Starting phenix.real_space_refine on Tue Aug 26 08:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fwb_29500/08_2025/8fwb_29500.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fwb_29500/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8fwb_29500/08_2025/8fwb_29500.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fwb_29500/08_2025/8fwb_29500.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fwb_29500/08_2025/8fwb_29500.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fwb_29500/08_2025/8fwb_29500.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.91, per 1000 atoms: 0.20 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: 2.67 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 1.33 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: 6.19 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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: 0.13 Found NCS groups: ncs_group { reference = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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: 5.470 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.520 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.100 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (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 ARG 0.005 0.001 ARG X 373 TYR 0.012 0.001 TYR c 192 PHE 0.021 0.002 PHE Z 361 TRP 0.010 0.001 TRP a 143 HIS 0.014 0.005 HIS e 297 Details of bonding type rmsd covalent geometry : bond 0.00540 (36000) covalent geometry : angle 0.82688 (48672) hydrogen bonds : bond 0.13449 ( 1464) hydrogen bonds : angle 6.52893 ( 4068) *********************** 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 : 1.423 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: 0.2311 time to fit residues: 375.9692 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 : 1.257 ------------------------------------------------------------------------------- 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 432 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 GLN U 191 ASN U 202 ASN U 291 ASN U 305 GLN V 80 GLN ** V 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 164 GLN X 191 ASN X 202 ASN X 291 ASN X 305 GLN Y 80 GLN ** Y 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 GLN a 191 ASN a 202 ASN a 291 ASN a 305 GLN b 80 GLN ** b 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 164 GLN d 191 ASN d 202 ASN d 291 ASN d 305 GLN e 80 GLN ** e 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102131 restraints weight = 55121.530| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.01 r_work: 0.3075 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1926 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 : 0.675 7.234 48672 Z= 0.351 Chirality : 0.045 0.154 5268 Planarity : 0.005 0.033 6420 Dihedral : 6.038 50.232 4952 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.79 % Allowed : 15.68 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.12), residues: 4524 helix: 0.35 (0.12), residues: 1944 sheet: -0.88 (0.31), residues: 360 loop : -3.32 (0.12), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG W 383 TYR 0.010 0.001 TYR c 367 PHE 0.012 0.001 PHE b 26 TRP 0.008 0.001 TRP Z 143 HIS 0.008 0.003 HIS e 297 Details of bonding type rmsd covalent geometry : bond 0.00324 (36000) covalent geometry : angle 0.67493 (48672) hydrogen bonds : bond 0.03670 ( 1464) hydrogen bonds : angle 4.82676 ( 4068) *********************** 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 842 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 738 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 49 GLN cc_start: 0.9007 (tp40) cc_final: 0.8669 (tp40) REVERT: U 153 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8294 (ttmm) REVERT: U 205 MET cc_start: 0.7807 (mtm) cc_final: 0.7463 (mtt) REVERT: U 249 ARG cc_start: 0.6558 (tpt170) cc_final: 0.4865 (ttt90) REVERT: U 265 GLU cc_start: 0.8751 (tp30) cc_final: 0.8098 (tt0) REVERT: U 285 LYS cc_start: 0.8352 (ttpp) cc_final: 0.7823 (tttp) REVERT: U 350 TYR cc_start: 0.9311 (m-80) cc_final: 0.8916 (m-80) REVERT: V 99 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8399 (mp10) REVERT: V 153 LYS cc_start: 0.8560 (ttmt) cc_final: 0.8249 (ttmt) REVERT: V 183 ASN cc_start: 0.7504 (m-40) cc_final: 0.7268 (m-40) REVERT: V 205 MET cc_start: 0.7934 (mtt) cc_final: 0.7717 (mmt) REVERT: V 215 GLN cc_start: 0.8707 (mt0) cc_final: 0.8507 (mt0) REVERT: V 249 ARG cc_start: 0.6610 (tpt170) cc_final: 0.5017 (ttt90) REVERT: V 355 GLU cc_start: 0.7935 (pt0) cc_final: 0.7704 (pt0) REVERT: W 49 GLN cc_start: 0.8958 (tp40) cc_final: 0.8569 (mm-40) REVERT: W 66 LEU cc_start: 0.9044 (mt) cc_final: 0.8749 (mt) REVERT: W 99 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8794 (mm-40) REVERT: W 153 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8498 (ttmt) REVERT: W 205 MET cc_start: 0.7968 (mtm) cc_final: 0.7519 (mmm) REVERT: W 249 ARG cc_start: 0.6778 (tpt170) cc_final: 0.4946 (ttt90) REVERT: W 285 LYS cc_start: 0.8474 (ttpp) cc_final: 0.8137 (tttp) REVERT: W 290 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8693 (tptp) REVERT: X 49 GLN cc_start: 0.9007 (tp40) cc_final: 0.8670 (tp40) REVERT: X 153 LYS cc_start: 0.8675 (ttmt) cc_final: 0.8293 (ttmm) REVERT: X 205 MET cc_start: 0.7819 (mtm) cc_final: 0.7454 (mtt) REVERT: X 249 ARG cc_start: 0.6572 (tpt170) cc_final: 0.4868 (ttt90) REVERT: X 265 GLU cc_start: 0.8743 (tp30) cc_final: 0.8093 (tt0) REVERT: X 285 LYS cc_start: 0.8350 (ttpp) cc_final: 0.7823 (tttp) REVERT: X 350 TYR cc_start: 0.9306 (m-80) cc_final: 0.8915 (m-80) REVERT: Y 99 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8393 (mp10) REVERT: Y 153 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8253 (ttmt) REVERT: Y 183 ASN cc_start: 0.7491 (m-40) cc_final: 0.7256 (m-40) REVERT: Y 205 MET cc_start: 0.7932 (mtt) cc_final: 0.7714 (mmt) REVERT: Y 249 ARG cc_start: 0.6609 (tpt170) cc_final: 0.5021 (ttt90) REVERT: Y 355 GLU cc_start: 0.7934 (pt0) cc_final: 0.7704 (pt0) REVERT: Z 49 GLN cc_start: 0.8953 (tp40) cc_final: 0.8564 (mm-40) REVERT: Z 66 LEU cc_start: 0.9040 (mt) cc_final: 0.8745 (mt) REVERT: Z 99 GLN cc_start: 0.9008 (mm-40) cc_final: 0.8798 (mm-40) REVERT: Z 153 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8496 (ttmt) REVERT: Z 205 MET cc_start: 0.7971 (mtm) cc_final: 0.7518 (mmm) REVERT: Z 249 ARG cc_start: 0.6818 (tpt170) cc_final: 0.4957 (ttt90) REVERT: Z 285 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8128 (tttp) REVERT: Z 290 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8692 (tptp) REVERT: a 49 GLN cc_start: 0.9004 (tp40) cc_final: 0.8666 (tp40) REVERT: a 153 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8297 (ttmm) REVERT: a 205 MET cc_start: 0.7821 (mtm) cc_final: 0.7460 (mtt) REVERT: a 249 ARG cc_start: 0.6572 (tpt170) cc_final: 0.4875 (ttt90) REVERT: a 265 GLU cc_start: 0.8759 (tp30) cc_final: 0.8101 (tt0) REVERT: a 285 LYS cc_start: 0.8341 (ttpp) cc_final: 0.7816 (tttp) REVERT: a 350 TYR cc_start: 0.9311 (m-80) cc_final: 0.8918 (m-80) REVERT: b 99 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8399 (mp10) REVERT: b 153 LYS cc_start: 0.8564 (ttmt) cc_final: 0.8249 (ttmt) REVERT: b 183 ASN cc_start: 0.7505 (m-40) cc_final: 0.7268 (m-40) REVERT: b 205 MET cc_start: 0.7940 (mtt) cc_final: 0.7717 (mmt) REVERT: b 215 GLN cc_start: 0.8710 (mt0) cc_final: 0.8509 (mt0) REVERT: b 249 ARG cc_start: 0.6604 (tpt170) cc_final: 0.5018 (ttt90) REVERT: b 355 GLU cc_start: 0.7934 (pt0) cc_final: 0.7704 (pt0) REVERT: c 49 GLN cc_start: 0.8951 (tp40) cc_final: 0.8565 (mm-40) REVERT: c 66 LEU cc_start: 0.9030 (mt) cc_final: 0.8736 (mt) REVERT: c 99 GLN cc_start: 0.9004 (mm-40) cc_final: 0.8793 (mm-40) REVERT: c 153 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8500 (ttmt) REVERT: c 205 MET cc_start: 0.7967 (mtm) cc_final: 0.7513 (mmm) REVERT: c 249 ARG cc_start: 0.6829 (tpt170) cc_final: 0.4961 (ttt90) REVERT: c 285 LYS cc_start: 0.8468 (ttpp) cc_final: 0.8131 (tttp) REVERT: c 290 LYS cc_start: 0.9002 (mmmt) cc_final: 0.8684 (tptp) REVERT: d 49 GLN cc_start: 0.9002 (tp40) cc_final: 0.8661 (tp40) REVERT: d 153 LYS cc_start: 0.8674 (ttmt) cc_final: 0.8293 (ttmm) REVERT: d 205 MET cc_start: 0.7823 (mtm) cc_final: 0.7468 (mtt) REVERT: d 249 ARG cc_start: 0.6586 (tpt170) cc_final: 0.4874 (ttt90) REVERT: d 265 GLU cc_start: 0.8752 (tp30) cc_final: 0.8101 (tt0) REVERT: d 285 LYS cc_start: 0.8345 (ttpp) cc_final: 0.7817 (tttp) REVERT: d 350 TYR cc_start: 0.9311 (m-80) cc_final: 0.8919 (m-80) REVERT: e 99 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8400 (mp10) REVERT: e 153 LYS cc_start: 0.8568 (ttmt) cc_final: 0.8255 (ttmt) REVERT: e 183 ASN cc_start: 0.7495 (m-40) cc_final: 0.7258 (m-40) REVERT: e 205 MET cc_start: 0.7930 (mtt) cc_final: 0.7712 (mmt) REVERT: e 215 GLN cc_start: 0.8712 (mt0) cc_final: 0.8507 (mt0) REVERT: e 249 ARG cc_start: 0.6609 (tpt170) cc_final: 0.5025 (ttt90) REVERT: e 355 GLU cc_start: 0.7928 (pt0) cc_final: 0.7698 (pt0) REVERT: f 49 GLN cc_start: 0.8955 (tp40) cc_final: 0.8567 (mm-40) REVERT: f 66 LEU cc_start: 0.9040 (mt) cc_final: 0.8743 (mt) REVERT: f 99 GLN cc_start: 0.9002 (mm-40) cc_final: 0.8792 (mm-40) REVERT: f 153 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8499 (ttmt) REVERT: f 249 ARG cc_start: 0.6790 (tpt170) cc_final: 0.4942 (ttt90) REVERT: f 285 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8137 (tttp) REVERT: f 290 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8690 (tptp) outliers start: 104 outliers final: 80 residues processed: 810 average time/residue: 0.2403 time to fit residues: 313.2352 Evaluate side-chains 719 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 639 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 74 ASP 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 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 258 GLU Chi-restraints excluded: chain W residue 371 PHE Chi-restraints excluded: chain W residue 391 ASP 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 245 VAL Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 74 ASP 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 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 258 GLU Chi-restraints excluded: chain Z residue 371 PHE Chi-restraints excluded: chain Z residue 391 ASP 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 245 VAL Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 74 ASP 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 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 258 GLU Chi-restraints excluded: chain c residue 371 PHE Chi-restraints excluded: chain c residue 391 ASP 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 245 VAL Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 74 ASP 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 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 258 GLU Chi-restraints excluded: chain f residue 371 PHE Chi-restraints excluded: chain f residue 391 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 180 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 225 optimal weight: 5.9990 chunk 98 optimal weight: 0.1980 chunk 121 optimal weight: 3.9990 chunk 430 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 348 optimal weight: 0.0670 chunk 313 optimal weight: 5.9990 chunk 433 optimal weight: 10.0000 overall best weight: 3.0524 ------------------------------------------------------------------------------- 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 ** Z 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 215 GLN ** c 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 215 GLN ** f 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.136516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097870 restraints weight = 54752.967| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.95 r_work: 0.3028 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 36000 Z= 0.197 Angle : 0.682 7.290 48672 Z= 0.351 Chirality : 0.046 0.204 5268 Planarity : 0.005 0.030 6420 Dihedral : 6.003 57.062 4940 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 4.39 % Allowed : 18.81 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.13), residues: 4524 helix: 0.64 (0.12), residues: 1968 sheet: -0.39 (0.33), residues: 360 loop : -3.12 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG b 50 TYR 0.013 0.001 TYR Z 367 PHE 0.012 0.001 PHE V 124 TRP 0.009 0.001 TRP Z 143 HIS 0.013 0.004 HIS b 297 Details of bonding type rmsd covalent geometry : bond 0.00477 (36000) covalent geometry : angle 0.68224 (48672) hydrogen bonds : bond 0.04026 ( 1464) hydrogen bonds : angle 4.62713 ( 4068) *********************** 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 848 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 684 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 89 MET cc_start: 0.6056 (mmm) cc_final: 0.5760 (mmm) REVERT: U 149 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7001 (p90) REVERT: U 249 ARG cc_start: 0.6477 (tpt170) cc_final: 0.4421 (ttm-80) REVERT: U 265 GLU cc_start: 0.8662 (tp30) cc_final: 0.7954 (tt0) REVERT: U 350 TYR cc_start: 0.9491 (m-80) cc_final: 0.9119 (m-80) REVERT: U 405 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8590 (p) REVERT: V 153 LYS cc_start: 0.8760 (ttmt) cc_final: 0.8450 (ttmm) REVERT: V 215 GLN cc_start: 0.8752 (mt0) cc_final: 0.8520 (mt0) REVERT: V 249 ARG cc_start: 0.6371 (tpt170) cc_final: 0.4830 (ttt90) REVERT: V 405 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8536 (p) REVERT: W 153 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8537 (ttmt) REVERT: W 157 TYR cc_start: 0.7884 (m-80) cc_final: 0.7465 (m-80) REVERT: W 212 THR cc_start: 0.8820 (t) cc_final: 0.8503 (t) REVERT: W 215 GLN cc_start: 0.9135 (OUTLIER) cc_final: 0.8844 (pt0) REVERT: W 228 MET cc_start: 0.9193 (mmp) cc_final: 0.8904 (mmm) REVERT: W 249 ARG cc_start: 0.6725 (tpt170) cc_final: 0.4789 (ttt90) REVERT: W 285 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8036 (tttp) REVERT: W 290 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8657 (tptp) REVERT: W 405 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8495 (p) REVERT: X 89 MET cc_start: 0.6049 (mmm) cc_final: 0.5753 (mmm) REVERT: X 149 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.6987 (p90) REVERT: X 249 ARG cc_start: 0.6463 (tpt170) cc_final: 0.4417 (ttm-80) REVERT: X 265 GLU cc_start: 0.8656 (tp30) cc_final: 0.7948 (tt0) REVERT: X 350 TYR cc_start: 0.9487 (m-80) cc_final: 0.9116 (m-80) REVERT: X 405 THR cc_start: 0.8791 (OUTLIER) cc_final: 0.8591 (p) REVERT: Y 153 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8450 (ttmm) REVERT: Y 249 ARG cc_start: 0.6381 (tpt170) cc_final: 0.4835 (ttt90) REVERT: Y 405 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8549 (p) REVERT: Z 153 LYS cc_start: 0.8865 (ttmt) cc_final: 0.8542 (ttmt) REVERT: Z 157 TYR cc_start: 0.7881 (m-80) cc_final: 0.7459 (m-80) REVERT: Z 212 THR cc_start: 0.8828 (t) cc_final: 0.8511 (t) REVERT: Z 215 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: Z 228 MET cc_start: 0.9188 (mmp) cc_final: 0.8897 (mmm) REVERT: Z 249 ARG cc_start: 0.6721 (tpt170) cc_final: 0.4805 (ttt90) REVERT: Z 285 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8036 (tttp) REVERT: Z 290 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8659 (tptp) REVERT: Z 405 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8496 (p) REVERT: a 89 MET cc_start: 0.6045 (mmm) cc_final: 0.5749 (mmm) REVERT: a 149 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.6993 (p90) REVERT: a 249 ARG cc_start: 0.6488 (tpt170) cc_final: 0.4420 (ttm-80) REVERT: a 265 GLU cc_start: 0.8667 (tp30) cc_final: 0.7965 (tt0) REVERT: a 350 TYR cc_start: 0.9489 (m-80) cc_final: 0.9116 (m-80) REVERT: a 405 THR cc_start: 0.8796 (OUTLIER) cc_final: 0.8595 (p) REVERT: b 153 LYS cc_start: 0.8767 (ttmt) cc_final: 0.8453 (ttmm) REVERT: b 215 GLN cc_start: 0.8751 (mt0) cc_final: 0.8518 (mt0) REVERT: b 249 ARG cc_start: 0.6381 (tpt170) cc_final: 0.4837 (ttt90) REVERT: b 405 THR cc_start: 0.8776 (OUTLIER) cc_final: 0.8543 (p) REVERT: c 153 LYS cc_start: 0.8869 (ttmt) cc_final: 0.8546 (ttmt) REVERT: c 157 TYR cc_start: 0.7884 (m-80) cc_final: 0.7465 (m-80) REVERT: c 212 THR cc_start: 0.8828 (t) cc_final: 0.8510 (t) REVERT: c 215 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8847 (pt0) REVERT: c 228 MET cc_start: 0.9182 (mmp) cc_final: 0.8889 (mmm) REVERT: c 249 ARG cc_start: 0.6709 (tpt170) cc_final: 0.4804 (ttt90) REVERT: c 285 LYS cc_start: 0.8488 (ttpp) cc_final: 0.8036 (tttp) REVERT: c 290 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8661 (tptp) REVERT: c 405 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8500 (p) REVERT: d 89 MET cc_start: 0.6043 (mmm) cc_final: 0.5746 (mmm) REVERT: d 149 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.6994 (p90) REVERT: d 249 ARG cc_start: 0.6487 (tpt170) cc_final: 0.4423 (ttm-80) REVERT: d 265 GLU cc_start: 0.8682 (tp30) cc_final: 0.7968 (tt0) REVERT: d 350 TYR cc_start: 0.9492 (m-80) cc_final: 0.9123 (m-80) REVERT: d 405 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8593 (p) REVERT: e 153 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8453 (ttmm) REVERT: e 215 GLN cc_start: 0.8751 (mt0) cc_final: 0.8518 (mt0) REVERT: e 249 ARG cc_start: 0.6372 (tpt170) cc_final: 0.4827 (ttt90) REVERT: e 405 THR cc_start: 0.8769 (OUTLIER) cc_final: 0.8538 (p) REVERT: f 153 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8538 (ttmt) REVERT: f 157 TYR cc_start: 0.7877 (m-80) cc_final: 0.7459 (m-80) REVERT: f 212 THR cc_start: 0.8822 (t) cc_final: 0.8504 (t) REVERT: f 215 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8845 (pt0) REVERT: f 228 MET cc_start: 0.9189 (mmp) cc_final: 0.8898 (mmm) REVERT: f 249 ARG cc_start: 0.6725 (tpt170) cc_final: 0.4787 (ttt90) REVERT: f 285 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8035 (tttp) REVERT: f 290 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8657 (tptp) REVERT: f 405 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8498 (p) outliers start: 164 outliers final: 112 residues processed: 800 average time/residue: 0.2411 time to fit residues: 310.7270 Evaluate side-chains 782 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 650 time to evaluate : 1.439 ------------------------------------------------------------------------------- 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 149 PHE 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 U residue 405 THR Chi-restraints excluded: chain V residue 74 ASP 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 V residue 405 THR 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 215 GLN 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 149 PHE 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 X residue 405 THR Chi-restraints excluded: chain Y residue 74 ASP 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 Y residue 405 THR 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 215 GLN 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 149 PHE 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 a residue 405 THR Chi-restraints excluded: chain b residue 74 ASP 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 b residue 405 THR 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 215 GLN 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 149 PHE 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 d residue 405 THR Chi-restraints excluded: chain e residue 74 ASP 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 e residue 405 THR 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 215 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 391 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 349 optimal weight: 0.0970 chunk 167 optimal weight: 0.9990 chunk 64 optimal weight: 0.0070 chunk 35 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN W 215 GLN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 105 ASN Z 105 ASN Z 215 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 105 ASN c 105 ASN c 215 GLN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 105 ASN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 105 ASN f 105 ASN f 215 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.141322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102446 restraints weight = 54386.327| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 2.95 r_work: 0.3077 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 36000 Z= 0.119 Angle : 0.617 7.335 48672 Z= 0.318 Chirality : 0.043 0.206 5268 Planarity : 0.004 0.033 6420 Dihedral : 5.794 59.614 4940 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 4.98 % Allowed : 19.86 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.13), residues: 4524 helix: 0.91 (0.12), residues: 2004 sheet: -0.51 (0.28), residues: 480 loop : -3.15 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 103 TYR 0.013 0.001 TYR c 367 PHE 0.014 0.001 PHE W 30 TRP 0.007 0.001 TRP X 143 HIS 0.005 0.001 HIS W 297 Details of bonding type rmsd covalent geometry : bond 0.00272 (36000) covalent geometry : angle 0.61656 (48672) hydrogen bonds : bond 0.02938 ( 1464) hydrogen bonds : angle 4.43085 ( 4068) *********************** 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 937 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 751 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 249 ARG cc_start: 0.6402 (tpt170) cc_final: 0.4651 (ttt90) REVERT: U 265 GLU cc_start: 0.8745 (tp30) cc_final: 0.7991 (tt0) REVERT: U 272 ASN cc_start: 0.8771 (p0) cc_final: 0.8509 (p0) REVERT: U 285 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7856 (tttp) REVERT: U 350 TYR cc_start: 0.9423 (m-80) cc_final: 0.8759 (m-80) REVERT: U 362 LEU cc_start: 0.8748 (mt) cc_final: 0.8522 (mt) REVERT: V 149 PHE cc_start: 0.8344 (OUTLIER) cc_final: 0.6661 (p90) REVERT: V 153 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8394 (ttmm) REVERT: V 215 GLN cc_start: 0.8651 (mt0) cc_final: 0.8439 (mt0) REVERT: V 249 ARG cc_start: 0.6181 (tpt170) cc_final: 0.4459 (ttt90) REVERT: V 285 LYS cc_start: 0.8335 (tttt) cc_final: 0.8067 (tttp) REVERT: V 290 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8664 (tptp) REVERT: V 367 TYR cc_start: 0.8301 (m-80) cc_final: 0.7947 (m-80) REVERT: W 99 GLN cc_start: 0.8911 (mm-40) cc_final: 0.8555 (mp10) REVERT: W 153 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8458 (ttmt) REVERT: W 212 THR cc_start: 0.8782 (OUTLIER) cc_final: 0.8479 (t) REVERT: W 228 MET cc_start: 0.9023 (mmp) cc_final: 0.8757 (mmm) REVERT: W 249 ARG cc_start: 0.6436 (tpt170) cc_final: 0.3268 (ttm170) REVERT: W 285 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8111 (tttp) REVERT: W 290 LYS cc_start: 0.8994 (mmmt) cc_final: 0.8651 (tptp) REVERT: W 381 LYS cc_start: 0.8026 (tppt) cc_final: 0.7751 (tppt) REVERT: W 391 ASP cc_start: 0.8945 (OUTLIER) cc_final: 0.8633 (t70) REVERT: X 249 ARG cc_start: 0.6388 (tpt170) cc_final: 0.4654 (ttt90) REVERT: X 265 GLU cc_start: 0.8739 (tp30) cc_final: 0.7994 (tt0) REVERT: X 272 ASN cc_start: 0.8777 (p0) cc_final: 0.8517 (p0) REVERT: X 285 LYS cc_start: 0.8329 (ttpp) cc_final: 0.7852 (tttp) REVERT: X 350 TYR cc_start: 0.9418 (m-80) cc_final: 0.8756 (m-80) REVERT: X 362 LEU cc_start: 0.8745 (mt) cc_final: 0.8522 (mt) REVERT: Y 149 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.6672 (p90) REVERT: Y 153 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8393 (ttmm) REVERT: Y 249 ARG cc_start: 0.6166 (tpt170) cc_final: 0.4449 (ttt90) REVERT: Y 285 LYS cc_start: 0.8340 (tttt) cc_final: 0.8072 (tttp) REVERT: Y 290 LYS cc_start: 0.8948 (mmmt) cc_final: 0.8668 (tptp) REVERT: Y 367 TYR cc_start: 0.8310 (m-80) cc_final: 0.7957 (m-80) REVERT: Z 99 GLN cc_start: 0.8910 (mm-40) cc_final: 0.8555 (mp10) REVERT: Z 153 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8460 (ttmt) REVERT: Z 205 MET cc_start: 0.8732 (mmm) cc_final: 0.8527 (mmp) REVERT: Z 212 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8477 (t) REVERT: Z 228 MET cc_start: 0.9026 (mmp) cc_final: 0.8759 (mmm) REVERT: Z 249 ARG cc_start: 0.6442 (tpt170) cc_final: 0.3272 (ttm170) REVERT: Z 285 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8101 (tttp) REVERT: Z 290 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8652 (tptp) REVERT: Z 381 LYS cc_start: 0.8017 (tppt) cc_final: 0.7740 (tppt) REVERT: Z 391 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8624 (t70) REVERT: a 249 ARG cc_start: 0.6401 (tpt170) cc_final: 0.4654 (ttt90) REVERT: a 265 GLU cc_start: 0.8741 (tp30) cc_final: 0.8000 (tt0) REVERT: a 272 ASN cc_start: 0.8782 (p0) cc_final: 0.8525 (p0) REVERT: a 285 LYS cc_start: 0.8324 (ttpp) cc_final: 0.7848 (tttp) REVERT: a 350 TYR cc_start: 0.9420 (m-80) cc_final: 0.8753 (m-80) REVERT: a 362 LEU cc_start: 0.8746 (mt) cc_final: 0.8521 (mt) REVERT: b 149 PHE cc_start: 0.8355 (OUTLIER) cc_final: 0.6675 (p90) REVERT: b 153 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8394 (ttmm) REVERT: b 215 GLN cc_start: 0.8653 (mt0) cc_final: 0.8442 (mt0) REVERT: b 249 ARG cc_start: 0.6169 (tpt170) cc_final: 0.4439 (ttt90) REVERT: b 285 LYS cc_start: 0.8323 (tttt) cc_final: 0.8053 (tttp) REVERT: b 290 LYS cc_start: 0.8944 (mmmt) cc_final: 0.8662 (tptp) REVERT: b 367 TYR cc_start: 0.8299 (m-80) cc_final: 0.7947 (m-80) REVERT: c 99 GLN cc_start: 0.8904 (mm-40) cc_final: 0.8549 (mp10) REVERT: c 153 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8460 (ttmt) REVERT: c 212 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8478 (t) REVERT: c 215 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8894 (pt0) REVERT: c 228 MET cc_start: 0.9026 (mmp) cc_final: 0.8757 (mmm) REVERT: c 249 ARG cc_start: 0.6455 (tpt170) cc_final: 0.3271 (ttm170) REVERT: c 285 LYS cc_start: 0.8459 (ttpp) cc_final: 0.8105 (tttp) REVERT: c 290 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8650 (tptp) REVERT: c 381 LYS cc_start: 0.8027 (tppt) cc_final: 0.7753 (tppt) REVERT: c 391 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8630 (t70) REVERT: d 249 ARG cc_start: 0.6402 (tpt170) cc_final: 0.4655 (ttt90) REVERT: d 265 GLU cc_start: 0.8738 (tp30) cc_final: 0.7990 (tt0) REVERT: d 272 ASN cc_start: 0.8778 (p0) cc_final: 0.8516 (p0) REVERT: d 285 LYS cc_start: 0.8325 (ttpp) cc_final: 0.7846 (tttp) REVERT: d 350 TYR cc_start: 0.9423 (m-80) cc_final: 0.8752 (m-80) REVERT: d 362 LEU cc_start: 0.8742 (mt) cc_final: 0.8518 (mt) REVERT: e 149 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.6676 (p90) REVERT: e 153 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8399 (ttmm) REVERT: e 215 GLN cc_start: 0.8653 (mt0) cc_final: 0.8442 (mt0) REVERT: e 249 ARG cc_start: 0.6183 (tpt170) cc_final: 0.4446 (ttt90) REVERT: e 285 LYS cc_start: 0.8332 (tttt) cc_final: 0.8066 (tttp) REVERT: e 290 LYS cc_start: 0.8943 (mmmt) cc_final: 0.8661 (tptp) REVERT: e 367 TYR cc_start: 0.8303 (m-80) cc_final: 0.7951 (m-80) REVERT: f 99 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8551 (mp10) REVERT: f 153 LYS cc_start: 0.8831 (ttmt) cc_final: 0.8465 (ttmt) REVERT: f 212 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8480 (t) REVERT: f 215 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8892 (pt0) REVERT: f 228 MET cc_start: 0.9017 (mmp) cc_final: 0.8748 (mmm) REVERT: f 249 ARG cc_start: 0.6441 (tpt170) cc_final: 0.3262 (ttm170) REVERT: f 285 LYS cc_start: 0.8460 (ttpp) cc_final: 0.8107 (tttp) REVERT: f 290 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8652 (tptp) REVERT: f 381 LYS cc_start: 0.8027 (tppt) cc_final: 0.7753 (tppt) REVERT: f 391 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8627 (t70) outliers start: 186 outliers final: 64 residues processed: 869 average time/residue: 0.2358 time to fit residues: 331.3146 Evaluate side-chains 752 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 674 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 371 PHE Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 168 GLU Chi-restraints excluded: chain V residue 236 ASP Chi-restraints excluded: chain V residue 245 VAL 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 212 THR 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 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 371 PHE Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 168 GLU Chi-restraints excluded: chain Y residue 236 ASP Chi-restraints excluded: chain Y residue 245 VAL 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 212 THR 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 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 371 PHE Chi-restraints excluded: chain b residue 149 PHE Chi-restraints excluded: chain b residue 168 GLU Chi-restraints excluded: chain b residue 236 ASP Chi-restraints excluded: chain b residue 245 VAL 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 212 THR Chi-restraints excluded: chain c residue 215 GLN 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 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 371 PHE Chi-restraints excluded: chain e residue 149 PHE Chi-restraints excluded: chain e residue 168 GLU Chi-restraints excluded: chain e residue 236 ASP Chi-restraints excluded: chain e residue 245 VAL 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 212 THR Chi-restraints excluded: chain f residue 215 GLN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 127 optimal weight: 10.0000 chunk 249 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 221 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 348 optimal weight: 6.9990 chunk 170 optimal weight: 0.0070 chunk 126 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 69 GLN W 69 GLN W 215 GLN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 69 GLN Z 69 GLN Z 215 GLN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 69 GLN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 69 GLN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 69 GLN ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 69 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.098173 restraints weight = 53953.869| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.90 r_work: 0.3039 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 36000 Z= 0.181 Angle : 0.657 7.203 48672 Z= 0.336 Chirality : 0.045 0.211 5268 Planarity : 0.005 0.074 6420 Dihedral : 5.650 52.682 4940 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 4.58 % Allowed : 21.86 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.13), residues: 4524 helix: 0.95 (0.12), residues: 1968 sheet: -0.51 (0.28), residues: 480 loop : -3.12 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG U 103 TYR 0.010 0.001 TYR f 367 PHE 0.017 0.001 PHE U 371 TRP 0.008 0.001 TRP V 143 HIS 0.004 0.001 HIS b 297 Details of bonding type rmsd covalent geometry : bond 0.00436 (36000) covalent geometry : angle 0.65714 (48672) hydrogen bonds : bond 0.03572 ( 1464) hydrogen bonds : angle 4.45968 ( 4068) *********************** 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 850 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 679 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 149 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.6942 (p90) REVERT: U 249 ARG cc_start: 0.6432 (tpt170) cc_final: 0.3440 (ttm170) REVERT: U 265 GLU cc_start: 0.8714 (tp30) cc_final: 0.8070 (tt0) REVERT: U 272 ASN cc_start: 0.8940 (p0) cc_final: 0.8686 (p0) REVERT: U 350 TYR cc_start: 0.9484 (m-80) cc_final: 0.9055 (m-80) REVERT: V 149 PHE cc_start: 0.8613 (OUTLIER) cc_final: 0.6864 (p90) REVERT: V 153 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8430 (ttmm) REVERT: V 215 GLN cc_start: 0.8730 (mt0) cc_final: 0.8505 (mt0) REVERT: V 249 ARG cc_start: 0.6337 (tpt170) cc_final: 0.4598 (ttt90) REVERT: W 99 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8572 (mp10) REVERT: W 149 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.8011 (p90) REVERT: W 153 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8558 (ttmt) REVERT: W 249 ARG cc_start: 0.6509 (tpt170) cc_final: 0.3373 (ttm170) REVERT: W 285 LYS cc_start: 0.8419 (ttpp) cc_final: 0.8066 (tttp) REVERT: W 290 LYS cc_start: 0.9013 (mmmt) cc_final: 0.8649 (tptp) REVERT: W 391 ASP cc_start: 0.9022 (OUTLIER) cc_final: 0.8677 (t70) REVERT: X 149 PHE cc_start: 0.8579 (OUTLIER) cc_final: 0.6939 (p90) REVERT: X 249 ARG cc_start: 0.6436 (tpt170) cc_final: 0.3435 (ttm170) REVERT: X 265 GLU cc_start: 0.8706 (tp30) cc_final: 0.8062 (tt0) REVERT: X 272 ASN cc_start: 0.8932 (p0) cc_final: 0.8677 (p0) REVERT: X 350 TYR cc_start: 0.9485 (m-80) cc_final: 0.9061 (m-80) REVERT: Y 149 PHE cc_start: 0.8616 (OUTLIER) cc_final: 0.6861 (p90) REVERT: Y 153 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8427 (ttmm) REVERT: Y 249 ARG cc_start: 0.6331 (tpt170) cc_final: 0.4592 (ttt90) REVERT: Z 99 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8572 (mp10) REVERT: Z 149 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8013 (p90) REVERT: Z 153 LYS cc_start: 0.8921 (ttmt) cc_final: 0.8555 (ttmt) REVERT: Z 205 MET cc_start: 0.8775 (mmm) cc_final: 0.8287 (mmt) REVERT: Z 249 ARG cc_start: 0.6503 (tpt170) cc_final: 0.3361 (ttm170) REVERT: Z 285 LYS cc_start: 0.8420 (ttpp) cc_final: 0.8062 (tttp) REVERT: Z 290 LYS cc_start: 0.9021 (mmmt) cc_final: 0.8655 (tptp) REVERT: Z 391 ASP cc_start: 0.9020 (OUTLIER) cc_final: 0.8673 (t70) REVERT: a 149 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.6941 (p90) REVERT: a 249 ARG cc_start: 0.6417 (tpt170) cc_final: 0.3428 (ttm170) REVERT: a 265 GLU cc_start: 0.8711 (tp30) cc_final: 0.8070 (tt0) REVERT: a 272 ASN cc_start: 0.8937 (p0) cc_final: 0.8681 (p0) REVERT: a 350 TYR cc_start: 0.9486 (m-80) cc_final: 0.9063 (m-80) REVERT: b 149 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.6867 (p90) REVERT: b 153 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8432 (ttmm) REVERT: b 215 GLN cc_start: 0.8733 (mt0) cc_final: 0.8509 (mt0) REVERT: b 249 ARG cc_start: 0.6321 (tpt170) cc_final: 0.4585 (ttt90) REVERT: c 99 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8572 (mp10) REVERT: c 149 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8025 (p90) REVERT: c 153 LYS cc_start: 0.8920 (ttmt) cc_final: 0.8554 (ttmt) REVERT: c 212 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8601 (t) REVERT: c 249 ARG cc_start: 0.6501 (tpt170) cc_final: 0.3353 (ttm170) REVERT: c 285 LYS cc_start: 0.8428 (ttpp) cc_final: 0.8069 (tttp) REVERT: c 290 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8660 (tptp) REVERT: c 391 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8679 (t70) REVERT: d 149 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.6948 (p90) REVERT: d 249 ARG cc_start: 0.6414 (tpt170) cc_final: 0.3431 (ttm170) REVERT: d 265 GLU cc_start: 0.8718 (tp30) cc_final: 0.8072 (tt0) REVERT: d 272 ASN cc_start: 0.8940 (p0) cc_final: 0.8686 (p0) REVERT: d 350 TYR cc_start: 0.9488 (m-80) cc_final: 0.9062 (m-80) REVERT: e 149 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.6863 (p90) REVERT: e 153 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8433 (ttmm) REVERT: e 215 GLN cc_start: 0.8734 (mt0) cc_final: 0.8511 (mt0) REVERT: e 249 ARG cc_start: 0.6337 (tpt170) cc_final: 0.4599 (ttt90) REVERT: f 99 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8572 (mp10) REVERT: f 149 PHE cc_start: 0.8630 (OUTLIER) cc_final: 0.8014 (p90) REVERT: f 153 LYS cc_start: 0.8925 (ttmt) cc_final: 0.8558 (ttmt) REVERT: f 212 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8598 (t) REVERT: f 249 ARG cc_start: 0.6478 (tpt170) cc_final: 0.3365 (ttm170) REVERT: f 285 LYS cc_start: 0.8420 (ttpp) cc_final: 0.8064 (tttp) REVERT: f 290 LYS cc_start: 0.9016 (mmmt) cc_final: 0.8653 (tptp) REVERT: f 391 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8681 (t70) outliers start: 171 outliers final: 92 residues processed: 800 average time/residue: 0.2361 time to fit residues: 305.2899 Evaluate side-chains 772 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 662 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 120 SER 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 345 THR Chi-restraints excluded: chain U residue 371 PHE Chi-restraints excluded: chain V residue 149 PHE 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 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 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 X residue 120 SER 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 345 THR Chi-restraints excluded: chain X residue 371 PHE Chi-restraints excluded: chain Y residue 149 PHE 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 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 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 a residue 120 SER 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 345 THR Chi-restraints excluded: chain a residue 371 PHE Chi-restraints excluded: chain b residue 149 PHE 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 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 209 VAL Chi-restraints excluded: chain c residue 212 THR 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 d residue 120 SER 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 345 THR Chi-restraints excluded: chain d residue 371 PHE Chi-restraints excluded: chain e residue 149 PHE 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 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 209 VAL Chi-restraints excluded: chain f residue 212 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 81 optimal weight: 0.5980 chunk 436 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 306 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 255 optimal weight: 7.9990 chunk 387 optimal weight: 20.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 215 GLN ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.099442 restraints weight = 54396.620| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.93 r_work: 0.3032 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3011 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= 0.153 Angle : 0.631 7.299 48672 Z= 0.322 Chirality : 0.044 0.195 5268 Planarity : 0.004 0.053 6420 Dihedral : 5.183 47.494 4916 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.39 % Allowed : 22.80 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.13), residues: 4524 helix: 1.00 (0.12), residues: 1968 sheet: -0.45 (0.28), residues: 480 loop : -3.03 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG U 103 TYR 0.009 0.001 TYR f 367 PHE 0.013 0.001 PHE a 371 TRP 0.008 0.001 TRP X 143 HIS 0.003 0.001 HIS X 297 Details of bonding type rmsd covalent geometry : bond 0.00365 (36000) covalent geometry : angle 0.63072 (48672) hydrogen bonds : bond 0.03249 ( 1464) hydrogen bonds : angle 4.39954 ( 4068) *********************** 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 848 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 684 time to evaluate : 1.325 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 127 MET cc_start: 0.7873 (mtt) cc_final: 0.7271 (mtp) REVERT: U 149 PHE cc_start: 0.8446 (OUTLIER) cc_final: 0.6891 (p90) REVERT: U 249 ARG cc_start: 0.6261 (tpt170) cc_final: 0.3344 (ttm170) REVERT: U 265 GLU cc_start: 0.8723 (tp30) cc_final: 0.7954 (tt0) REVERT: U 272 ASN cc_start: 0.8888 (p0) cc_final: 0.8622 (p0) REVERT: U 350 TYR cc_start: 0.9423 (m-80) cc_final: 0.8727 (m-80) REVERT: U 361 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.6774 (p90) REVERT: V 149 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.6751 (p90) REVERT: V 153 LYS cc_start: 0.8702 (ttmt) cc_final: 0.8378 (ttmm) REVERT: V 215 GLN cc_start: 0.8644 (mt0) cc_final: 0.8411 (mt0) REVERT: V 249 ARG cc_start: 0.6343 (tpt170) cc_final: 0.4112 (ttm-80) REVERT: V 391 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8626 (t0) REVERT: W 99 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8593 (mp10) REVERT: W 149 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7925 (p90) REVERT: W 153 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8529 (ttmt) REVERT: W 249 ARG cc_start: 0.6199 (tpt170) cc_final: 0.3370 (ttm170) REVERT: W 290 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8662 (tptp) REVERT: W 391 ASP cc_start: 0.8960 (OUTLIER) cc_final: 0.8620 (t70) REVERT: X 127 MET cc_start: 0.7902 (mtt) cc_final: 0.7315 (mtp) REVERT: X 149 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.6887 (p90) REVERT: X 249 ARG cc_start: 0.6300 (tpt170) cc_final: 0.3352 (ttm170) REVERT: X 265 GLU cc_start: 0.8720 (tp30) cc_final: 0.7953 (tt0) REVERT: X 272 ASN cc_start: 0.8887 (p0) cc_final: 0.8623 (p0) REVERT: X 350 TYR cc_start: 0.9420 (m-80) cc_final: 0.8729 (m-80) REVERT: X 361 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.6795 (p90) REVERT: Y 149 PHE cc_start: 0.8464 (OUTLIER) cc_final: 0.6838 (p90) REVERT: Y 153 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8377 (ttmm) REVERT: Y 249 ARG cc_start: 0.6333 (tpt170) cc_final: 0.4099 (ttm-80) REVERT: Y 391 ASP cc_start: 0.8979 (OUTLIER) cc_final: 0.8623 (t0) REVERT: Z 99 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8591 (mp10) REVERT: Z 149 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7948 (p90) REVERT: Z 153 LYS cc_start: 0.8912 (ttmt) cc_final: 0.8530 (ttmt) REVERT: Z 249 ARG cc_start: 0.6212 (tpt170) cc_final: 0.3366 (ttm170) REVERT: Z 290 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8663 (tptp) REVERT: Z 391 ASP cc_start: 0.8961 (OUTLIER) cc_final: 0.8619 (t70) REVERT: a 127 MET cc_start: 0.7908 (mtt) cc_final: 0.7326 (mtp) REVERT: a 149 PHE cc_start: 0.8448 (OUTLIER) cc_final: 0.6892 (p90) REVERT: a 249 ARG cc_start: 0.6298 (tpt170) cc_final: 0.3353 (ttm170) REVERT: a 265 GLU cc_start: 0.8710 (tp30) cc_final: 0.7947 (tt0) REVERT: a 272 ASN cc_start: 0.8891 (p0) cc_final: 0.8627 (p0) REVERT: a 350 TYR cc_start: 0.9417 (m-80) cc_final: 0.8724 (m-80) REVERT: a 361 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.6787 (p90) REVERT: b 149 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.6748 (p90) REVERT: b 153 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8381 (ttmm) REVERT: b 205 MET cc_start: 0.8425 (mmp) cc_final: 0.8058 (mmp) REVERT: b 215 GLN cc_start: 0.8648 (mt0) cc_final: 0.8416 (mt0) REVERT: b 249 ARG cc_start: 0.6330 (tpt170) cc_final: 0.4098 (ttm-80) REVERT: b 391 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8626 (t0) REVERT: c 99 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8583 (mp10) REVERT: c 149 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7945 (p90) REVERT: c 153 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8530 (ttmt) REVERT: c 212 THR cc_start: 0.8715 (t) cc_final: 0.8487 (t) REVERT: c 249 ARG cc_start: 0.6196 (tpt170) cc_final: 0.3366 (ttm170) REVERT: c 290 LYS cc_start: 0.9057 (mmmt) cc_final: 0.8667 (tptp) REVERT: c 391 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8620 (t70) REVERT: d 127 MET cc_start: 0.7907 (mtt) cc_final: 0.7321 (mtp) REVERT: d 149 PHE cc_start: 0.8449 (OUTLIER) cc_final: 0.6895 (p90) REVERT: d 249 ARG cc_start: 0.6281 (tpt170) cc_final: 0.3351 (ttm170) REVERT: d 265 GLU cc_start: 0.8721 (tp30) cc_final: 0.7959 (tt0) REVERT: d 272 ASN cc_start: 0.8892 (p0) cc_final: 0.8630 (p0) REVERT: d 350 TYR cc_start: 0.9424 (m-80) cc_final: 0.8731 (m-80) REVERT: d 361 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.6801 (p90) REVERT: e 149 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.6753 (p90) REVERT: e 153 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8380 (ttmm) REVERT: e 205 MET cc_start: 0.8423 (mmp) cc_final: 0.8056 (mmp) REVERT: e 215 GLN cc_start: 0.8643 (mt0) cc_final: 0.8410 (mt0) REVERT: e 249 ARG cc_start: 0.6334 (tpt170) cc_final: 0.4114 (ttm-80) REVERT: e 391 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8627 (t0) REVERT: f 99 GLN cc_start: 0.9006 (mm-40) cc_final: 0.8583 (mp10) REVERT: f 149 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.7929 (p90) REVERT: f 153 LYS cc_start: 0.8913 (ttmt) cc_final: 0.8575 (ttmt) REVERT: f 249 ARG cc_start: 0.6169 (tpt170) cc_final: 0.3359 (ttm170) REVERT: f 290 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8663 (tptp) REVERT: f 391 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8627 (t70) outliers start: 164 outliers final: 96 residues processed: 792 average time/residue: 0.2404 time to fit residues: 310.2395 Evaluate side-chains 798 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 678 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 120 SER 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 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 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 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 X residue 120 SER 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 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 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 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 a residue 120 SER 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 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 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 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 d residue 120 SER 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 222 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 349 optimal weight: 20.0000 chunk 427 optimal weight: 5.9990 chunk 301 optimal weight: 7.9990 chunk 165 optimal weight: 8.9990 chunk 25 optimal weight: 0.0470 chunk 173 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 319 optimal weight: 1.9990 chunk 343 optimal weight: 10.0000 overall best weight: 2.1684 ------------------------------------------------------------------------------- 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 105 ASN ** V 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 215 GLN 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 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.137721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099100 restraints weight = 53980.180| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.87 r_work: 0.3053 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3111 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= 0.154 Angle : 0.630 7.282 48672 Z= 0.321 Chirality : 0.044 0.201 5268 Planarity : 0.005 0.079 6420 Dihedral : 4.932 26.183 4904 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.69 % Allowed : 23.20 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.24 (0.13), residues: 4524 helix: 1.03 (0.12), residues: 1968 sheet: -0.38 (0.28), residues: 480 loop : -2.94 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG c 50 TYR 0.018 0.001 TYR b 367 PHE 0.015 0.001 PHE U 371 TRP 0.013 0.001 TRP V 143 HIS 0.002 0.001 HIS V 297 Details of bonding type rmsd covalent geometry : bond 0.00366 (36000) covalent geometry : angle 0.63010 (48672) hydrogen bonds : bond 0.03288 ( 1464) hydrogen bonds : angle 4.37521 ( 4068) *********************** 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 864 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 689 time to evaluate : 1.419 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: 0.8554 (OUTLIER) cc_final: 0.6914 (p90) REVERT: U 249 ARG cc_start: 0.6251 (tpt170) cc_final: 0.3367 (ttm170) REVERT: U 350 TYR cc_start: 0.9499 (m-80) cc_final: 0.8894 (m-80) REVERT: U 361 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.6914 (p90) REVERT: U 403 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8564 (pp20) REVERT: V 149 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.6819 (p90) REVERT: V 153 LYS cc_start: 0.8755 (ttmt) cc_final: 0.8450 (ttmm) REVERT: V 195 MET cc_start: 0.9025 (tpt) cc_final: 0.8705 (tpt) REVERT: V 205 MET cc_start: 0.8523 (mmt) cc_final: 0.8141 (mmt) REVERT: V 249 ARG cc_start: 0.6282 (tpt170) cc_final: 0.3358 (ttm170) REVERT: V 391 ASP cc_start: 0.9007 (OUTLIER) cc_final: 0.8658 (t0) REVERT: V 403 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: W 99 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8523 (mp10) REVERT: W 149 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7959 (p90) REVERT: W 153 LYS cc_start: 0.8951 (ttmt) cc_final: 0.8607 (ttmt) REVERT: W 249 ARG cc_start: 0.6316 (tpt170) cc_final: 0.3507 (ttm170) REVERT: W 290 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8622 (tptp) REVERT: W 361 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7422 (p90) REVERT: W 391 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8646 (t70) REVERT: W 403 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: X 149 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.6910 (p90) REVERT: X 249 ARG cc_start: 0.6304 (tpt170) cc_final: 0.3383 (ttm170) REVERT: X 350 TYR cc_start: 0.9500 (m-80) cc_final: 0.8901 (m-80) REVERT: X 360 MET cc_start: 0.8917 (ttm) cc_final: 0.8686 (ttm) REVERT: X 361 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6917 (p90) REVERT: X 403 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8558 (pp20) REVERT: Y 149 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.6893 (p90) REVERT: Y 153 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8449 (ttmm) REVERT: Y 195 MET cc_start: 0.9019 (tpt) cc_final: 0.8697 (tpt) REVERT: Y 205 MET cc_start: 0.8522 (mmt) cc_final: 0.8131 (mmt) REVERT: Y 249 ARG cc_start: 0.6274 (tpt170) cc_final: 0.3351 (ttm170) REVERT: Y 391 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8666 (t0) REVERT: Y 403 GLU cc_start: 0.9084 (OUTLIER) cc_final: 0.8586 (pp20) REVERT: Z 99 GLN cc_start: 0.9054 (mm-40) cc_final: 0.8523 (mp10) REVERT: Z 149 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.7999 (p90) REVERT: Z 153 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8616 (ttmt) REVERT: Z 249 ARG cc_start: 0.6306 (tpt170) cc_final: 0.3492 (ttm170) REVERT: Z 290 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8626 (tptp) REVERT: Z 361 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7781 (p90) REVERT: Z 391 ASP cc_start: 0.8984 (OUTLIER) cc_final: 0.8645 (t70) REVERT: Z 403 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8626 (pp20) REVERT: a 149 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.6918 (p90) REVERT: a 249 ARG cc_start: 0.6281 (tpt170) cc_final: 0.3365 (ttm170) REVERT: a 350 TYR cc_start: 0.9494 (m-80) cc_final: 0.8894 (m-80) REVERT: a 360 MET cc_start: 0.8916 (ttm) cc_final: 0.8686 (ttm) REVERT: a 361 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.6912 (p90) REVERT: a 403 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8562 (pp20) REVERT: b 149 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.6816 (p90) REVERT: b 153 LYS cc_start: 0.8761 (ttmt) cc_final: 0.8455 (ttmm) REVERT: b 195 MET cc_start: 0.9026 (tpt) cc_final: 0.8699 (tpt) REVERT: b 249 ARG cc_start: 0.6268 (tpt170) cc_final: 0.3357 (ttm170) REVERT: b 391 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8665 (t0) REVERT: b 403 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8581 (pp20) REVERT: c 99 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8520 (mp10) REVERT: c 149 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8006 (p90) REVERT: c 153 LYS cc_start: 0.8941 (ttmt) cc_final: 0.8628 (ttmt) REVERT: c 212 THR cc_start: 0.8750 (t) cc_final: 0.8546 (t) REVERT: c 249 ARG cc_start: 0.6314 (tpt170) cc_final: 0.3485 (ttm170) REVERT: c 290 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8631 (tptp) REVERT: c 361 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7423 (p90) REVERT: c 391 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8641 (t70) REVERT: c 403 GLU cc_start: 0.9162 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: d 149 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.6913 (p90) REVERT: d 249 ARG cc_start: 0.6269 (tpt170) cc_final: 0.3361 (ttm170) REVERT: d 350 TYR cc_start: 0.9500 (m-80) cc_final: 0.8898 (m-80) REVERT: d 360 MET cc_start: 0.8914 (ttm) cc_final: 0.8686 (ttm) REVERT: d 361 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.6914 (p90) REVERT: d 403 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8573 (pp20) REVERT: e 149 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.6892 (p90) REVERT: e 153 LYS cc_start: 0.8751 (ttmt) cc_final: 0.8445 (ttmm) REVERT: e 195 MET cc_start: 0.9027 (tpt) cc_final: 0.8710 (tpt) REVERT: e 249 ARG cc_start: 0.6279 (tpt170) cc_final: 0.3362 (ttm170) REVERT: e 391 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8668 (t0) REVERT: e 403 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8590 (pp20) REVERT: f 99 GLN cc_start: 0.9056 (mm-40) cc_final: 0.8521 (mp10) REVERT: f 149 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7964 (p90) REVERT: f 153 LYS cc_start: 0.8950 (ttmt) cc_final: 0.8607 (ttmt) REVERT: f 249 ARG cc_start: 0.6273 (tpt170) cc_final: 0.3490 (ttm170) REVERT: f 290 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8629 (tptp) REVERT: f 361 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7794 (p90) REVERT: f 391 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8642 (t70) REVERT: f 403 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8633 (pp20) outliers start: 175 outliers final: 110 residues processed: 814 average time/residue: 0.2310 time to fit residues: 305.8050 Evaluate side-chains 832 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 682 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 120 SER 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 U residue 403 GLU Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 PHE 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 391 ASP 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 149 PHE 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 W residue 396 ILE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 120 SER 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 403 GLU Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 119 LEU Chi-restraints excluded: chain Y residue 149 PHE 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 391 ASP 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 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 Z residue 396 ILE Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 120 SER 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 403 GLU Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 149 PHE 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 391 ASP 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 149 PHE 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 c residue 396 ILE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 120 SER 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 403 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 149 PHE 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 391 ASP 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 149 PHE 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 Chi-restraints excluded: chain f residue 396 ILE Chi-restraints excluded: chain f residue 403 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 69 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 395 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 366 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 300 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 293 optimal weight: 4.9990 chunk 243 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 105 ASN ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.135505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.096598 restraints weight = 54212.503| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.88 r_work: 0.3011 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 36000 Z= 0.225 Angle : 0.680 7.438 48672 Z= 0.346 Chirality : 0.046 0.202 5268 Planarity : 0.005 0.075 6420 Dihedral : 5.131 26.373 4904 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 5.04 % Allowed : 23.47 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.13), residues: 4524 helix: 0.94 (0.12), residues: 1968 sheet: -0.30 (0.28), residues: 480 loop : -2.94 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 103 TYR 0.015 0.002 TYR V 367 PHE 0.021 0.002 PHE U 371 TRP 0.009 0.001 TRP V 143 HIS 0.004 0.001 HIS b 297 Details of bonding type rmsd covalent geometry : bond 0.00543 (36000) covalent geometry : angle 0.68018 (48672) hydrogen bonds : bond 0.03851 ( 1464) hydrogen bonds : angle 4.44723 ( 4068) *********************** 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 872 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 684 time to evaluate : 1.435 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 127 MET cc_start: 0.8076 (mtt) cc_final: 0.7566 (mtp) REVERT: U 149 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.6999 (p90) REVERT: U 249 ARG cc_start: 0.6362 (tpt170) cc_final: 0.3391 (ttm170) REVERT: U 350 TYR cc_start: 0.9490 (m-80) cc_final: 0.9066 (m-80) REVERT: U 361 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7020 (p90) REVERT: U 403 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8571 (pp20) REVERT: V 149 PHE cc_start: 0.8580 (OUTLIER) cc_final: 0.6940 (p90) REVERT: V 153 LYS cc_start: 0.8716 (ttmt) cc_final: 0.8368 (ttmm) REVERT: V 249 ARG cc_start: 0.6309 (tpt170) cc_final: 0.3317 (ttm170) REVERT: V 391 ASP cc_start: 0.9060 (OUTLIER) cc_final: 0.8695 (t0) REVERT: V 403 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8611 (pp20) REVERT: W 37 LYS cc_start: 0.8573 (ptmt) cc_final: 0.8316 (pttt) REVERT: W 99 GLN cc_start: 0.9105 (mm-40) cc_final: 0.8637 (mp10) REVERT: W 149 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7970 (p90) REVERT: W 153 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8646 (ttmt) REVERT: W 205 MET cc_start: 0.8598 (mmp) cc_final: 0.8355 (mmp) REVERT: W 249 ARG cc_start: 0.6508 (tpt170) cc_final: 0.3302 (ttm170) REVERT: W 285 LYS cc_start: 0.8421 (ttpp) cc_final: 0.8045 (ttpp) REVERT: W 290 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8682 (tptp) REVERT: W 361 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7731 (p90) REVERT: W 391 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8797 (t70) REVERT: W 403 GLU cc_start: 0.9186 (OUTLIER) cc_final: 0.8655 (pp20) REVERT: X 127 MET cc_start: 0.8079 (mtt) cc_final: 0.7569 (mtp) REVERT: X 149 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.6978 (p90) REVERT: X 249 ARG cc_start: 0.6372 (tpt170) cc_final: 0.3385 (ttm170) REVERT: X 350 TYR cc_start: 0.9489 (m-80) cc_final: 0.9063 (m-80) REVERT: X 360 MET cc_start: 0.8880 (ttm) cc_final: 0.8637 (ttm) REVERT: X 361 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7023 (p90) REVERT: X 403 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8565 (pp20) REVERT: Y 149 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.6933 (p90) REVERT: Y 153 LYS cc_start: 0.8718 (ttmt) cc_final: 0.8368 (ttmm) REVERT: Y 249 ARG cc_start: 0.6308 (tpt170) cc_final: 0.3311 (ttm170) REVERT: Y 289 MET cc_start: 0.9097 (mmm) cc_final: 0.8714 (mmm) REVERT: Y 391 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8701 (t0) REVERT: Y 403 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: Z 37 LYS cc_start: 0.8574 (ptmt) cc_final: 0.8318 (pttt) REVERT: Z 99 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8561 (mp10) REVERT: Z 149 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7982 (p90) REVERT: Z 153 LYS cc_start: 0.8948 (ttmt) cc_final: 0.8633 (ttmt) REVERT: Z 205 MET cc_start: 0.8536 (mmt) cc_final: 0.8066 (mmt) REVERT: Z 249 ARG cc_start: 0.6484 (tpt170) cc_final: 0.3286 (ttm170) REVERT: Z 290 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8691 (tptp) REVERT: Z 361 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7767 (p90) REVERT: Z 391 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8793 (t70) REVERT: Z 403 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8651 (pp20) REVERT: a 127 MET cc_start: 0.8029 (mtt) cc_final: 0.7503 (mtp) REVERT: a 149 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.6977 (p90) REVERT: a 249 ARG cc_start: 0.6372 (tpt170) cc_final: 0.3381 (ttm170) REVERT: a 350 TYR cc_start: 0.9482 (m-80) cc_final: 0.9055 (m-80) REVERT: a 360 MET cc_start: 0.8880 (ttm) cc_final: 0.8642 (ttm) REVERT: a 361 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7023 (p90) REVERT: a 403 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8568 (pp20) REVERT: b 149 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.6933 (p90) REVERT: b 153 LYS cc_start: 0.8725 (ttmt) cc_final: 0.8379 (ttmm) REVERT: b 249 ARG cc_start: 0.6300 (tpt170) cc_final: 0.3301 (ttm170) REVERT: b 289 MET cc_start: 0.9100 (mmm) cc_final: 0.8719 (mmm) REVERT: b 391 ASP cc_start: 0.9065 (OUTLIER) cc_final: 0.8705 (t0) REVERT: b 403 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: c 37 LYS cc_start: 0.8584 (ptmt) cc_final: 0.8329 (pttt) REVERT: c 99 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8632 (mp10) REVERT: c 149 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7992 (p90) REVERT: c 153 LYS cc_start: 0.8954 (ttmt) cc_final: 0.8645 (ttmt) REVERT: c 205 MET cc_start: 0.8601 (mmp) cc_final: 0.8356 (mmp) REVERT: c 249 ARG cc_start: 0.6464 (tpt170) cc_final: 0.3266 (ttm170) REVERT: c 290 LYS cc_start: 0.9053 (mmmt) cc_final: 0.8690 (tptp) REVERT: c 361 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7734 (p90) REVERT: c 391 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8797 (t70) REVERT: c 403 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8662 (pp20) REVERT: d 127 MET cc_start: 0.8076 (mtt) cc_final: 0.7611 (mtp) REVERT: d 149 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.6987 (p90) REVERT: d 249 ARG cc_start: 0.6381 (tpt170) cc_final: 0.3377 (ttm170) REVERT: d 350 TYR cc_start: 0.9489 (m-80) cc_final: 0.9060 (m-80) REVERT: d 360 MET cc_start: 0.8883 (ttm) cc_final: 0.8646 (ttm) REVERT: d 361 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7026 (p90) REVERT: d 403 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8572 (pp20) REVERT: e 149 PHE cc_start: 0.8584 (OUTLIER) cc_final: 0.6931 (p90) REVERT: e 153 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8374 (ttmm) REVERT: e 249 ARG cc_start: 0.6299 (tpt170) cc_final: 0.3313 (ttm170) REVERT: e 289 MET cc_start: 0.9101 (mmm) cc_final: 0.8721 (mmm) REVERT: e 391 ASP cc_start: 0.9068 (OUTLIER) cc_final: 0.8709 (t0) REVERT: e 403 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8615 (pp20) REVERT: f 37 LYS cc_start: 0.8639 (ptmt) cc_final: 0.8417 (pttt) REVERT: f 99 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8630 (mp10) REVERT: f 149 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7972 (p90) REVERT: f 153 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8642 (ttmt) REVERT: f 249 ARG cc_start: 0.6478 (tpt170) cc_final: 0.3288 (ttm170) REVERT: f 285 LYS cc_start: 0.8418 (ttpp) cc_final: 0.8041 (ttpp) REVERT: f 290 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8682 (tptp) REVERT: f 361 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7756 (p90) REVERT: f 391 ASP cc_start: 0.9131 (OUTLIER) cc_final: 0.8793 (t70) REVERT: f 403 GLU cc_start: 0.9198 (OUTLIER) cc_final: 0.8672 (pp20) outliers start: 188 outliers final: 117 residues processed: 812 average time/residue: 0.2220 time to fit residues: 294.1083 Evaluate side-chains 828 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 671 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 49 GLN Chi-restraints excluded: chain U residue 120 SER 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 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 119 LEU Chi-restraints excluded: chain V residue 149 PHE 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 391 ASP Chi-restraints excluded: chain V residue 403 GLU Chi-restraints excluded: chain W residue 49 GLN Chi-restraints excluded: chain W residue 74 ASP 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 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 W residue 396 ILE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 49 GLN Chi-restraints excluded: chain X residue 108 MET Chi-restraints excluded: chain X residue 120 SER 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 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 X residue 403 GLU Chi-restraints excluded: chain Y residue 69 GLN Chi-restraints excluded: chain Y residue 119 LEU 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 391 ASP Chi-restraints excluded: chain Y residue 403 GLU Chi-restraints excluded: chain Z residue 49 GLN Chi-restraints excluded: chain Z residue 74 ASP 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 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 Z residue 396 ILE Chi-restraints excluded: chain Z residue 403 GLU Chi-restraints excluded: chain a residue 49 GLN Chi-restraints excluded: chain a residue 120 SER 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 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 a residue 403 GLU Chi-restraints excluded: chain b residue 69 GLN Chi-restraints excluded: chain b residue 119 LEU Chi-restraints excluded: chain b residue 149 PHE 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 391 ASP Chi-restraints excluded: chain b residue 403 GLU Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 74 ASP 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 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 c residue 396 ILE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 49 GLN Chi-restraints excluded: chain d residue 108 MET Chi-restraints excluded: chain d residue 120 SER 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 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 d residue 403 GLU Chi-restraints excluded: chain e residue 69 GLN Chi-restraints excluded: chain e residue 119 LEU Chi-restraints excluded: chain e residue 149 PHE 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 391 ASP Chi-restraints excluded: chain e residue 403 GLU Chi-restraints excluded: chain f residue 49 GLN Chi-restraints excluded: chain f residue 74 ASP 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 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 Chi-restraints excluded: chain f residue 396 ILE 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 379 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 234 optimal weight: 0.2980 chunk 377 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 230 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 391 optimal weight: 2.9990 chunk 295 optimal weight: 0.2980 chunk 369 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Z 105 ASN a 105 ASN ** a 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** d 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100934 restraints weight = 53636.472| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.88 r_work: 0.3083 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3320 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= 0.120 Angle : 0.614 7.821 48672 Z= 0.314 Chirality : 0.043 0.189 5268 Planarity : 0.005 0.063 6420 Dihedral : 4.918 26.594 4904 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 4.21 % Allowed : 24.44 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.13), residues: 4524 helix: 1.13 (0.12), residues: 1956 sheet: 0.09 (0.32), residues: 360 loop : -2.74 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 103 TYR 0.014 0.001 TYR e 367 PHE 0.016 0.001 PHE f 361 TRP 0.011 0.001 TRP c 121 HIS 0.001 0.000 HIS V 297 Details of bonding type rmsd covalent geometry : bond 0.00275 (36000) covalent geometry : angle 0.61384 (48672) hydrogen bonds : bond 0.02902 ( 1464) hydrogen bonds : angle 4.35951 ( 4068) *********************** 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 855 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 698 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 149 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.6909 (p90) REVERT: U 232 ILE cc_start: 0.8652 (mm) cc_final: 0.8442 (tp) REVERT: U 249 ARG cc_start: 0.6176 (tpt170) cc_final: 0.3332 (ttm170) REVERT: U 350 TYR cc_start: 0.9480 (m-80) cc_final: 0.8880 (m-80) REVERT: U 361 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.6915 (p90) REVERT: U 403 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8534 (pp20) REVERT: V 149 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.6808 (p90) REVERT: V 153 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8387 (ttmm) REVERT: V 249 ARG cc_start: 0.6210 (tpt170) cc_final: 0.3312 (ttm170) REVERT: V 289 MET cc_start: 0.9044 (mmm) cc_final: 0.8693 (mmm) REVERT: V 391 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8606 (t0) REVERT: V 403 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8583 (pp20) REVERT: W 37 LYS cc_start: 0.8546 (ptmt) cc_final: 0.8297 (pttt) REVERT: W 99 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8503 (mp10) REVERT: W 149 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7781 (p90) REVERT: W 153 LYS cc_start: 0.8938 (ttmt) cc_final: 0.8616 (ttmt) REVERT: W 249 ARG cc_start: 0.6292 (tpt170) cc_final: 0.3519 (ttm170) REVERT: W 285 LYS cc_start: 0.8354 (ttpp) cc_final: 0.8082 (tttp) REVERT: W 290 LYS cc_start: 0.9091 (mmmt) cc_final: 0.8730 (tptp) REVERT: W 361 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7594 (p90) REVERT: W 391 ASP cc_start: 0.9040 (OUTLIER) cc_final: 0.8746 (t70) REVERT: W 403 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8656 (pp20) REVERT: X 127 MET cc_start: 0.8015 (mtt) cc_final: 0.7457 (mtp) REVERT: X 149 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.6894 (p90) REVERT: X 232 ILE cc_start: 0.8653 (mm) cc_final: 0.8450 (tp) REVERT: X 249 ARG cc_start: 0.6206 (tpt170) cc_final: 0.3332 (ttm170) REVERT: X 350 TYR cc_start: 0.9474 (m-80) cc_final: 0.8780 (m-80) REVERT: X 361 PHE cc_start: 0.8156 (OUTLIER) cc_final: 0.6924 (p90) REVERT: X 403 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8531 (pp20) REVERT: Y 149 PHE cc_start: 0.8405 (OUTLIER) cc_final: 0.6802 (p90) REVERT: Y 153 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8374 (ttmm) REVERT: Y 249 ARG cc_start: 0.6195 (tpt170) cc_final: 0.3313 (ttm170) REVERT: Y 289 MET cc_start: 0.9037 (mmm) cc_final: 0.8682 (mmm) REVERT: Y 391 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8612 (t0) REVERT: Y 403 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8569 (pp20) REVERT: Z 37 LYS cc_start: 0.8542 (ptmt) cc_final: 0.8292 (pttt) REVERT: Z 99 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8485 (mp10) REVERT: Z 149 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.7844 (p90) REVERT: Z 153 LYS cc_start: 0.8928 (ttmt) cc_final: 0.8603 (ttmt) REVERT: Z 249 ARG cc_start: 0.6227 (tpt170) cc_final: 0.3476 (ttm170) REVERT: Z 290 LYS cc_start: 0.9093 (mmmt) cc_final: 0.8731 (tptp) REVERT: Z 361 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7558 (p90) REVERT: Z 391 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8741 (t70) REVERT: Z 403 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: a 149 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.6906 (p90) REVERT: a 232 ILE cc_start: 0.8661 (mm) cc_final: 0.8454 (tp) REVERT: a 249 ARG cc_start: 0.6187 (tpt170) cc_final: 0.3323 (ttm170) REVERT: a 350 TYR cc_start: 0.9469 (m-80) cc_final: 0.8773 (m-80) REVERT: a 361 PHE cc_start: 0.8153 (OUTLIER) cc_final: 0.6922 (p90) REVERT: a 403 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8536 (pp20) REVERT: b 149 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.6796 (p90) REVERT: b 153 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8386 (ttmm) REVERT: b 249 ARG cc_start: 0.6182 (tpt170) cc_final: 0.3309 (ttm170) REVERT: b 289 MET cc_start: 0.9041 (mmm) cc_final: 0.8686 (mmm) REVERT: b 391 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8610 (t0) REVERT: b 403 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8570 (pp20) REVERT: c 37 LYS cc_start: 0.8556 (ptmt) cc_final: 0.8309 (pttt) REVERT: c 99 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8499 (mp10) REVERT: c 149 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7853 (p90) REVERT: c 153 LYS cc_start: 0.8934 (ttmt) cc_final: 0.8612 (ttmt) REVERT: c 249 ARG cc_start: 0.6242 (tpt170) cc_final: 0.3483 (ttm170) REVERT: c 290 LYS cc_start: 0.9087 (mmmt) cc_final: 0.8721 (tptp) REVERT: c 361 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7621 (p90) REVERT: c 391 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8747 (t70) REVERT: c 403 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8672 (pp20) REVERT: d 127 MET cc_start: 0.8000 (mtt) cc_final: 0.7444 (mtp) REVERT: d 149 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.6905 (p90) REVERT: d 232 ILE cc_start: 0.8657 (mm) cc_final: 0.8447 (tp) REVERT: d 249 ARG cc_start: 0.6186 (tpt170) cc_final: 0.3314 (ttm170) REVERT: d 350 TYR cc_start: 0.9477 (m-80) cc_final: 0.8779 (m-80) REVERT: d 361 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.6922 (p90) REVERT: d 403 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8535 (pp20) REVERT: e 149 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.6792 (p90) REVERT: e 153 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8374 (ttmm) REVERT: e 249 ARG cc_start: 0.6189 (tpt170) cc_final: 0.3300 (ttm170) REVERT: e 289 MET cc_start: 0.9033 (mmm) cc_final: 0.8686 (mmm) REVERT: e 391 ASP cc_start: 0.8943 (OUTLIER) cc_final: 0.8616 (t0) REVERT: e 403 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8576 (pp20) REVERT: f 99 GLN cc_start: 0.9025 (mm-40) cc_final: 0.8487 (mp10) REVERT: f 149 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.7837 (p90) REVERT: f 153 LYS cc_start: 0.8931 (ttmt) cc_final: 0.8604 (ttmt) REVERT: f 249 ARG cc_start: 0.6223 (tpt170) cc_final: 0.3481 (ttm170) REVERT: f 285 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8074 (tttp) REVERT: f 290 LYS cc_start: 0.9092 (mmmt) cc_final: 0.8731 (tptp) REVERT: f 361 PHE cc_start: 0.8033 (OUTLIER) cc_final: 0.7364 (p90) REVERT: f 391 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8740 (t70) REVERT: f 403 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.8667 (pp20) outliers start: 157 outliers final: 86 residues processed: 815 average time/residue: 0.2142 time to fit residues: 284.2389 Evaluate side-chains 798 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 672 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 345 THR Chi-restraints excluded: chain V residue 391 ASP 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 131 VAL Chi-restraints excluded: chain W residue 149 PHE 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 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 W residue 396 ILE Chi-restraints excluded: chain W residue 403 GLU Chi-restraints excluded: chain X residue 108 MET 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 372 ASP 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 345 THR Chi-restraints excluded: chain Y residue 391 ASP 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 131 VAL Chi-restraints excluded: chain Z residue 149 PHE 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 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 391 ASP Chi-restraints excluded: chain Z residue 396 ILE 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 372 ASP 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 345 THR Chi-restraints excluded: chain b residue 391 ASP 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 149 PHE 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 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 c residue 396 ILE Chi-restraints excluded: chain c residue 403 GLU Chi-restraints excluded: chain d residue 108 MET 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 372 ASP 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 345 THR Chi-restraints excluded: chain e residue 391 ASP 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 149 PHE 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 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 391 ASP Chi-restraints excluded: chain f residue 396 ILE 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 408 optimal weight: 5.9990 chunk 336 optimal weight: 0.7980 chunk 166 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 355 optimal weight: 8.9990 chunk 364 optimal weight: 0.6980 chunk 372 optimal weight: 0.0670 chunk 212 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- 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 V 140 ASN W 105 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 140 ASN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 105 ASN ** 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** a 140 ASN a 215 GLN ** b 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 140 ASN ** c 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 140 ASN ** e 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 140 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102301 restraints weight = 54427.342| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.92 r_work: 0.3079 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 36000 Z= 0.116 Angle : 0.617 8.216 48672 Z= 0.313 Chirality : 0.043 0.178 5268 Planarity : 0.005 0.080 6420 Dihedral : 4.779 26.287 4904 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 3.22 % Allowed : 25.35 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.13), residues: 4524 helix: 1.16 (0.12), residues: 1956 sheet: -0.27 (0.27), residues: 480 loop : -2.81 (0.13), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG a 103 TYR 0.014 0.001 TYR b 367 PHE 0.019 0.001 PHE e 207 TRP 0.010 0.001 TRP V 73 HIS 0.001 0.000 HIS e 297 Details of bonding type rmsd covalent geometry : bond 0.00261 (36000) covalent geometry : angle 0.61682 (48672) hydrogen bonds : bond 0.02777 ( 1464) hydrogen bonds : angle 4.24601 ( 4068) ********************** 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 844 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 724 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 149 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.6801 (p90) REVERT: U 153 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8567 (ttpt) REVERT: U 232 ILE cc_start: 0.8571 (mm) cc_final: 0.8353 (tp) REVERT: U 249 ARG cc_start: 0.6203 (tpt170) cc_final: 0.3321 (ttm170) REVERT: U 345 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8997 (p) REVERT: U 350 TYR cc_start: 0.9485 (m-80) cc_final: 0.8701 (m-80) REVERT: U 361 PHE cc_start: 0.7790 (OUTLIER) cc_final: 0.6984 (p90) REVERT: V 149 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.6757 (p90) REVERT: V 153 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8317 (ttmm) REVERT: V 183 ASN cc_start: 0.7555 (m-40) cc_final: 0.7351 (m110) REVERT: V 249 ARG cc_start: 0.6044 (tpt170) cc_final: 0.5209 (tpt170) REVERT: V 289 MET cc_start: 0.8939 (mmm) cc_final: 0.8581 (mmm) REVERT: V 391 ASP cc_start: 0.8903 (OUTLIER) cc_final: 0.8582 (t0) REVERT: V 403 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8575 (pp20) REVERT: W 37 LYS cc_start: 0.8512 (ptmt) cc_final: 0.8262 (pttt) REVERT: W 99 GLN cc_start: 0.9012 (mm-40) cc_final: 0.8489 (mp10) REVERT: W 149 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7761 (p90) REVERT: W 153 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8471 (ttmt) REVERT: W 205 MET cc_start: 0.8092 (mmp) cc_final: 0.7551 (mmt) REVERT: W 249 ARG cc_start: 0.6233 (tpt170) cc_final: 0.3493 (ttm170) REVERT: W 265 GLU cc_start: 0.8714 (tp30) cc_final: 0.7957 (tt0) REVERT: W 285 LYS cc_start: 0.8345 (ttpp) cc_final: 0.8083 (tttp) REVERT: W 290 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8587 (tptp) REVERT: W 361 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7537 (p90) REVERT: W 403 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8630 (pp20) REVERT: X 127 MET cc_start: 0.7943 (mtt) cc_final: 0.7360 (mtp) REVERT: X 149 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.6795 (p90) REVERT: X 153 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8564 (ttpt) REVERT: X 205 MET cc_start: 0.8290 (mmt) cc_final: 0.8007 (tpp) REVERT: X 232 ILE cc_start: 0.8577 (mm) cc_final: 0.8358 (tp) REVERT: X 249 ARG cc_start: 0.6235 (tpt170) cc_final: 0.3342 (ttm170) REVERT: X 345 THR cc_start: 0.9247 (OUTLIER) cc_final: 0.8999 (p) REVERT: X 350 TYR cc_start: 0.9485 (m-80) cc_final: 0.8698 (m-80) REVERT: X 361 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.6819 (p90) REVERT: Y 149 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.6757 (p90) REVERT: Y 153 LYS cc_start: 0.8608 (ttmt) cc_final: 0.8302 (ttmm) REVERT: Y 183 ASN cc_start: 0.7556 (m-40) cc_final: 0.7356 (m110) REVERT: Y 249 ARG cc_start: 0.6050 (tpt170) cc_final: 0.5209 (tpt170) REVERT: Y 289 MET cc_start: 0.8931 (mmm) cc_final: 0.8571 (mmm) REVERT: Y 391 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8578 (t0) REVERT: Y 403 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8568 (pp20) REVERT: Z 37 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8260 (pttt) REVERT: Z 99 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8490 (mp10) REVERT: Z 149 PHE cc_start: 0.8469 (OUTLIER) cc_final: 0.7845 (p90) REVERT: Z 153 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8456 (ttmt) REVERT: Z 161 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8021 (mm-30) REVERT: Z 249 ARG cc_start: 0.6241 (tpt170) cc_final: 0.3484 (ttm170) REVERT: Z 265 GLU cc_start: 0.8714 (tp30) cc_final: 0.7968 (tt0) REVERT: Z 290 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8574 (tptp) REVERT: Z 361 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7490 (p90) REVERT: Z 403 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8633 (pp20) REVERT: a 149 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.6810 (p90) REVERT: a 153 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8564 (ttpt) REVERT: a 205 MET cc_start: 0.8285 (mmt) cc_final: 0.7997 (tpp) REVERT: a 215 GLN cc_start: 0.8541 (mt0) cc_final: 0.8292 (mt0) REVERT: a 232 ILE cc_start: 0.8573 (mm) cc_final: 0.8354 (tp) REVERT: a 249 ARG cc_start: 0.6230 (tpt170) cc_final: 0.3359 (ttm170) REVERT: a 345 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.9000 (p) REVERT: a 350 TYR cc_start: 0.9485 (m-80) cc_final: 0.8697 (m-80) REVERT: a 361 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6817 (p90) REVERT: b 149 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.6751 (p90) REVERT: b 153 LYS cc_start: 0.8602 (ttmt) cc_final: 0.8286 (ttmm) REVERT: b 183 ASN cc_start: 0.7558 (m-40) cc_final: 0.7355 (m110) REVERT: b 249 ARG cc_start: 0.6051 (tpt170) cc_final: 0.5213 (tpt170) REVERT: b 289 MET cc_start: 0.8939 (mmm) cc_final: 0.8580 (mmm) REVERT: b 391 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8584 (t0) REVERT: b 403 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8562 (pp20) REVERT: c 37 LYS cc_start: 0.8504 (ptmt) cc_final: 0.8253 (pttt) REVERT: c 99 GLN cc_start: 0.9001 (mm-40) cc_final: 0.8481 (mp10) REVERT: c 149 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7828 (p90) REVERT: c 153 LYS cc_start: 0.8836 (ttmt) cc_final: 0.8456 (ttmt) REVERT: c 161 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8016 (mm-30) REVERT: c 205 MET cc_start: 0.8082 (mmp) cc_final: 0.7546 (mmt) REVERT: c 249 ARG cc_start: 0.6266 (tpt170) cc_final: 0.3485 (ttm170) REVERT: c 265 GLU cc_start: 0.8719 (tp30) cc_final: 0.7976 (tt0) REVERT: c 290 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8574 (tptp) REVERT: c 361 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.7538 (p90) REVERT: c 403 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.8614 (pp20) REVERT: d 127 MET cc_start: 0.7938 (mtt) cc_final: 0.7359 (mtp) REVERT: d 149 PHE cc_start: 0.8347 (OUTLIER) cc_final: 0.6805 (p90) REVERT: d 153 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8565 (ttpt) REVERT: d 205 MET cc_start: 0.8283 (mmt) cc_final: 0.7998 (tpp) REVERT: d 232 ILE cc_start: 0.8578 (mm) cc_final: 0.8353 (tp) REVERT: d 249 ARG cc_start: 0.6198 (tpt170) cc_final: 0.3332 (ttm170) REVERT: d 345 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.9000 (p) REVERT: d 350 TYR cc_start: 0.9489 (m-80) cc_final: 0.8702 (m-80) REVERT: d 361 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.6823 (p90) REVERT: e 149 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.6748 (p90) REVERT: e 153 LYS cc_start: 0.8617 (ttmt) cc_final: 0.8300 (ttmm) REVERT: e 183 ASN cc_start: 0.7546 (m-40) cc_final: 0.7343 (m110) REVERT: e 249 ARG cc_start: 0.6034 (tpt170) cc_final: 0.5204 (tpt170) REVERT: e 289 MET cc_start: 0.8938 (mmm) cc_final: 0.8578 (mmm) REVERT: e 391 ASP cc_start: 0.8906 (OUTLIER) cc_final: 0.8592 (t0) REVERT: e 403 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8568 (pp20) REVERT: f 99 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8489 (mp10) REVERT: f 149 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.7770 (p90) REVERT: f 153 LYS cc_start: 0.8825 (ttmt) cc_final: 0.8467 (ttmt) REVERT: f 249 ARG cc_start: 0.6251 (tpt170) cc_final: 0.3484 (ttm170) REVERT: f 265 GLU cc_start: 0.8731 (tp30) cc_final: 0.7975 (tt0) REVERT: f 290 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8573 (tptp) REVERT: f 361 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7430 (p90) REVERT: f 403 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.8632 (pp20) outliers start: 120 outliers final: 67 residues processed: 808 average time/residue: 0.2182 time to fit residues: 286.4558 Evaluate side-chains 794 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 691 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 372 ASP Chi-restraints excluded: chain V residue 119 LEU Chi-restraints excluded: chain V residue 149 PHE Chi-restraints excluded: chain V residue 245 VAL Chi-restraints excluded: chain V residue 345 THR Chi-restraints excluded: chain V residue 391 ASP 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 201 ILE 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 345 THR 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 108 MET 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 Y residue 119 LEU Chi-restraints excluded: chain Y residue 149 PHE Chi-restraints excluded: chain Y residue 245 VAL Chi-restraints excluded: chain Y residue 391 ASP 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 131 VAL Chi-restraints excluded: chain Z residue 149 PHE 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 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 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 b residue 149 PHE Chi-restraints excluded: chain b residue 245 VAL Chi-restraints excluded: chain b residue 345 THR Chi-restraints excluded: chain b residue 391 ASP 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 131 VAL Chi-restraints excluded: chain c residue 149 PHE 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 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 403 GLU Chi-restraints excluded: chain d residue 108 MET 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 e residue 149 PHE Chi-restraints excluded: chain e residue 245 VAL Chi-restraints excluded: chain e residue 345 THR Chi-restraints excluded: chain e residue 391 ASP 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 131 VAL Chi-restraints excluded: chain f residue 149 PHE 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 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 403 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 96 optimal weight: 10.0000 chunk 113 optimal weight: 0.6980 chunk 267 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 316 optimal weight: 0.1980 chunk 95 optimal weight: 6.9990 chunk 242 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 270 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** W 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 183 ASN ** X 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 215 GLN ** Z 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 183 ASN ** a 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 98 GLN a 215 GLN ** b 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 105 ASN ** c 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 183 ASN d 98 GLN ** e 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 105 ASN f 183 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102736 restraints weight = 53950.778| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.90 r_work: 0.3085 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 36000 Z= 0.118 Angle : 0.620 8.473 48672 Z= 0.313 Chirality : 0.043 0.171 5268 Planarity : 0.005 0.069 6420 Dihedral : 4.718 27.511 4896 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.79 % Favored : 89.21 % Rotamer: Outliers : 3.38 % Allowed : 25.54 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.13), residues: 4524 helix: 1.35 (0.13), residues: 1896 sheet: 0.16 (0.32), residues: 360 loop : -2.76 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d 103 TYR 0.014 0.001 TYR Y 367 PHE 0.020 0.001 PHE e 207 TRP 0.010 0.001 TRP U 73 HIS 0.001 0.000 HIS e 297 Details of bonding type rmsd covalent geometry : bond 0.00270 (36000) covalent geometry : angle 0.62030 (48672) hydrogen bonds : bond 0.02792 ( 1464) hydrogen bonds : angle 4.17379 ( 4068) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9219.24 seconds wall clock time: 158 minutes 44.76 seconds (9524.76 seconds total)