8855 (ttmt) cc_final: 0.8484 (ttmt) REVERT: c 249 ARG cc_start: 0.6403 (tpt170) cc_final: 0.3261 (ttm170) REVERT: c 290 LYS cc_start: 0.9066 (mmmt) cc_final: 0.8720 (tptp) REVERT: c 391 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8634 (t70) REVERT: c 405 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8508 (p) REVERT: d 149 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6880 (p90) REVERT: d 205 MET cc_start: 0.7833 (mtm) cc_final: 0.7607 (mtt) REVERT: d 249 ARG cc_start: 0.6373 (tpt170) cc_final: 0.3440 (ttm170) REVERT: d 265 GLU cc_start: 0.8710 (tp30) cc_final: 0.7973 (tt0) REVERT: d 350 TYR cc_start: 0.9437 (m-80) cc_final: 0.8762 (m-80) REVERT: e 149 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6725 (p90) REVERT: e 153 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8372 (ttmm) REVERT: e 205 MET cc_start: 0.8769 (mmm) cc_final: 0.8165 (mmt) REVERT: e 249 ARG cc_start: 0.6178 (tpt170) cc_final: 0.3295 (ttm170) REVERT: e 285 LYS cc_start: 0.8306 (tttt) cc_final: 0.8025 (tttp) REVERT: e 367 TYR cc_start: 0.8268 (m-80) cc_final: 0.7966 (m-80) REVERT: f 99 GLN cc_start: 0.8924 (mm-40) cc_final: 0.8511 (mp10) REVERT: f 149 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7870 (p90) REVERT: f 153 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8489 (ttmt) REVERT: f 249 ARG cc_start: 0.6394 (tpt170) cc_final: 0.3252 (ttm170) REVERT: f 290 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8711 (tptp) REVERT: f 391 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8640 (t70) REVERT: f 405 THR cc_start: 0.8717 (OUTLIER) cc_final: 0.8508 (p) outliers start: 172 outliers final: 100 residues processed: 787 average time/residue: 0.4681 time to fit residues: 594.1116 Evaluate side-chains 782 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 662 time to evaluate : 4.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 168 GLU Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain W residue 405 THR Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain c residue 405 THR Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 168 GLU Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Chi-restraints excluded: chain f residue 405 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 158 optimal weight: 3.9990 chunk 166 optimal weight: 0.6980 chunk 278 optimal weight: 0.0670 chunk 101 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 267 optimal weight: 10.0000 chunk 384 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 337 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 417 optimal weight: 3.9990 overall best weight: 1.7524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 105 ASN W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 ASN ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100502 restraints weight = 54460.783| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.94 r_work: 0.3049 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36000 Z= 0.141 Angle : 0.622 7.349 48672 Z= 0.317 Chirality : 0.044 0.199 5268 Planarity : 0.004 0.074 6420 Dihedral : 5.108 51.416 4916 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 4.50 % Allowed : 22.03 % Favored : 73.47 % 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: -1.24 (0.13), residues: 4524 helix: 1.08 (0.12), residues: 1968 sheet: -0.32 (0.28), residues: 480 loop : -3.00 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 143 HIS 0.002 0.001 HIS V 297 PHE 0.011 0.001 PHE a 371 TYR 0.011 0.001 TYR b 367 ARG 0.004 0.000 ARG U 103 Details of bonding type rmsd hydrogen bonds : bond 0.03144 ( 1464) hydrogen bonds : angle 4.37942 ( 4068) covalent geometry : bond 0.00334 (36000) covalent geometry : angle 0.62150 (48672) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 684 time to evaluate : 4.038 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: U 149 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.6813 (p90) REVERT: U 205 MET cc_start: 0.8052 (mmt) cc_final: 0.7837 (mmt) REVERT: U 249 ARG cc_start: 0.6322 (tpt170) cc_final: 0.3397 (ttm170) REVERT: U 350 TYR cc_start: 0.9421 (m-80) cc_final: 0.8721 (m-80) REVERT: U 361 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6765 (p90) REVERT: V 149 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.6713 (p90) REVERT: V 153 LYS cc_start: 0.8731 (ttmt) cc_final: 0.8417 (ttmm) REVERT: V 249 ARG cc_start: 0.6192 (tpt170) cc_final: 0.3271 (ttm170) REVERT: V 367 TYR cc_start: 0.8316 (m-80) cc_final: 0.8000 (m-80) REVERT: V 371 PHE cc_start: 0.6115 (OUTLIER) cc_final: 0.5167 (p90) REVERT: V 391 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8622 (t0) REVERT: W 99 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8552 (mp10) REVERT: W 149 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7905 (p90) REVERT: W 153 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8479 (ttmt) REVERT: W 205 MET cc_start: 0.8666 (mmm) cc_final: 0.8420 (mmt) REVERT: W 249 ARG cc_start: 0.6356 (tpt170) cc_final: 0.3204 (ttm170) REVERT: W 290 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8687 (tptp) REVERT: W 391 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8638 (t70) REVERT: X 149 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.6820 (p90) REVERT: X 205 MET cc_start: 0.7808 (mtm) cc_final: 0.7577 (mtt) REVERT: X 249 ARG cc_start: 0.6325 (tpt170) cc_final: 0.3402 (ttm170) REVERT: X 350 TYR cc_start: 0.9416 (m-80) cc_final: 0.8722 (m-80) REVERT: X 361 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.6841 (p90) REVERT: Y 149 PHE cc_start: 0.8450 (OUTLIER) cc_final: 0.6718 (p90) REVERT: Y 153 LYS cc_start: 0.8733 (ttmt) cc_final: 0.8418 (ttmm) REVERT: Y 249 ARG cc_start: 0.6182 (tpt170) cc_final: 0.3265 (ttm170) REVERT: Y 367 TYR cc_start: 0.8313 (m-80) cc_final: 0.7997 (m-80) REVERT: Y 371 PHE cc_start: 0.6095 (OUTLIER) cc_final: 0.5134 (p90) REVERT: Y 391 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8619 (t0) REVERT: Z 99 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8552 (mp10) REVERT: Z 149 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7922 (p90) REVERT: Z 153 LYS cc_start: 0.8872 (ttmt) cc_final: 0.8488 (ttmt) REVERT: Z 205 MET cc_start: 0.8671 (mmm) cc_final: 0.8415 (mmt) REVERT: Z 249 ARG cc_start: 0.6346 (tpt170) cc_final: 0.3198 (ttm170) REVERT: Z 290 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8682 (tptp) REVERT: Z 391 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8637 (t70) REVERT: a 149 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.6819 (p90) REVERT: a 205 MET cc_start: 0.7810 (mtm) cc_final: 0.7580 (mtt) REVERT: a 249 ARG cc_start: 0.6323 (tpt170) cc_final: 0.3398 (ttm170) REVERT: a 350 TYR cc_start: 0.9417 (m-80) cc_final: 0.8720 (m-80) REVERT: a 361 PHE cc_start: 0.8006 (OUTLIER) cc_final: 0.6838 (p90) REVERT: b 149 PHE cc_start: 0.8454 (OUTLIER) cc_final: 0.6725 (p90) REVERT: b 153 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8413 (ttmm) REVERT: b 249 ARG cc_start: 0.6170 (tpt170) cc_final: 0.3258 (ttm170) REVERT: b 367 TYR cc_start: 0.8309 (m-80) cc_final: 0.7994 (m-80) REVERT: b 371 PHE cc_start: 0.6100 (OUTLIER) cc_final: 0.5141 (p90) REVERT: b 391 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8630 (t0) REVERT: c 99 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8543 (mp10) REVERT: c 149 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7921 (p90) REVERT: c 153 LYS cc_start: 0.8867 (ttmt) cc_final: 0.8482 (ttmt) REVERT: c 205 MET cc_start: 0.8670 (mmm) cc_final: 0.8414 (mmt) REVERT: c 249 ARG cc_start: 0.6346 (tpt170) cc_final: 0.3197 (ttm170) REVERT: c 290 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8688 (tptp) REVERT: c 391 ASP cc_start: 0.8968 (OUTLIER) cc_final: 0.8635 (t70) REVERT: d 149 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.6821 (p90) REVERT: d 205 MET cc_start: 0.7821 (mtm) cc_final: 0.7594 (mtt) REVERT: d 249 ARG cc_start: 0.6317 (tpt170) cc_final: 0.3399 (ttm170) REVERT: d 350 TYR cc_start: 0.9423 (m-80) cc_final: 0.8727 (m-80) REVERT: d 361 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.6838 (p90) REVERT: e 149 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.6720 (p90) REVERT: e 153 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8414 (ttmm) REVERT: e 249 ARG cc_start: 0.6175 (tpt170) cc_final: 0.3251 (ttm170) REVERT: e 367 TYR cc_start: 0.8313 (m-80) cc_final: 0.8000 (m-80) REVERT: e 371 PHE cc_start: 0.6107 (OUTLIER) cc_final: 0.5150 (p90) REVERT: e 391 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8627 (t0) REVERT: f 99 GLN cc_start: 0.8953 (mm-40) cc_final: 0.8546 (mp10) REVERT: f 149 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7911 (p90) REVERT: f 153 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8491 (ttmt) REVERT: f 249 ARG cc_start: 0.6337 (tpt170) cc_final: 0.3188 (ttm170) REVERT: f 290 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8684 (tptp) REVERT: f 391 ASP cc_start: 0.8970 (OUTLIER) cc_final: 0.8640 (t70) outliers start: 168 outliers final: 110 residues processed: 796 average time/residue: 0.4598 time to fit residues: 593.3413 Evaluate side-chains 818 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 680 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 391 ASP Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 355 GLU Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 391 ASP Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 69 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 168 GLU Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 355 GLU Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 69 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 168 GLU Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 355 GLU Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 391 ASP Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 69 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 143 optimal weight: 5.9990 chunk 292 optimal weight: 0.4980 chunk 412 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 236 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 8.9990 chunk 217 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 ASN ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.138172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099550 restraints weight = 53896.537| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.88 r_work: 0.3058 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 36000 Z= 0.158 Angle : 0.635 7.398 48672 Z= 0.323 Chirality : 0.044 0.195 5268 Planarity : 0.004 0.055 6420 Dihedral : 5.014 45.235 4910 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.30 % Favored : 88.70 % Rotamer: Outliers : 4.64 % Allowed : 22.64 % Favored : 72.72 % 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: -1.19 (0.13), residues: 4524 helix: 1.10 (0.12), residues: 1968 sheet: -0.28 (0.27), residues: 480 loop : -2.96 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 143 HIS 0.003 0.001 HIS Y 297 PHE 0.014 0.001 PHE U 371 TYR 0.015 0.001 TYR f 367 ARG 0.006 0.000 ARG a 103 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 1464) hydrogen bonds : angle 4.39412 ( 4068) covalent geometry : bond 0.00377 (36000) covalent geometry : angle 0.63482 (48672) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 869 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 696 time to evaluate : 4.052 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: U 149 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.6917 (p90) REVERT: U 249 ARG cc_start: 0.6313 (tpt170) cc_final: 0.3412 (ttm170) REVERT: U 350 TYR cc_start: 0.9478 (m-80) cc_final: 0.8751 (m-80) REVERT: U 361 PHE cc_start: 0.8074 (OUTLIER) cc_final: 0.6964 (p90) REVERT: V 149 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.6786 (p90) REVERT: V 153 LYS cc_start: 0.8775 (ttmt) cc_final: 0.8547 (ttpt) REVERT: V 249 ARG cc_start: 0.6264 (tpt170) cc_final: 0.3377 (ttm170) REVERT: V 285 LYS cc_start: 0.8488 (tttt) cc_final: 0.8250 (tttp) REVERT: V 371 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5133 (p90) REVERT: V 391 ASP cc_start: 0.9018 (OUTLIER) cc_final: 0.8673 (t0) REVERT: W 99 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8502 (mp10) REVERT: W 149 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8008 (p90) REVERT: W 153 LYS cc_start: 0.8926 (ttmt) cc_final: 0.8611 (ttmt) REVERT: W 205 MET cc_start: 0.8596 (mmm) cc_final: 0.8075 (mmp) REVERT: W 249 ARG cc_start: 0.6488 (tpt170) cc_final: 0.3389 (ttm170) REVERT: W 290 LYS cc_start: 0.9061 (mmmt) cc_final: 0.8692 (tptp) REVERT: W 361 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7675 (p90) REVERT: W 391 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8655 (t70) REVERT: X 149 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.6884 (p90) REVERT: X 205 MET cc_start: 0.7830 (mtm) cc_final: 0.7582 (mtt) REVERT: X 249 ARG cc_start: 0.6322 (tpt170) cc_final: 0.3411 (ttm170) REVERT: X 350 TYR cc_start: 0.9474 (m-80) cc_final: 0.8750 (m-80) REVERT: X 361 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6880 (p90) REVERT: Y 149 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.6792 (p90) REVERT: Y 153 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8547 (ttpt) REVERT: Y 249 ARG cc_start: 0.6262 (tpt170) cc_final: 0.3373 (ttm170) REVERT: Y 285 LYS cc_start: 0.8486 (tttt) cc_final: 0.8249 (tttp) REVERT: Y 371 PHE cc_start: 0.6083 (OUTLIER) cc_final: 0.5108 (p90) REVERT: Y 391 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8679 (t0) REVERT: Z 99 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8504 (mp10) REVERT: Z 149 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8008 (p90) REVERT: Z 153 LYS cc_start: 0.8923 (ttmt) cc_final: 0.8607 (ttmt) REVERT: Z 205 MET cc_start: 0.8598 (mmm) cc_final: 0.8080 (mmp) REVERT: Z 249 ARG cc_start: 0.6491 (tpt170) cc_final: 0.3382 (ttm170) REVERT: Z 290 LYS cc_start: 0.9064 (mmmt) cc_final: 0.8697 (tptp) REVERT: Z 361 PHE cc_start: 0.8195 (OUTLIER) cc_final: 0.7681 (p90) REVERT: Z 391 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8656 (t70) REVERT: a 149 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.6895 (p90) REVERT: a 205 MET cc_start: 0.7832 (mtm) cc_final: 0.7586 (mtt) REVERT: a 249 ARG cc_start: 0.6329 (tpt170) cc_final: 0.3404 (ttm170) REVERT: a 350 TYR cc_start: 0.9474 (m-80) cc_final: 0.8751 (m-80) REVERT: a 361 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6878 (p90) REVERT: b 149 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.6790 (p90) REVERT: b 153 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8554 (ttpt) REVERT: b 249 ARG cc_start: 0.6265 (tpt170) cc_final: 0.3376 (ttm170) REVERT: b 285 LYS cc_start: 0.8487 (tttt) cc_final: 0.8248 (tttp) REVERT: b 371 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5106 (p90) REVERT: b 391 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8687 (t0) REVERT: c 99 GLN cc_start: 0.9040 (mm-40) cc_final: 0.8501 (mp10) REVERT: c 149 PHE cc_start: 0.8626 (OUTLIER) cc_final: 0.8013 (p90) REVERT: c 153 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8619 (ttmt) REVERT: c 205 MET cc_start: 0.8598 (mmm) cc_final: 0.8077 (mmp) REVERT: c 249 ARG cc_start: 0.6490 (tpt170) cc_final: 0.3377 (ttm170) REVERT: c 290 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8694 (tptp) REVERT: c 361 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7681 (p90) REVERT: c 391 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8657 (t70) REVERT: d 149 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.6897 (p90) REVERT: d 205 MET cc_start: 0.7843 (mtm) cc_final: 0.7597 (mtt) REVERT: d 249 ARG cc_start: 0.6336 (tpt170) cc_final: 0.3415 (ttm170) REVERT: d 350 TYR cc_start: 0.9478 (m-80) cc_final: 0.8756 (m-80) REVERT: d 361 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.6876 (p90) REVERT: e 149 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.6791 (p90) REVERT: e 153 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8544 (ttpt) REVERT: e 249 ARG cc_start: 0.6254 (tpt170) cc_final: 0.3381 (ttm170) REVERT: e 285 LYS cc_start: 0.8493 (tttt) cc_final: 0.8257 (tttp) REVERT: e 371 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.5127 (p90) REVERT: e 391 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8685 (t0) REVERT: f 99 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8502 (mp10) REVERT: f 149 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8011 (p90) REVERT: f 153 LYS cc_start: 0.8929 (ttmt) cc_final: 0.8616 (ttmt) REVERT: f 249 ARG cc_start: 0.6467 (tpt170) cc_final: 0.3385 (ttm170) REVERT: f 290 LYS cc_start: 0.9060 (mmmt) cc_final: 0.8694 (tptp) REVERT: f 361 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7667 (p90) REVERT: f 391 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8654 (t70) outliers start: 173 outliers final: 111 residues processed: 816 average time/residue: 0.4633 time to fit residues: 617.8751 Evaluate side-chains 836 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 693 time to evaluate : 3.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 232 ILE Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 246 THR Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 232 ILE Chi-restraints excluded: chain V residue 241 SER Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 391 ASP Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 232 ILE Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 246 THR Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 372 ASP Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 232 ILE Chi-restraints excluded: chain Y residue 241 SER Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 391 ASP Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 69 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 232 ILE Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 246 THR Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 372 ASP Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 232 ILE Chi-restraints excluded: chain b residue 241 SER Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 391 ASP Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 69 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 232 ILE Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 246 THR Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 372 ASP Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 232 ILE Chi-restraints excluded: chain e residue 241 SER Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 391 ASP Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 69 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 12 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 359 optimal weight: 0.5980 chunk 170 optimal weight: 0.0370 chunk 372 optimal weight: 3.9990 chunk 44 optimal weight: 0.3980 chunk 329 optimal weight: 0.0020 chunk 340 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 450 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 overall best weight: 0.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 140 ASN W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 ASN Z 105 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN c 105 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 ASN f 105 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103270 restraints weight = 54162.017| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.93 r_work: 0.3092 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 36000 Z= 0.114 Angle : 0.605 7.568 48672 Z= 0.308 Chirality : 0.043 0.185 5268 Planarity : 0.004 0.074 6420 Dihedral : 4.757 27.880 4904 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.25 % Favored : 88.75 % Rotamer: Outliers : 3.80 % Allowed : 23.90 % Favored : 72.29 % 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: -1.00 (0.13), residues: 4524 helix: 1.21 (0.13), residues: 1956 sheet: 0.18 (0.33), residues: 360 loop : -2.73 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 143 HIS 0.001 0.000 HIS b 54 PHE 0.013 0.001 PHE U 30 TYR 0.011 0.001 TYR f 367 ARG 0.005 0.000 ARG X 103 Details of bonding type rmsd hydrogen bonds : bond 0.02696 ( 1464) hydrogen bonds : angle 4.26915 ( 4068) covalent geometry : bond 0.00255 (36000) covalent geometry : angle 0.60490 (48672) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 762 time to evaluate : 4.048 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: U 149 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.6736 (p90) REVERT: U 249 ARG cc_start: 0.6137 (tpt170) cc_final: 0.3328 (ttm170) REVERT: U 345 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.9025 (p) REVERT: U 350 TYR cc_start: 0.9449 (m-80) cc_final: 0.8659 (m-80) REVERT: U 361 PHE cc_start: 0.7795 (OUTLIER) cc_final: 0.6915 (p90) REVERT: U 403 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.8529 (pp20) REVERT: V 149 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6638 (p90) REVERT: V 153 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8430 (ttpt) REVERT: V 208 ASP cc_start: 0.8253 (t0) cc_final: 0.7815 (p0) REVERT: V 249 ARG cc_start: 0.6068 (tpt170) cc_final: 0.5299 (tpt170) REVERT: V 285 LYS cc_start: 0.8340 (tttt) cc_final: 0.8072 (tttp) REVERT: V 403 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8611 (pp20) REVERT: W 99 GLN cc_start: 0.8997 (mm-40) cc_final: 0.8491 (mp10) REVERT: W 149 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7891 (p90) REVERT: W 153 LYS cc_start: 0.8845 (ttmt) cc_final: 0.8495 (ttmt) REVERT: W 205 MET cc_start: 0.8640 (mmm) cc_final: 0.8158 (mmt) REVERT: W 228 MET cc_start: 0.9093 (mmp) cc_final: 0.8703 (mmm) REVERT: W 249 ARG cc_start: 0.6142 (tpt170) cc_final: 0.3369 (ttm170) REVERT: W 290 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8660 (tptp) REVERT: W 361 PHE cc_start: 0.7937 (OUTLIER) cc_final: 0.7264 (p90) REVERT: W 403 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8618 (pp20) REVERT: X 149 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.6738 (p90) REVERT: X 205 MET cc_start: 0.7681 (mtm) cc_final: 0.7407 (mtt) REVERT: X 208 ASP cc_start: 0.8079 (t0) cc_final: 0.7824 (m-30) REVERT: X 249 ARG cc_start: 0.6175 (tpt170) cc_final: 0.3341 (ttm170) REVERT: X 345 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.9022 (p) REVERT: X 350 TYR cc_start: 0.9441 (m-80) cc_final: 0.8654 (m-80) REVERT: X 361 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.6883 (p90) REVERT: X 403 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8522 (pp20) REVERT: Y 149 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.6662 (p90) REVERT: Y 153 LYS cc_start: 0.8661 (ttmt) cc_final: 0.8434 (ttpt) REVERT: Y 208 ASP cc_start: 0.8252 (t0) cc_final: 0.7815 (p0) REVERT: Y 249 ARG cc_start: 0.6081 (tpt170) cc_final: 0.5306 (tpt170) REVERT: Y 285 LYS cc_start: 0.8339 (tttt) cc_final: 0.8072 (tttp) REVERT: Y 403 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8605 (pp20) REVERT: Z 99 GLN cc_start: 0.8995 (mm-40) cc_final: 0.8492 (mp10) REVERT: Z 149 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7900 (p90) REVERT: Z 153 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8498 (ttmt) REVERT: Z 205 MET cc_start: 0.8642 (mmm) cc_final: 0.8157 (mmt) REVERT: Z 228 MET cc_start: 0.9095 (mmp) cc_final: 0.8706 (mmm) REVERT: Z 249 ARG cc_start: 0.6159 (tpt170) cc_final: 0.3378 (ttm170) REVERT: Z 290 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8661 (tptp) REVERT: Z 361 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7271 (p90) REVERT: Z 403 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: a 149 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.6740 (p90) REVERT: a 205 MET cc_start: 0.7681 (mtm) cc_final: 0.7406 (mtt) REVERT: a 208 ASP cc_start: 0.8071 (t0) cc_final: 0.7819 (m-30) REVERT: a 249 ARG cc_start: 0.6188 (tpt170) cc_final: 0.3350 (ttm170) REVERT: a 345 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.9023 (p) REVERT: a 350 TYR cc_start: 0.9442 (m-80) cc_final: 0.8656 (m-80) REVERT: a 361 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.6879 (p90) REVERT: a 403 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8520 (pp20) REVERT: b 149 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.6672 (p90) REVERT: b 153 LYS cc_start: 0.8656 (ttmt) cc_final: 0.8429 (ttpt) REVERT: b 208 ASP cc_start: 0.8237 (t0) cc_final: 0.7808 (p0) REVERT: b 249 ARG cc_start: 0.6059 (tpt170) cc_final: 0.5296 (tpt170) REVERT: b 285 LYS cc_start: 0.8347 (tttt) cc_final: 0.8079 (tttp) REVERT: b 403 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8598 (pp20) REVERT: c 99 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8483 (mp10) REVERT: c 149 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.7890 (p90) REVERT: c 153 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8499 (ttmt) REVERT: c 205 MET cc_start: 0.8637 (mmm) cc_final: 0.8157 (mmt) REVERT: c 228 MET cc_start: 0.9088 (mmp) cc_final: 0.8699 (mmm) REVERT: c 249 ARG cc_start: 0.6177 (tpt170) cc_final: 0.3377 (ttm170) REVERT: c 290 LYS cc_start: 0.9048 (mmmt) cc_final: 0.8663 (tptp) REVERT: c 361 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7265 (p90) REVERT: c 403 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8623 (pp20) REVERT: d 149 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.6736 (p90) REVERT: d 205 MET cc_start: 0.7701 (mtm) cc_final: 0.7429 (mtt) REVERT: d 208 ASP cc_start: 0.8076 (t0) cc_final: 0.7826 (m-30) REVERT: d 249 ARG cc_start: 0.6168 (tpt170) cc_final: 0.3339 (ttm170) REVERT: d 345 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.9019 (p) REVERT: d 350 TYR cc_start: 0.9444 (m-80) cc_final: 0.8656 (m-80) REVERT: d 361 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.6882 (p90) REVERT: d 403 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8525 (pp20) REVERT: e 149 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.6661 (p90) REVERT: e 153 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8435 (ttpt) REVERT: e 208 ASP cc_start: 0.8253 (t0) cc_final: 0.7818 (p0) REVERT: e 249 ARG cc_start: 0.6062 (tpt170) cc_final: 0.5300 (tpt170) REVERT: e 285 LYS cc_start: 0.8346 (tttt) cc_final: 0.8076 (tttp) REVERT: e 403 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8603 (pp20) REVERT: f 99 GLN cc_start: 0.8991 (mm-40) cc_final: 0.8486 (mp10) REVERT: f 149 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7895 (p90) REVERT: f 153 LYS cc_start: 0.8852 (ttmt) cc_final: 0.8503 (ttmt) REVERT: f 228 MET cc_start: 0.9086 (mmp) cc_final: 0.8700 (mmm) REVERT: f 249 ARG cc_start: 0.6172 (tpt170) cc_final: 0.3366 (ttm170) REVERT: f 290 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8659 (tptp) REVERT: f 361 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7263 (p90) REVERT: f 403 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8629 (pp20) outliers start: 142 outliers final: 85 residues processed: 863 average time/residue: 0.4691 time to fit residues: 659.6117 Evaluate side-chains 811 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 690 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 258 GLU Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 372 ASP Chi-restraints excluded: chain U residue 403 GLU Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 355 GLU Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 258 GLU Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 403 GLU Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 355 GLU Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 258 GLU Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 355 GLU Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 258 GLU Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 403 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 95 optimal weight: 5.9990 chunk 367 optimal weight: 0.3980 chunk 220 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 53 optimal weight: 0.0170 chunk 439 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 374 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN U 140 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 ASN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 140 ASN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.142512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103577 restraints weight = 54421.020| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.94 r_work: 0.3095 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36000 Z= 0.113 Angle : 0.605 8.271 48672 Z= 0.307 Chirality : 0.043 0.173 5268 Planarity : 0.004 0.052 6420 Dihedral : 4.629 27.010 4896 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 3.78 % Allowed : 24.30 % Favored : 71.92 % 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: -0.95 (0.13), residues: 4524 helix: 1.23 (0.13), residues: 1956 sheet: 0.06 (0.32), residues: 360 loop : -2.64 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Y 143 HIS 0.001 0.000 HIS Y 297 PHE 0.012 0.001 PHE a 30 TYR 0.017 0.001 TYR Y 367 ARG 0.004 0.000 ARG a 103 Details of bonding type rmsd hydrogen bonds : bond 0.02699 ( 1464) hydrogen bonds : angle 4.20344 ( 4068) covalent geometry : bond 0.00257 (36000) covalent geometry : angle 0.60476 (48672) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 706 time to evaluate : 4.618 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: U 149 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.6795 (p90) REVERT: U 249 ARG cc_start: 0.6104 (tpt170) cc_final: 0.3340 (ttm170) REVERT: U 345 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.9012 (p) REVERT: U 350 TYR cc_start: 0.9465 (m-80) cc_final: 0.8666 (m-80) REVERT: U 361 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6883 (p90) REVERT: U 403 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: V 149 PHE cc_start: 0.8332 (OUTLIER) cc_final: 0.6740 (p90) REVERT: V 153 LYS cc_start: 0.8662 (ttmt) cc_final: 0.8432 (ttpt) REVERT: V 183 ASN cc_start: 0.7506 (m-40) cc_final: 0.7304 (m110) REVERT: V 208 ASP cc_start: 0.8324 (t0) cc_final: 0.7805 (p0) REVERT: V 249 ARG cc_start: 0.6048 (tpt170) cc_final: 0.5257 (tpt170) REVERT: V 371 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.4925 (p90) REVERT: V 403 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8600 (pp20) REVERT: W 99 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8500 (mp10) REVERT: W 153 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8432 (ttmt) REVERT: W 228 MET cc_start: 0.9098 (mmp) cc_final: 0.8730 (mmm) REVERT: W 249 ARG cc_start: 0.6131 (tpt170) cc_final: 0.3398 (ttm170) REVERT: W 265 GLU cc_start: 0.8680 (tp30) cc_final: 0.7944 (tt0) REVERT: W 290 LYS cc_start: 0.8971 (mmmt) cc_final: 0.8626 (tptp) REVERT: W 361 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7367 (p90) REVERT: W 403 GLU cc_start: 0.9137 (OUTLIER) cc_final: 0.8621 (pp20) REVERT: X 149 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.6784 (p90) REVERT: X 205 MET cc_start: 0.7645 (mtm) cc_final: 0.7344 (mtt) REVERT: X 208 ASP cc_start: 0.8078 (t0) cc_final: 0.7830 (m-30) REVERT: X 249 ARG cc_start: 0.6139 (tpt170) cc_final: 0.3353 (ttm170) REVERT: X 345 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.9009 (p) REVERT: X 350 TYR cc_start: 0.9456 (m-80) cc_final: 0.8651 (m-80) REVERT: X 361 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.6981 (p90) REVERT: X 403 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8510 (pp20) REVERT: Y 149 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.6769 (p90) REVERT: Y 153 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8444 (ttpt) REVERT: Y 183 ASN cc_start: 0.7503 (m-40) cc_final: 0.7302 (m110) REVERT: Y 208 ASP cc_start: 0.8238 (t0) cc_final: 0.7807 (p0) REVERT: Y 249 ARG cc_start: 0.6065 (tpt170) cc_final: 0.5267 (tpt170) REVERT: Y 371 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4925 (p90) REVERT: Y 403 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8590 (pp20) REVERT: Z 99 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8498 (mp10) REVERT: Z 149 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7982 (p90) REVERT: Z 153 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8431 (ttmt) REVERT: Z 228 MET cc_start: 0.9100 (mmp) cc_final: 0.8733 (mmm) REVERT: Z 249 ARG cc_start: 0.6148 (tpt170) cc_final: 0.3402 (ttm170) REVERT: Z 265 GLU cc_start: 0.8680 (tp30) cc_final: 0.7950 (tt0) REVERT: Z 290 LYS cc_start: 0.8966 (mmmt) cc_final: 0.8619 (tptp) REVERT: Z 361 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7371 (p90) REVERT: Z 403 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8626 (pp20) REVERT: a 149 PHE cc_start: 0.8297 (OUTLIER) cc_final: 0.6777 (p90) REVERT: a 205 MET cc_start: 0.7650 (mtm) cc_final: 0.7349 (mtt) REVERT: a 208 ASP cc_start: 0.8080 (t0) cc_final: 0.7834 (m-30) REVERT: a 249 ARG cc_start: 0.6156 (tpt170) cc_final: 0.3360 (ttm170) REVERT: a 345 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.9008 (p) REVERT: a 350 TYR cc_start: 0.9456 (m-80) cc_final: 0.8656 (m-80) REVERT: a 361 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.6985 (p90) REVERT: a 403 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8516 (pp20) REVERT: b 149 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.6775 (p90) REVERT: b 153 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8436 (ttpt) REVERT: b 183 ASN cc_start: 0.7514 (m-40) cc_final: 0.7314 (m110) REVERT: b 208 ASP cc_start: 0.8227 (t0) cc_final: 0.7807 (p0) REVERT: b 249 ARG cc_start: 0.6037 (tpt170) cc_final: 0.5252 (tpt170) REVERT: b 371 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.4925 (p90) REVERT: b 403 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: c 99 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8495 (mp10) REVERT: c 153 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8438 (ttmt) REVERT: c 228 MET cc_start: 0.9099 (mmp) cc_final: 0.8731 (mmm) REVERT: c 249 ARG cc_start: 0.6146 (tpt170) cc_final: 0.3398 (ttm170) REVERT: c 265 GLU cc_start: 0.8680 (tp30) cc_final: 0.7951 (tt0) REVERT: c 290 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8625 (tptp) REVERT: c 361 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7372 (p90) REVERT: c 403 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8623 (pp20) REVERT: d 149 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.6783 (p90) REVERT: d 205 MET cc_start: 0.7664 (mtm) cc_final: 0.7363 (mtt) REVERT: d 208 ASP cc_start: 0.8084 (t0) cc_final: 0.7838 (m-30) REVERT: d 249 ARG cc_start: 0.6127 (tpt170) cc_final: 0.3351 (ttm170) REVERT: d 345 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.9009 (p) REVERT: d 350 TYR cc_start: 0.9461 (m-80) cc_final: 0.8659 (m-80) REVERT: d 361 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6982 (p90) REVERT: d 403 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8522 (pp20) REVERT: e 149 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6761 (p90) REVERT: e 153 LYS cc_start: 0.8671 (ttmt) cc_final: 0.8439 (ttpt) REVERT: e 183 ASN cc_start: 0.7509 (m-40) cc_final: 0.7305 (m110) REVERT: e 208 ASP cc_start: 0.8240 (t0) cc_final: 0.7811 (p0) REVERT: e 249 ARG cc_start: 0.6039 (tpt170) cc_final: 0.5249 (tpt170) REVERT: e 371 PHE cc_start: 0.6096 (OUTLIER) cc_final: 0.4923 (p90) REVERT: e 403 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8591 (pp20) REVERT: f 99 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8497 (mp10) REVERT: f 153 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8442 (ttmt) REVERT: f 228 MET cc_start: 0.9098 (mmp) cc_final: 0.8732 (mmm) REVERT: f 249 ARG cc_start: 0.6139 (tpt170) cc_final: 0.3386 (ttm170) REVERT: f 265 GLU cc_start: 0.8680 (tp30) cc_final: 0.7946 (tt0) REVERT: f 290 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8619 (tptp) REVERT: f 361 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7359 (p90) REVERT: f 403 GLU cc_start: 0.9141 (OUTLIER) cc_final: 0.8627 (pp20) outliers start: 141 outliers final: 91 residues processed: 799 average time/residue: 0.5013 time to fit residues: 647.9780 Evaluate side-chains 797 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 669 time to evaluate : 6.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 403 GLU Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 371 PHE Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 69 GLN Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 355 GLU Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 403 GLU Chi-restraints excluded: chain Y residue 140 ASN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 236 ASP Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 371 PHE Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 69 GLN Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 355 GLU Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain b residue 140 ASN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 236 ASP Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 371 PHE Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 69 GLN Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 355 GLU Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 403 GLU Chi-restraints excluded: chain e residue 140 ASN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 236 ASP Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 371 PHE Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 69 GLN Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 137 optimal weight: 0.0270 chunk 184 optimal weight: 0.8980 chunk 239 optimal weight: 9.9990 chunk 455 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 362 optimal weight: 0.7980 chunk 214 optimal weight: 2.9990 chunk 446 optimal weight: 5.9990 chunk 313 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 GLN V 215 GLN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN X 105 ASN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 ASN Y 215 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN a 105 ASN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN b 215 GLN ** d 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 ASN e 215 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.142691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.103533 restraints weight = 54382.185| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.94 r_work: 0.3095 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36000 Z= 0.117 Angle : 0.619 7.921 48672 Z= 0.312 Chirality : 0.043 0.187 5268 Planarity : 0.004 0.050 6420 Dihedral : 4.619 27.163 4896 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.27 % Allowed : 24.76 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.13), residues: 4524 helix: 1.24 (0.13), residues: 1956 sheet: 0.12 (0.32), residues: 360 loop : -2.65 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 143 HIS 0.001 0.000 HIS e 297 PHE 0.018 0.001 PHE Y 371 TYR 0.015 0.001 TYR V 367 ARG 0.005 0.000 ARG a 103 Details of bonding type rmsd hydrogen bonds : bond 0.02701 ( 1464) hydrogen bonds : angle 4.16629 ( 4068) covalent geometry : bond 0.00273 (36000) covalent geometry : angle 0.61897 (48672) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9048 Ramachandran restraints generated. 4524 Oldfield, 0 Emsley, 4524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 689 time to evaluate : 3.985 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: U 52 MET cc_start: 0.9185 (mmm) cc_final: 0.8821 (mmt) REVERT: U 149 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.6759 (p90) REVERT: U 205 MET cc_start: 0.6829 (mmm) cc_final: 0.6384 (mmm) REVERT: U 249 ARG cc_start: 0.6247 (tpt170) cc_final: 0.3388 (ttm170) REVERT: U 345 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8996 (p) REVERT: U 350 TYR cc_start: 0.9451 (m-80) cc_final: 0.8637 (m-80) REVERT: U 361 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6865 (p90) REVERT: U 403 GLU cc_start: 0.9105 (OUTLIER) cc_final: 0.8525 (pp20) REVERT: V 149 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.6709 (p90) REVERT: V 153 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8430 (ttpt) REVERT: V 183 ASN cc_start: 0.7507 (m-40) cc_final: 0.7301 (m110) REVERT: V 208 ASP cc_start: 0.8367 (t0) cc_final: 0.7657 (p0) REVERT: V 249 ARG cc_start: 0.6049 (tpt170) cc_final: 0.5241 (tpt170) REVERT: V 403 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8592 (pp20) REVERT: W 37 LYS cc_start: 0.8432 (ptmt) cc_final: 0.8208 (pttt) REVERT: W 99 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8483 (mp10) REVERT: W 149 PHE cc_start: 0.8487 (OUTLIER) cc_final: 0.7977 (p90) REVERT: W 153 LYS cc_start: 0.8830 (ttmt) cc_final: 0.8448 (ttmt) REVERT: W 249 ARG cc_start: 0.6137 (tpt170) cc_final: 0.3385 (ttm170) REVERT: W 265 GLU cc_start: 0.8736 (tp30) cc_final: 0.7988 (tt0) REVERT: W 290 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8627 (tptp) REVERT: W 361 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7293 (p90) REVERT: W 403 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8621 (pp20) REVERT: X 52 MET cc_start: 0.9189 (mmm) cc_final: 0.8823 (mmt) REVERT: X 149 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.6752 (p90) REVERT: X 205 MET cc_start: 0.7566 (mtm) cc_final: 0.7271 (mtt) REVERT: X 208 ASP cc_start: 0.8082 (t0) cc_final: 0.7828 (m-30) REVERT: X 249 ARG cc_start: 0.6284 (tpt170) cc_final: 0.3398 (ttm170) REVERT: X 345 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (p) REVERT: X 350 TYR cc_start: 0.9447 (m-80) cc_final: 0.8633 (m-80) REVERT: X 361 PHE cc_start: 0.7757 (OUTLIER) cc_final: 0.7003 (p90) REVERT: X 403 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8515 (pp20) REVERT: Y 140 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8129 (m-40) REVERT: Y 149 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6752 (p90) REVERT: Y 153 LYS cc_start: 0.8673 (ttmt) cc_final: 0.8439 (ttpt) REVERT: Y 183 ASN cc_start: 0.7505 (m-40) cc_final: 0.7299 (m110) REVERT: Y 208 ASP cc_start: 0.8360 (t0) cc_final: 0.7755 (p0) REVERT: Y 249 ARG cc_start: 0.6052 (tpt170) cc_final: 0.5207 (tpt170) REVERT: Y 403 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8586 (pp20) REVERT: Z 37 LYS cc_start: 0.8448 (ptmt) cc_final: 0.8222 (pttt) REVERT: Z 99 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8479 (mp10) REVERT: Z 149 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.7923 (p90) REVERT: Z 153 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8452 (ttmt) REVERT: Z 249 ARG cc_start: 0.6163 (tpt170) cc_final: 0.3387 (ttm170) REVERT: Z 265 GLU cc_start: 0.8736 (tp30) cc_final: 0.7992 (tt0) REVERT: Z 290 LYS cc_start: 0.8982 (mmmt) cc_final: 0.8622 (tptp) REVERT: Z 361 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.7296 (p90) REVERT: Z 403 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8622 (pp20) REVERT: a 52 MET cc_start: 0.9183 (mmm) cc_final: 0.8816 (mmt) REVERT: a 149 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.6748 (p90) REVERT: a 205 MET cc_start: 0.7569 (mtm) cc_final: 0.7274 (mtt) REVERT: a 208 ASP cc_start: 0.8081 (t0) cc_final: 0.7827 (m-30) REVERT: a 249 ARG cc_start: 0.6294 (tpt170) cc_final: 0.3399 (ttm170) REVERT: a 345 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8998 (p) REVERT: a 350 TYR cc_start: 0.9448 (m-80) cc_final: 0.8640 (m-80) REVERT: a 361 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7011 (p90) REVERT: a 403 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8517 (pp20) REVERT: b 140 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8123 (m-40) REVERT: b 149 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6755 (p90) REVERT: b 153 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8432 (ttpt) REVERT: b 183 ASN cc_start: 0.7517 (m-40) cc_final: 0.7310 (m110) REVERT: b 208 ASP cc_start: 0.8360 (t0) cc_final: 0.7654 (p0) REVERT: b 249 ARG cc_start: 0.6033 (tpt170) cc_final: 0.5201 (tpt170) REVERT: b 403 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: c 37 LYS cc_start: 0.8441 (ptmt) cc_final: 0.8219 (pttt) REVERT: c 99 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8478 (mp10) REVERT: c 149 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7980 (p90) REVERT: c 153 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8457 (ttmt) REVERT: c 249 ARG cc_start: 0.6183 (tpt170) cc_final: 0.3390 (ttm170) REVERT: c 265 GLU cc_start: 0.8730 (tp30) cc_final: 0.7991 (tt0) REVERT: c 290 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8628 (tptp) REVERT: c 361 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7296 (p90) REVERT: c 403 GLU cc_start: 0.9134 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: d 149 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.6750 (p90) REVERT: d 205 MET cc_start: 0.7578 (mtm) cc_final: 0.7284 (mtt) REVERT: d 208 ASP cc_start: 0.8087 (t0) cc_final: 0.7836 (m-30) REVERT: d 249 ARG cc_start: 0.6259 (tpt170) cc_final: 0.3397 (ttm170) REVERT: d 345 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.9000 (p) REVERT: d 350 TYR cc_start: 0.9451 (m-80) cc_final: 0.8641 (m-80) REVERT: d 361 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7013 (p90) REVERT: d 403 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8519 (pp20) REVERT: e 140 ASN cc_start: 0.8547 (OUTLIER) cc_final: 0.8127 (m-40) REVERT: e 149 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6753 (p90) REVERT: e 153 LYS cc_start: 0.8667 (ttmt) cc_final: 0.8431 (ttpt) REVERT: e 183 ASN cc_start: 0.7511 (m-40) cc_final: 0.7300 (m110) REVERT: e 208 ASP cc_start: 0.8358 (t0) cc_final: 0.7756 (p0) REVERT: e 249 ARG cc_start: 0.6038 (tpt170) cc_final: 0.5234 (tpt170) REVERT: e 403 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8583 (pp20) REVERT: f 99 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8477 (mp10) REVERT: f 149 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.7990 (p90) REVERT: f 153 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8438 (ttmt) REVERT: f 228 MET cc_start: 0.9097 (mmp) cc_final: 0.8710 (mmm) REVERT: f 249 ARG cc_start: 0.6160 (tpt170) cc_final: 0.3381 (ttm170) REVERT: f 265 GLU cc_start: 0.8740 (tp30) cc_final: 0.7998 (tt0) REVERT: f 290 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8623 (tptp) REVERT: f 361 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7306 (p90) REVERT: f 403 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8626 (pp20) outliers start: 122 outliers final: 80 residues processed: 778 average time/residue: 0.4688 time to fit residues: 594.6302 Evaluate side-chains 783 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 664 time to evaluate : 3.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 131 VAL Chi-restraints excluded: chain U residue 149 PHE Chi-restraints excluded: chain U residue 209 VAL Chi-restraints excluded: chain U residue 245 VAL Chi-restraints excluded: chain U residue 345 THR Chi-restraints excluded: chain U residue 361 PHE Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain U residue 403 GLU Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 246 THR Chi-restraints excluded: chain V residue 293 LEU Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 102 GLN Chi-restraints excluded: chain W residue 131 VAL Chi-restraints excluded: chain W residue 149 PHE Chi-restraints excluded: chain W residue 195 MET Chi-restraints excluded: chain W residue 201 ILE Chi-restraints excluded: chain W residue 209 VAL Chi-restraints excluded: chain W residue 236 ASP Chi-restraints excluded: chain W residue 246 THR Chi-restraints excluded: chain W residue 258 GLU Chi-restraints excluded: chain W residue 267 LYS Chi-restraints excluded: chain W residue 345 THR Chi-restraints excluded: chain W residue 355 GLU Chi-restraints excluded: chain W residue 361 PHE Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 131 VAL Chi-restraints excluded: chain X residue 149 PHE Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 245 VAL Chi-restraints excluded: chain X residue 345 THR Chi-restraints excluded: chain X residue 361 PHE Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain X residue 403 GLU Chi-restraints excluded: chain Y residue 140 ASN Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 236 ASP Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 246 THR Chi-restraints excluded: chain Y residue 293 LEU Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 102 GLN Chi-restraints excluded: chain Z residue 131 VAL Chi-restraints excluded: chain Z residue 149 PHE Chi-restraints excluded: chain Z residue 195 MET Chi-restraints excluded: chain Z residue 201 ILE Chi-restraints excluded: chain Z residue 209 VAL Chi-restraints excluded: chain Z residue 236 ASP Chi-restraints excluded: chain Z residue 246 THR Chi-restraints excluded: chain Z residue 258 GLU Chi-restraints excluded: chain Z residue 267 LYS Chi-restraints excluded: chain Z residue 345 THR Chi-restraints excluded: chain Z residue 355 GLU Chi-restraints excluded: chain Z residue 361 PHE Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 149 PHE Chi-restraints excluded: chain a residue 209 VAL Chi-restraints excluded: chain a residue 245 VAL Chi-restraints excluded: chain a residue 345 THR Chi-restraints excluded: chain a residue 361 PHE Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain a residue 403 GLU Chi-restraints excluded: chain b residue 140 ASN Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 236 ASP Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 246 THR Chi-restraints excluded: chain b residue 293 LEU Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 102 GLN Chi-restraints excluded: chain c residue 131 VAL Chi-restraints excluded: chain c residue 149 PHE Chi-restraints excluded: chain c residue 195 MET Chi-restraints excluded: chain c residue 201 ILE Chi-restraints excluded: chain c residue 209 VAL Chi-restraints excluded: chain c residue 236 ASP Chi-restraints excluded: chain c residue 246 THR Chi-restraints excluded: chain c residue 258 GLU Chi-restraints excluded: chain c residue 267 LYS Chi-restraints excluded: chain c residue 345 THR Chi-restraints excluded: chain c residue 355 GLU Chi-restraints excluded: chain c residue 361 PHE Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 131 VAL Chi-restraints excluded: chain d residue 149 PHE Chi-restraints excluded: chain d residue 209 VAL Chi-restraints excluded: chain d residue 245 VAL Chi-restraints excluded: chain d residue 345 THR Chi-restraints excluded: chain d residue 361 PHE Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain d residue 403 GLU Chi-restraints excluded: chain e residue 140 ASN Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 236 ASP Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 246 THR Chi-restraints excluded: chain e residue 293 LEU Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 102 GLN Chi-restraints excluded: chain f residue 131 VAL Chi-restraints excluded: chain f residue 149 PHE Chi-restraints excluded: chain f residue 195 MET Chi-restraints excluded: chain f residue 201 ILE Chi-restraints excluded: chain f residue 209 VAL Chi-restraints excluded: chain f residue 236 ASP Chi-restraints excluded: chain f residue 246 THR Chi-restraints excluded: chain f residue 258 GLU Chi-restraints excluded: chain f residue 267 LYS Chi-restraints excluded: chain f residue 345 THR Chi-restraints excluded: chain f residue 355 GLU Chi-restraints excluded: chain f residue 361 PHE Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 277 optimal weight: 3.9990 chunk 444 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 436 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 377 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 428 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 105 ASN ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 140 ASN ** Z 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN d 98 GLN e 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102332 restraints weight = 54467.092| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.94 r_work: 0.3077 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 36000 Z= 0.132 Angle : 0.628 7.668 48672 Z= 0.315 Chirality : 0.044 0.195 5268 Planarity : 0.004 0.043 6420 Dihedral : 4.637 27.098 4896 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.46 % Allowed : 24.65 % Favored : 71.89 % 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: -0.88 (0.13), residues: 4524 helix: 1.27 (0.13), residues: 1956 sheet: 0.15 (0.32), residues: 360 loop : -2.61 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Y 143 HIS 0.003 0.001 HIS e 297 PHE 0.018 0.001 PHE Y 371 TYR 0.015 0.001 TYR b 367 ARG 0.005 0.000 ARG d 103 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 1464) hydrogen bonds : angle 4.14259 ( 4068) covalent geometry : bond 0.00315 (36000) covalent geometry : angle 0.62803 (48672) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19127.12 seconds wall clock time: 329 minutes 34.44 seconds (19774.44 seconds total)