Starting phenix.real_space_refine on Wed Aug 27 01:11:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wk4_37595/08_2025/8wk4_37595.map" } resolution = 3.7 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= -0.001 sd= 0.046 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 108 5.16 5 C 27220 2.51 5 N 8295 2.21 5 O 9067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 414 residue(s): 0.03s 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: 44690 Number of models: 1 Model: "" Number of chains: 45 Chain: "i" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "k" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "l" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "m" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "n" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 129 Classifications: {'peptide': 19} Link IDs: {'TRANS': 18} Chain: "o" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 116 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "p" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "q" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 119 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "r" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 119 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "s" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 118 Classifications: {'peptide': 17} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 1, 'TRANS': 15} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "B" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "C" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "D" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "E" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "F" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "G" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "H" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "I" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "J" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "K" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "L" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "M" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "N" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "O" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "P" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "Q" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "R" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "S" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "T" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "U" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "V" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "W" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "X" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "Y" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "Z" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "a" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "b" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "c" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "d" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "e" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "f" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "g" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "h" Number of atoms: 1275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1275 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Time building chain proxies: 9.23, per 1000 atoms: 0.21 Number of scatterers: 44690 At special positions: 0 Unit cell: (266.4, 265.2, 102, 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 108 16.00 O 9067 8.00 N 8295 7.00 C 27220 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: 3.64 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 715.3 nanoseconds 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10894 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 70 sheets defined 29.0% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'i' and resid 3 through 21 Processing helix chain 'j' and resid 4 through 21 Processing helix chain 'k' and resid 4 through 21 Processing helix chain 'l' and resid 4 through 21 Processing helix chain 'm' and resid 4 through 21 Processing helix chain 'n' and resid 4 through 21 Processing helix chain 'A' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE B 252 " --> pdb=" O ARG B 248 " (cutoff:3.500A) Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'C' and resid 230 through 258 removed outlier: 3.609A pdb=" N ILE C 252 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Proline residue: C 255 - end of helix Processing helix chain 'C' and resid 405 through 421 Processing helix chain 'D' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE D 252 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 405 through 421 Processing helix chain 'E' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE E 252 " --> pdb=" O ARG E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 405 through 421 Processing helix chain 'F' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE F 252 " --> pdb=" O ARG F 248 " (cutoff:3.500A) Proline residue: F 255 - end of helix Processing helix chain 'F' and resid 405 through 421 Processing helix chain 'G' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE G 252 " --> pdb=" O ARG G 248 " (cutoff:3.500A) Proline residue: G 255 - end of helix Processing helix chain 'G' and resid 405 through 421 Processing helix chain 'H' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE H 252 " --> pdb=" O ARG H 248 " (cutoff:3.500A) Proline residue: H 255 - end of helix Processing helix chain 'H' and resid 405 through 421 Processing helix chain 'I' and resid 230 through 258 removed outlier: 3.609A pdb=" N ILE I 252 " --> pdb=" O ARG I 248 " (cutoff:3.500A) Proline residue: I 255 - end of helix Processing helix chain 'I' and resid 405 through 421 Processing helix chain 'J' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE J 252 " --> pdb=" O ARG J 248 " (cutoff:3.500A) Proline residue: J 255 - end of helix Processing helix chain 'J' and resid 405 through 421 Processing helix chain 'K' and resid 230 through 258 removed outlier: 3.606A pdb=" N ILE K 252 " --> pdb=" O ARG K 248 " (cutoff:3.500A) Proline residue: K 255 - end of helix Processing helix chain 'K' and resid 405 through 421 Processing helix chain 'L' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE L 252 " --> pdb=" O ARG L 248 " (cutoff:3.500A) Proline residue: L 255 - end of helix Processing helix chain 'L' and resid 405 through 421 Processing helix chain 'M' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE M 252 " --> pdb=" O ARG M 248 " (cutoff:3.500A) Proline residue: M 255 - end of helix Processing helix chain 'M' and resid 405 through 421 Processing helix chain 'N' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE N 252 " --> pdb=" O ARG N 248 " (cutoff:3.500A) Proline residue: N 255 - end of helix Processing helix chain 'N' and resid 405 through 421 Processing helix chain 'O' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE O 252 " --> pdb=" O ARG O 248 " (cutoff:3.500A) Proline residue: O 255 - end of helix Processing helix chain 'O' and resid 405 through 421 Processing helix chain 'P' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE P 252 " --> pdb=" O ARG P 248 " (cutoff:3.500A) Proline residue: P 255 - end of helix Processing helix chain 'P' and resid 405 through 421 Processing helix chain 'Q' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Q 252 " --> pdb=" O ARG Q 248 " (cutoff:3.500A) Proline residue: Q 255 - end of helix Processing helix chain 'Q' and resid 405 through 421 Processing helix chain 'R' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE R 252 " --> pdb=" O ARG R 248 " (cutoff:3.500A) Proline residue: R 255 - end of helix Processing helix chain 'R' and resid 405 through 421 Processing helix chain 'S' and resid 230 through 258 removed outlier: 3.609A pdb=" N ILE S 252 " --> pdb=" O ARG S 248 " (cutoff:3.500A) Proline residue: S 255 - end of helix Processing helix chain 'S' and resid 405 through 421 Processing helix chain 'T' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE T 252 " --> pdb=" O ARG T 248 " (cutoff:3.500A) Proline residue: T 255 - end of helix Processing helix chain 'T' and resid 405 through 421 Processing helix chain 'U' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE U 252 " --> pdb=" O ARG U 248 " (cutoff:3.500A) Proline residue: U 255 - end of helix Processing helix chain 'U' and resid 405 through 421 Processing helix chain 'V' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE V 252 " --> pdb=" O ARG V 248 " (cutoff:3.500A) Proline residue: V 255 - end of helix Processing helix chain 'V' and resid 405 through 421 Processing helix chain 'W' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE W 252 " --> pdb=" O ARG W 248 " (cutoff:3.500A) Proline residue: W 255 - end of helix Processing helix chain 'W' and resid 405 through 421 Processing helix chain 'X' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE X 252 " --> pdb=" O ARG X 248 " (cutoff:3.500A) Proline residue: X 255 - end of helix Processing helix chain 'X' and resid 405 through 421 Processing helix chain 'Y' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE Y 252 " --> pdb=" O ARG Y 248 " (cutoff:3.500A) Proline residue: Y 255 - end of helix Processing helix chain 'Y' and resid 405 through 421 Processing helix chain 'Z' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE Z 252 " --> pdb=" O ARG Z 248 " (cutoff:3.500A) Proline residue: Z 255 - end of helix Processing helix chain 'Z' and resid 405 through 421 Processing helix chain 'a' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE a 252 " --> pdb=" O ARG a 248 " (cutoff:3.500A) Proline residue: a 255 - end of helix Processing helix chain 'a' and resid 405 through 421 Processing helix chain 'b' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE b 252 " --> pdb=" O ARG b 248 " (cutoff:3.500A) Proline residue: b 255 - end of helix Processing helix chain 'b' and resid 405 through 421 Processing helix chain 'c' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE c 252 " --> pdb=" O ARG c 248 " (cutoff:3.500A) Proline residue: c 255 - end of helix Processing helix chain 'c' and resid 405 through 421 Processing helix chain 'd' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE d 252 " --> pdb=" O ARG d 248 " (cutoff:3.500A) Proline residue: d 255 - end of helix Processing helix chain 'd' and resid 405 through 421 Processing helix chain 'e' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE e 252 " --> pdb=" O ARG e 248 " (cutoff:3.500A) Proline residue: e 255 - end of helix Processing helix chain 'e' and resid 405 through 421 Processing helix chain 'f' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE f 252 " --> pdb=" O ARG f 248 " (cutoff:3.500A) Proline residue: f 255 - end of helix Processing helix chain 'f' and resid 405 through 421 Processing helix chain 'g' and resid 230 through 258 removed outlier: 3.608A pdb=" N ILE g 252 " --> pdb=" O ARG g 248 " (cutoff:3.500A) Proline residue: g 255 - end of helix Processing helix chain 'g' and resid 405 through 421 Processing helix chain 'h' and resid 230 through 258 removed outlier: 3.607A pdb=" N ILE h 252 " --> pdb=" O ARG h 248 " (cutoff:3.500A) Proline residue: h 255 - end of helix Processing helix chain 'h' and resid 405 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS A 263 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL A 389 " --> pdb=" O HIS A 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN A 265 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL A 387 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR A 267 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU A 385 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN A 269 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 292 through 303 removed outlier: 5.370A pdb=" N LEU A 293 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU A 367 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 295 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG B 294 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU B 293 " --> pdb=" O GLU B 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU B 367 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 295 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG C 294 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU C 293 " --> pdb=" O GLU C 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU C 367 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER C 295 " --> pdb=" O ASN C 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG D 294 " --> pdb=" O TYR C 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU D 293 " --> pdb=" O GLU D 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU D 367 " --> pdb=" O LEU D 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER D 295 " --> pdb=" O ASN D 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG E 294 " --> pdb=" O TYR D 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU E 293 " --> pdb=" O GLU E 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU E 367 " --> pdb=" O LEU E 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER E 295 " --> pdb=" O ASN E 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG F 294 " --> pdb=" O TYR E 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU F 293 " --> pdb=" O GLU F 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU F 367 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER F 295 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG G 294 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU G 293 " --> pdb=" O GLU G 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU G 367 " --> pdb=" O LEU G 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER G 295 " --> pdb=" O ASN G 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG H 294 " --> pdb=" O TYR G 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU H 293 " --> pdb=" O GLU H 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU H 367 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER H 295 " --> pdb=" O ASN H 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG I 294 " --> pdb=" O TYR H 366 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU I 293 " --> pdb=" O GLU I 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU I 367 " --> pdb=" O LEU I 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER I 295 " --> pdb=" O ASN I 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG J 294 " --> pdb=" O TYR I 366 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU J 293 " --> pdb=" O GLU J 367 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLU J 367 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER J 295 " --> pdb=" O ASN J 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG K 294 " --> pdb=" O TYR J 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU K 293 " --> pdb=" O GLU K 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU K 367 " --> pdb=" O LEU K 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER K 295 " --> pdb=" O ASN K 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG L 294 " --> pdb=" O TYR K 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU L 293 " --> pdb=" O GLU L 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU L 367 " --> pdb=" O LEU L 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER L 295 " --> pdb=" O ASN L 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG M 294 " --> pdb=" O TYR L 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU M 293 " --> pdb=" O GLU M 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU M 367 " --> pdb=" O LEU M 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER M 295 " --> pdb=" O ASN M 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG N 294 " --> pdb=" O TYR M 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU N 293 " --> pdb=" O GLU N 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU N 367 " --> pdb=" O LEU N 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER N 295 " --> pdb=" O ASN N 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG O 294 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU O 293 " --> pdb=" O GLU O 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU O 367 " --> pdb=" O LEU O 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER O 295 " --> pdb=" O ASN O 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG P 294 " --> pdb=" O TYR O 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU P 293 " --> pdb=" O GLU P 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU P 367 " --> pdb=" O LEU P 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER P 295 " --> pdb=" O ASN P 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG Q 294 " --> pdb=" O TYR P 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Q 293 " --> pdb=" O GLU Q 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Q 367 " --> pdb=" O LEU Q 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER Q 295 " --> pdb=" O ASN Q 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG R 294 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU R 293 " --> pdb=" O GLU R 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU R 367 " --> pdb=" O LEU R 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 295 " --> pdb=" O ASN R 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG S 294 " --> pdb=" O TYR R 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU S 293 " --> pdb=" O GLU S 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU S 367 " --> pdb=" O LEU S 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER S 295 " --> pdb=" O ASN S 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG T 294 " --> pdb=" O TYR S 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU T 293 " --> pdb=" O GLU T 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU T 367 " --> pdb=" O LEU T 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER T 295 " --> pdb=" O ASN T 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG U 294 " --> pdb=" O TYR T 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU U 293 " --> pdb=" O GLU U 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU U 367 " --> pdb=" O LEU U 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER U 295 " --> pdb=" O ASN U 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG V 294 " --> pdb=" O TYR U 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU V 293 " --> pdb=" O GLU V 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU V 367 " --> pdb=" O LEU V 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER V 295 " --> pdb=" O ASN V 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG W 294 " --> pdb=" O TYR V 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU W 293 " --> pdb=" O GLU W 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU W 367 " --> pdb=" O LEU W 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER W 295 " --> pdb=" O ASN W 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG X 294 " --> pdb=" O TYR W 366 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU X 293 " --> pdb=" O GLU X 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU X 367 " --> pdb=" O LEU X 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER X 295 " --> pdb=" O ASN X 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Y 294 " --> pdb=" O TYR X 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Y 293 " --> pdb=" O GLU Y 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU Y 367 " --> pdb=" O LEU Y 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Y 295 " --> pdb=" O ASN Y 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG Z 294 " --> pdb=" O TYR Y 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU Z 293 " --> pdb=" O GLU Z 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU Z 367 " --> pdb=" O LEU Z 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER Z 295 " --> pdb=" O ASN Z 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG a 294 " --> pdb=" O TYR Z 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU a 293 " --> pdb=" O GLU a 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU a 367 " --> pdb=" O LEU a 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER a 295 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG b 294 " --> pdb=" O TYR a 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU b 293 " --> pdb=" O GLU b 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU b 367 " --> pdb=" O LEU b 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER b 295 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG c 294 " --> pdb=" O TYR b 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU c 293 " --> pdb=" O GLU c 367 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU c 367 " --> pdb=" O LEU c 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER c 295 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ARG d 294 " --> pdb=" O TYR c 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU d 293 " --> pdb=" O GLU d 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU d 367 " --> pdb=" O LEU d 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER d 295 " --> pdb=" O ASN d 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG e 294 " --> pdb=" O TYR d 366 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU e 293 " --> pdb=" O GLU e 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU e 367 " --> pdb=" O LEU e 293 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER e 295 " --> pdb=" O ASN e 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG f 294 " --> pdb=" O TYR e 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU f 293 " --> pdb=" O GLU f 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU f 367 " --> pdb=" O LEU f 293 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER f 295 " --> pdb=" O ASN f 365 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ARG g 294 " --> pdb=" O TYR f 366 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU g 293 " --> pdb=" O GLU g 367 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N GLU g 367 " --> pdb=" O LEU g 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER g 295 " --> pdb=" O ASN g 365 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ARG h 294 " --> pdb=" O TYR g 366 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N LEU h 293 " --> pdb=" O GLU h 367 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLU h 367 " --> pdb=" O LEU h 293 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER h 295 " --> pdb=" O ASN h 365 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ARG A 294 " --> pdb=" O TYR h 366 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AA5, first strand: chain 'B' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS B 263 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 389 " --> pdb=" O HIS B 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN B 265 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL B 387 " --> pdb=" O GLN B 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR B 267 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU B 385 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN B 269 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS C 263 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL C 389 " --> pdb=" O HIS C 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN C 265 " --> pdb=" O VAL C 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL C 387 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR C 267 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU C 385 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN C 269 " --> pdb=" O GLU C 383 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'D' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS D 263 " --> pdb=" O VAL D 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL D 389 " --> pdb=" O HIS D 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN D 265 " --> pdb=" O VAL D 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL D 387 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR D 267 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU D 385 " --> pdb=" O THR D 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN D 269 " --> pdb=" O GLU D 383 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'E' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS E 263 " --> pdb=" O VAL E 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL E 389 " --> pdb=" O HIS E 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN E 265 " --> pdb=" O VAL E 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL E 387 " --> pdb=" O GLN E 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR E 267 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU E 385 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN E 269 " --> pdb=" O GLU E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 394 through 395 Processing sheet with id=AB4, first strand: chain 'F' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS F 263 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL F 389 " --> pdb=" O HIS F 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN F 265 " --> pdb=" O VAL F 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL F 387 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR F 267 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU F 385 " --> pdb=" O THR F 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN F 269 " --> pdb=" O GLU F 383 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 394 through 395 Processing sheet with id=AB6, first strand: chain 'G' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS G 263 " --> pdb=" O VAL G 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL G 389 " --> pdb=" O HIS G 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN G 265 " --> pdb=" O VAL G 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL G 387 " --> pdb=" O GLN G 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR G 267 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU G 385 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN G 269 " --> pdb=" O GLU G 383 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 394 through 395 Processing sheet with id=AB8, first strand: chain 'H' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS H 263 " --> pdb=" O VAL H 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL H 389 " --> pdb=" O HIS H 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN H 265 " --> pdb=" O VAL H 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H 387 " --> pdb=" O GLN H 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR H 267 " --> pdb=" O LEU H 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU H 385 " --> pdb=" O THR H 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN H 269 " --> pdb=" O GLU H 383 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 394 through 395 Processing sheet with id=AC1, first strand: chain 'I' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS I 263 " --> pdb=" O VAL I 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL I 389 " --> pdb=" O HIS I 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN I 265 " --> pdb=" O VAL I 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL I 387 " --> pdb=" O GLN I 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR I 267 " --> pdb=" O LEU I 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU I 385 " --> pdb=" O THR I 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN I 269 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 394 through 395 Processing sheet with id=AC3, first strand: chain 'J' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS J 263 " --> pdb=" O VAL J 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL J 389 " --> pdb=" O HIS J 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN J 265 " --> pdb=" O VAL J 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL J 387 " --> pdb=" O GLN J 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR J 267 " --> pdb=" O LEU J 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU J 385 " --> pdb=" O THR J 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN J 269 " --> pdb=" O GLU J 383 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'J' and resid 394 through 395 Processing sheet with id=AC5, first strand: chain 'K' and resid 262 through 271 removed outlier: 6.924A pdb=" N HIS K 263 " --> pdb=" O VAL K 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL K 389 " --> pdb=" O HIS K 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN K 265 " --> pdb=" O VAL K 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL K 387 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR K 267 " --> pdb=" O LEU K 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU K 385 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN K 269 " --> pdb=" O GLU K 383 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 394 through 395 Processing sheet with id=AC7, first strand: chain 'L' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS L 263 " --> pdb=" O VAL L 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL L 389 " --> pdb=" O HIS L 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN L 265 " --> pdb=" O VAL L 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL L 387 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR L 267 " --> pdb=" O LEU L 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU L 385 " --> pdb=" O THR L 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN L 269 " --> pdb=" O GLU L 383 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'L' and resid 394 through 395 Processing sheet with id=AC9, first strand: chain 'M' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS M 263 " --> pdb=" O VAL M 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL M 389 " --> pdb=" O HIS M 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN M 265 " --> pdb=" O VAL M 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL M 387 " --> pdb=" O GLN M 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR M 267 " --> pdb=" O LEU M 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU M 385 " --> pdb=" O THR M 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN M 269 " --> pdb=" O GLU M 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 394 through 395 Processing sheet with id=AD2, first strand: chain 'N' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS N 263 " --> pdb=" O VAL N 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL N 389 " --> pdb=" O HIS N 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN N 265 " --> pdb=" O VAL N 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL N 387 " --> pdb=" O GLN N 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR N 267 " --> pdb=" O LEU N 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU N 385 " --> pdb=" O THR N 267 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLN N 269 " --> pdb=" O GLU N 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 394 through 395 Processing sheet with id=AD4, first strand: chain 'O' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS O 263 " --> pdb=" O VAL O 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL O 389 " --> pdb=" O HIS O 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN O 265 " --> pdb=" O VAL O 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL O 387 " --> pdb=" O GLN O 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR O 267 " --> pdb=" O LEU O 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU O 385 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN O 269 " --> pdb=" O GLU O 383 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 394 through 395 Processing sheet with id=AD6, first strand: chain 'P' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS P 263 " --> pdb=" O VAL P 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL P 389 " --> pdb=" O HIS P 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN P 265 " --> pdb=" O VAL P 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL P 387 " --> pdb=" O GLN P 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR P 267 " --> pdb=" O LEU P 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU P 385 " --> pdb=" O THR P 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN P 269 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 394 through 395 Processing sheet with id=AD8, first strand: chain 'Q' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Q 263 " --> pdb=" O VAL Q 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Q 389 " --> pdb=" O HIS Q 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN Q 265 " --> pdb=" O VAL Q 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL Q 387 " --> pdb=" O GLN Q 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR Q 267 " --> pdb=" O LEU Q 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Q 385 " --> pdb=" O THR Q 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN Q 269 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Q' and resid 394 through 395 Processing sheet with id=AE1, first strand: chain 'R' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS R 263 " --> pdb=" O VAL R 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL R 389 " --> pdb=" O HIS R 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN R 265 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL R 387 " --> pdb=" O GLN R 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR R 267 " --> pdb=" O LEU R 385 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU R 385 " --> pdb=" O THR R 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN R 269 " --> pdb=" O GLU R 383 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'R' and resid 394 through 395 Processing sheet with id=AE3, first strand: chain 'S' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS S 263 " --> pdb=" O VAL S 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL S 389 " --> pdb=" O HIS S 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN S 265 " --> pdb=" O VAL S 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL S 387 " --> pdb=" O GLN S 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR S 267 " --> pdb=" O LEU S 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU S 385 " --> pdb=" O THR S 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN S 269 " --> pdb=" O GLU S 383 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 394 through 395 Processing sheet with id=AE5, first strand: chain 'T' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS T 263 " --> pdb=" O VAL T 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL T 389 " --> pdb=" O HIS T 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN T 265 " --> pdb=" O VAL T 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL T 387 " --> pdb=" O GLN T 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR T 267 " --> pdb=" O LEU T 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU T 385 " --> pdb=" O THR T 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN T 269 " --> pdb=" O GLU T 383 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'T' and resid 394 through 395 Processing sheet with id=AE7, first strand: chain 'U' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS U 263 " --> pdb=" O VAL U 389 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL U 389 " --> pdb=" O HIS U 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN U 265 " --> pdb=" O VAL U 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL U 387 " --> pdb=" O GLN U 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR U 267 " --> pdb=" O LEU U 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU U 385 " --> pdb=" O THR U 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN U 269 " --> pdb=" O GLU U 383 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'U' and resid 394 through 395 Processing sheet with id=AE9, first strand: chain 'V' and resid 262 through 271 removed outlier: 6.924A pdb=" N HIS V 263 " --> pdb=" O VAL V 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL V 389 " --> pdb=" O HIS V 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN V 265 " --> pdb=" O VAL V 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL V 387 " --> pdb=" O GLN V 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR V 267 " --> pdb=" O LEU V 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU V 385 " --> pdb=" O THR V 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN V 269 " --> pdb=" O GLU V 383 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'V' and resid 394 through 395 Processing sheet with id=AF2, first strand: chain 'W' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS W 263 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL W 389 " --> pdb=" O HIS W 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN W 265 " --> pdb=" O VAL W 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL W 387 " --> pdb=" O GLN W 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR W 267 " --> pdb=" O LEU W 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU W 385 " --> pdb=" O THR W 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN W 269 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 394 through 395 Processing sheet with id=AF4, first strand: chain 'X' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS X 263 " --> pdb=" O VAL X 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL X 389 " --> pdb=" O HIS X 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN X 265 " --> pdb=" O VAL X 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL X 387 " --> pdb=" O GLN X 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR X 267 " --> pdb=" O LEU X 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU X 385 " --> pdb=" O THR X 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN X 269 " --> pdb=" O GLU X 383 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'X' and resid 394 through 395 Processing sheet with id=AF6, first strand: chain 'Y' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS Y 263 " --> pdb=" O VAL Y 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL Y 389 " --> pdb=" O HIS Y 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN Y 265 " --> pdb=" O VAL Y 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL Y 387 " --> pdb=" O GLN Y 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR Y 267 " --> pdb=" O LEU Y 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Y 385 " --> pdb=" O THR Y 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN Y 269 " --> pdb=" O GLU Y 383 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Y' and resid 394 through 395 Processing sheet with id=AF8, first strand: chain 'Z' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS Z 263 " --> pdb=" O VAL Z 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL Z 389 " --> pdb=" O HIS Z 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN Z 265 " --> pdb=" O VAL Z 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL Z 387 " --> pdb=" O GLN Z 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR Z 267 " --> pdb=" O LEU Z 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU Z 385 " --> pdb=" O THR Z 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN Z 269 " --> pdb=" O GLU Z 383 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Z' and resid 394 through 395 Processing sheet with id=AG1, first strand: chain 'a' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS a 263 " --> pdb=" O VAL a 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL a 389 " --> pdb=" O HIS a 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN a 265 " --> pdb=" O VAL a 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL a 387 " --> pdb=" O GLN a 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR a 267 " --> pdb=" O LEU a 385 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N LEU a 385 " --> pdb=" O THR a 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN a 269 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AG3, first strand: chain 'b' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS b 263 " --> pdb=" O VAL b 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL b 389 " --> pdb=" O HIS b 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN b 265 " --> pdb=" O VAL b 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL b 387 " --> pdb=" O GLN b 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR b 267 " --> pdb=" O LEU b 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU b 385 " --> pdb=" O THR b 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN b 269 " --> pdb=" O GLU b 383 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AG5, first strand: chain 'c' and resid 262 through 271 removed outlier: 6.922A pdb=" N HIS c 263 " --> pdb=" O VAL c 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL c 389 " --> pdb=" O HIS c 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN c 265 " --> pdb=" O VAL c 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL c 387 " --> pdb=" O GLN c 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR c 267 " --> pdb=" O LEU c 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU c 385 " --> pdb=" O THR c 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN c 269 " --> pdb=" O GLU c 383 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 394 through 395 Processing sheet with id=AG7, first strand: chain 'd' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS d 263 " --> pdb=" O VAL d 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL d 389 " --> pdb=" O HIS d 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN d 265 " --> pdb=" O VAL d 387 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N VAL d 387 " --> pdb=" O GLN d 265 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N THR d 267 " --> pdb=" O LEU d 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU d 385 " --> pdb=" O THR d 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN d 269 " --> pdb=" O GLU d 383 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 394 through 395 Processing sheet with id=AG9, first strand: chain 'e' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS e 263 " --> pdb=" O VAL e 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL e 389 " --> pdb=" O HIS e 263 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN e 265 " --> pdb=" O VAL e 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL e 387 " --> pdb=" O GLN e 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR e 267 " --> pdb=" O LEU e 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU e 385 " --> pdb=" O THR e 267 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN e 269 " --> pdb=" O GLU e 383 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 394 through 395 Processing sheet with id=AH2, first strand: chain 'f' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS f 263 " --> pdb=" O VAL f 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL f 389 " --> pdb=" O HIS f 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN f 265 " --> pdb=" O VAL f 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL f 387 " --> pdb=" O GLN f 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR f 267 " --> pdb=" O LEU f 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU f 385 " --> pdb=" O THR f 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN f 269 " --> pdb=" O GLU f 383 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 394 through 395 Processing sheet with id=AH4, first strand: chain 'g' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS g 263 " --> pdb=" O VAL g 389 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL g 389 " --> pdb=" O HIS g 263 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLN g 265 " --> pdb=" O VAL g 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL g 387 " --> pdb=" O GLN g 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR g 267 " --> pdb=" O LEU g 385 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N LEU g 385 " --> pdb=" O THR g 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN g 269 " --> pdb=" O GLU g 383 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 394 through 395 Processing sheet with id=AH6, first strand: chain 'h' and resid 262 through 271 removed outlier: 6.923A pdb=" N HIS h 263 " --> pdb=" O VAL h 389 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL h 389 " --> pdb=" O HIS h 263 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLN h 265 " --> pdb=" O VAL h 387 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL h 387 " --> pdb=" O GLN h 265 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N THR h 267 " --> pdb=" O LEU h 385 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU h 385 " --> pdb=" O THR h 267 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN h 269 " --> pdb=" O GLU h 383 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 394 through 395 2703 hydrogen bonds defined for protein. 7497 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: 11.36 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12702 1.33 - 1.45: 6279 1.45 - 1.57: 25973 1.57 - 1.69: 0 1.69 - 1.81: 216 Bond restraints: 45170 Sorted by residual: bond pdb=" N VAL V 257 " pdb=" CA VAL V 257 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.34e-02 5.57e+03 1.22e+01 bond pdb=" N VAL a 257 " pdb=" CA VAL a 257 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" N VAL J 257 " pdb=" CA VAL J 257 " ideal model delta sigma weight residual 1.459 1.505 -0.047 1.34e-02 5.57e+03 1.21e+01 bond pdb=" N VAL h 257 " pdb=" CA VAL h 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.20e+01 bond pdb=" N VAL L 257 " pdb=" CA VAL L 257 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.34e-02 5.57e+03 1.20e+01 ... (remaining 45165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 58327 1.54 - 3.08: 1998 3.08 - 4.62: 516 4.62 - 6.16: 103 6.16 - 7.70: 71 Bond angle restraints: 61015 Sorted by residual: angle pdb=" C HIS r 72 " pdb=" N ILE r 73 " pdb=" CA ILE r 73 " ideal model delta sigma weight residual 123.04 116.28 6.76 9.20e-01 1.18e+00 5.40e+01 angle pdb=" CA HIS r 72 " pdb=" CB HIS r 72 " pdb=" CG HIS r 72 " ideal model delta sigma weight residual 113.80 106.50 7.30 1.00e+00 1.00e+00 5.32e+01 angle pdb=" N ASN h 261 " pdb=" CA ASN h 261 " pdb=" C ASN h 261 " ideal model delta sigma weight residual 113.02 106.53 6.49 1.20e+00 6.94e-01 2.93e+01 angle pdb=" N ASN K 261 " pdb=" CA ASN K 261 " pdb=" C ASN K 261 " ideal model delta sigma weight residual 113.02 106.54 6.48 1.20e+00 6.94e-01 2.92e+01 angle pdb=" N ASN E 261 " pdb=" CA ASN E 261 " pdb=" C ASN E 261 " ideal model delta sigma weight residual 113.02 106.54 6.48 1.20e+00 6.94e-01 2.91e+01 ... (remaining 61010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 23677 16.80 - 33.60: 2905 33.60 - 50.40: 1151 50.40 - 67.20: 266 67.20 - 84.00: 102 Dihedral angle restraints: 28101 sinusoidal: 11413 harmonic: 16688 Sorted by residual: dihedral pdb=" N LEU k 14 " pdb=" CA LEU k 14 " pdb=" CB LEU k 14 " pdb=" CG LEU k 14 " ideal model delta sinusoidal sigma weight residual -180.00 -120.30 -59.70 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG Y 294 " pdb=" CB ARG Y 294 " pdb=" CG ARG Y 294 " pdb=" CD ARG Y 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.98 59.02 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG D 294 " pdb=" CB ARG D 294 " pdb=" CG ARG D 294 " pdb=" CD ARG D 294 " ideal model delta sinusoidal sigma weight residual 180.00 120.98 59.02 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 28098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5860 0.053 - 0.106: 839 0.106 - 0.159: 288 0.159 - 0.213: 19 0.213 - 0.266: 6 Chirality restraints: 7012 Sorted by residual: chirality pdb=" CA ILE l 4 " pdb=" N ILE l 4 " pdb=" C ILE l 4 " pdb=" CB ILE l 4 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE j 4 " pdb=" N ILE j 4 " pdb=" C ILE j 4 " pdb=" CB ILE j 4 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE n 4 " pdb=" N ILE n 4 " pdb=" C ILE n 4 " pdb=" CB ILE n 4 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 7009 not shown) Planarity restraints: 8251 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE b 256 " -0.017 2.00e-02 2.50e+03 3.22e-02 1.03e+01 pdb=" C ILE b 256 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE b 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL b 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 256 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE E 256 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE E 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL E 257 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE f 256 " -0.017 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE f 256 " 0.056 2.00e-02 2.50e+03 pdb=" O ILE f 256 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL f 257 " -0.019 2.00e-02 2.50e+03 ... (remaining 8248 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 198 2.55 - 3.14: 31624 3.14 - 3.72: 67646 3.72 - 4.31: 96156 4.31 - 4.90: 164206 Nonbonded interactions: 359830 Sorted by model distance: nonbonded pdb=" O GLN q 76 " pdb=" OE1 GLN U 297 " model vdw 1.960 3.040 nonbonded pdb=" O VAL r 78 " pdb=" ND2 ASN N 299 " model vdw 1.988 3.120 nonbonded pdb=" OG1 THR r 68 " pdb=" CE1 HIS r 72 " model vdw 2.069 3.260 nonbonded pdb=" CG1 VAL s 78 " pdb=" ND2 ASN H 299 " model vdw 2.136 3.540 nonbonded pdb=" CG2 ILE m 7 " pdb=" CG2 THR G 278 " model vdw 2.252 3.880 ... (remaining 359825 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = 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' selection = chain 'g' selection = chain 'h' } ncs_group { reference = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } ncs_group { reference = (chain 'o' and (resid 62 through 74 or (resid 75 and (name N or name CA or name \ C or name O )) or resid 76 through 77)) selection = (chain 'q' and (resid 62 through 74 or (resid 75 and (name N or name CA or name \ C or name O )) or resid 76 through 77)) selection = (chain 'r' and (resid 62 through 74 or (resid 75 and (name N or name CA or name \ C or name O )) or resid 76 through 77)) selection = (chain 's' and resid 62 through 77) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 39.190 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 45170 Z= 0.275 Angle : 0.751 7.705 61015 Z= 0.493 Chirality : 0.044 0.266 7012 Planarity : 0.004 0.032 8251 Dihedral : 18.101 83.996 17207 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.14 % Allowed : 32.12 % Favored : 66.74 % 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: 1.81 (0.12), residues: 5613 helix: 3.94 (0.12), residues: 1530 sheet: 0.82 (0.11), residues: 2482 loop : -1.01 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG f 296 TYR 0.004 0.001 TYR F 366 PHE 0.007 0.001 PHE J 237 HIS 0.022 0.001 HIS r 72 Details of bonding type rmsd covalent geometry : bond 0.00413 (45170) covalent geometry : angle 0.75089 (61015) hydrogen bonds : bond 0.17844 ( 2703) hydrogen bonds : angle 5.88987 ( 7497) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2350 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 2294 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: r 76 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: A 280 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7893 (tt0) REVERT: A 384 ARG cc_start: 0.8287 (ttm170) cc_final: 0.8051 (ttp-110) REVERT: B 414 ASP cc_start: 0.8154 (m-30) cc_final: 0.7781 (m-30) REVERT: B 432 VAL cc_start: 0.8814 (t) cc_final: 0.8462 (t) REVERT: C 232 ASP cc_start: 0.7688 (m-30) cc_final: 0.6911 (t0) REVERT: C 271 ASP cc_start: 0.7049 (t0) cc_final: 0.6839 (t0) REVERT: C 425 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8198 (pttm) REVERT: D 297 GLN cc_start: 0.8293 (tt0) cc_final: 0.8014 (mp10) REVERT: D 298 LEU cc_start: 0.9036 (tp) cc_final: 0.8699 (tt) REVERT: D 372 ILE cc_start: 0.9265 (mt) cc_final: 0.9025 (tt) REVERT: E 276 GLU cc_start: 0.7178 (tt0) cc_final: 0.6849 (tt0) REVERT: E 281 HIS cc_start: 0.7461 (m-70) cc_final: 0.7118 (m170) REVERT: E 282 TYR cc_start: 0.8623 (m-80) cc_final: 0.8093 (m-10) REVERT: G 256 ILE cc_start: 0.9006 (pt) cc_final: 0.8536 (mp) REVERT: G 361 ASN cc_start: 0.8334 (m-40) cc_final: 0.7774 (m-40) REVERT: G 381 ASP cc_start: 0.7782 (m-30) cc_final: 0.7412 (t70) REVERT: G 411 GLN cc_start: 0.8250 (mt0) cc_final: 0.7708 (mm-40) REVERT: I 283 SER cc_start: 0.9264 (m) cc_final: 0.8932 (p) REVERT: J 270 LEU cc_start: 0.8782 (mt) cc_final: 0.7800 (mp) REVERT: J 303 GLN cc_start: 0.7738 (mt0) cc_final: 0.7529 (tm-30) REVERT: J 428 ASP cc_start: 0.8119 (m-30) cc_final: 0.7531 (m-30) REVERT: K 424 ASP cc_start: 0.7561 (m-30) cc_final: 0.7248 (p0) REVERT: L 394 LYS cc_start: 0.7465 (mmmt) cc_final: 0.6960 (mmmm) REVERT: M 282 TYR cc_start: 0.8783 (m-80) cc_final: 0.8381 (m-80) REVERT: M 381 ASP cc_start: 0.7718 (m-30) cc_final: 0.7279 (m-30) REVERT: M 414 ASP cc_start: 0.7961 (m-30) cc_final: 0.7517 (m-30) REVERT: N 266 VAL cc_start: 0.8789 (t) cc_final: 0.8413 (t) REVERT: N 283 SER cc_start: 0.9389 (m) cc_final: 0.9116 (p) REVERT: O 232 ASP cc_start: 0.7684 (m-30) cc_final: 0.6944 (t0) REVERT: O 259 ASN cc_start: 0.8282 (m-40) cc_final: 0.8018 (m110) REVERT: O 261 ASN cc_start: 0.7525 (m-40) cc_final: 0.7084 (m-40) REVERT: O 292 THR cc_start: 0.8811 (m) cc_final: 0.8377 (t) REVERT: P 360 ARG cc_start: 0.8460 (ttm-80) cc_final: 0.7833 (ttt-90) REVERT: P 382 ILE cc_start: 0.8993 (mt) cc_final: 0.8680 (mt) REVERT: P 430 LEU cc_start: 0.8239 (tp) cc_final: 0.7422 (tp) REVERT: P 432 VAL cc_start: 0.8419 (t) cc_final: 0.8013 (t) REVERT: P 434 ASN cc_start: 0.7062 (t0) cc_final: 0.6746 (t0) REVERT: Q 290 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8092 (ptpp) REVERT: S 283 SER cc_start: 0.9197 (m) cc_final: 0.8714 (p) REVERT: S 298 LEU cc_start: 0.8595 (tp) cc_final: 0.8081 (tp) REVERT: S 358 THR cc_start: 0.8511 (m) cc_final: 0.8099 (p) REVERT: S 414 ASP cc_start: 0.8771 (m-30) cc_final: 0.8203 (m-30) REVERT: T 283 SER cc_start: 0.9152 (m) cc_final: 0.8715 (p) REVERT: T 420 MET cc_start: 0.8362 (ptm) cc_final: 0.7992 (ptm) REVERT: U 383 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6737 (mt-10) REVERT: V 242 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6768 (pt0) REVERT: V 249 ILE cc_start: 0.8768 (mt) cc_final: 0.8553 (mt) REVERT: V 290 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7862 (ptmt) REVERT: V 428 ASP cc_start: 0.7966 (m-30) cc_final: 0.7708 (m-30) REVERT: W 369 ASP cc_start: 0.7879 (m-30) cc_final: 0.7642 (m-30) REVERT: X 282 TYR cc_start: 0.8338 (m-80) cc_final: 0.7939 (m-10) REVERT: X 295 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8083 (p) REVERT: X 385 LEU cc_start: 0.8422 (tp) cc_final: 0.8208 (tt) REVERT: X 394 LYS cc_start: 0.7310 (mmmt) cc_final: 0.6836 (mtmt) REVERT: Y 289 SER cc_start: 0.8471 (p) cc_final: 0.8068 (t) REVERT: Z 239 ASN cc_start: 0.7967 (t0) cc_final: 0.7701 (t0) REVERT: Z 295 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.8244 (p) REVERT: a 242 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7520 (mt-10) REVERT: a 359 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7377 (tt0) REVERT: a 394 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8326 (mtmm) REVERT: a 417 ARG cc_start: 0.8380 (mtt90) cc_final: 0.8003 (mtt-85) REVERT: c 375 THR cc_start: 0.8793 (m) cc_final: 0.8544 (t) REVERT: e 265 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7730 (mm-40) REVERT: e 359 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8296 (tt0) REVERT: e 418 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7542 (mm-30) REVERT: f 266 VAL cc_start: 0.8514 (t) cc_final: 0.7103 (t) REVERT: f 381 ASP cc_start: 0.6488 (m-30) cc_final: 0.4751 (m-30) REVERT: g 261 ASN cc_start: 0.8130 (m-40) cc_final: 0.7847 (t0) REVERT: g 270 LEU cc_start: 0.8298 (mt) cc_final: 0.8035 (mp) REVERT: g 370 ARG cc_start: 0.8529 (tmm-80) cc_final: 0.8143 (ttt90) REVERT: g 384 ARG cc_start: 0.8753 (ttm170) cc_final: 0.8236 (ttp-110) REVERT: g 394 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7444 (mtmt) REVERT: g 407 ASP cc_start: 0.7461 (t0) cc_final: 0.6922 (t0) outliers start: 56 outliers final: 9 residues processed: 2335 average time/residue: 0.2663 time to fit residues: 985.7350 Evaluate side-chains 1327 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1315 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 15 GLN Chi-restraints excluded: chain k residue 11 ILE Chi-restraints excluded: chain n residue 15 GLN Chi-restraints excluded: chain n residue 19 MET Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain q residue 71 HIS Chi-restraints excluded: chain r residue 76 GLN Chi-restraints excluded: chain s residue 65 LEU Chi-restraints excluded: chain V residue 295 SER Chi-restraints excluded: chain X residue 295 SER Chi-restraints excluded: chain Z residue 295 SER Chi-restraints excluded: chain h residue 295 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 0.3980 chunk 41 optimal weight: 0.7980 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 7.9990 chunk 414 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 76 GLN r 76 GLN ** s 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN A 359 GLN ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 HIS B 378 ASN ** B 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN C 374 HIS C 434 ASN D 303 GLN D 374 HIS E 374 HIS E 434 ASN F 234 GLN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 GLN G 239 ASN G 297 GLN G 374 HIS G 408 GLN H 231 ASN H 261 ASN H 265 GLN H 297 GLN H 374 HIS H 378 ASN I 431 ASN J 303 GLN J 374 HIS L 303 GLN M 263 HIS M 269 GLN M 277 GLN M 303 GLN M 374 HIS M 408 GLN N 274 ASN N 374 HIS O 374 HIS Q 259 ASN S 246 GLN S 259 ASN T 277 GLN T 374 HIS ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 ASN U 297 GLN V 434 ASN W 374 HIS X 261 ASN X 281 HIS Y 374 HIS ** Z 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 374 HIS b 374 HIS c 246 GLN c 277 GLN c 281 HIS d 431 ASN e 303 GLN e 374 HIS f 431 ASN f 434 ASN g 374 HIS ** g 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 277 GLN h 374 HIS Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102654 restraints weight = 78920.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.105566 restraints weight = 37824.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107433 restraints weight = 22964.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108618 restraints weight = 16420.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109379 restraints weight = 13152.425| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 45170 Z= 0.169 Angle : 0.622 9.549 61015 Z= 0.328 Chirality : 0.042 0.158 7012 Planarity : 0.005 0.090 8251 Dihedral : 4.523 58.824 6225 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 5.56 % Allowed : 25.43 % Favored : 69.01 % 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: 1.90 (0.12), residues: 5613 helix: 3.86 (0.12), residues: 1530 sheet: 0.69 (0.11), residues: 2618 loop : -0.51 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 244 TYR 0.014 0.002 TYR G 393 PHE 0.024 0.002 PHE c 422 HIS 0.011 0.001 HIS s 72 Details of bonding type rmsd covalent geometry : bond 0.00372 (45170) covalent geometry : angle 0.62155 (61015) hydrogen bonds : bond 0.03879 ( 2703) hydrogen bonds : angle 4.34431 ( 7497) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1719 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 1445 time to evaluate : 2.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 11 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7795 (pt) REVERT: q 72 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7829 (p-80) REVERT: A 271 ASP cc_start: 0.6833 (t0) cc_final: 0.6609 (t0) REVERT: A 302 GLU cc_start: 0.7300 (tp30) cc_final: 0.6953 (tp30) REVERT: A 303 GLN cc_start: 0.6227 (tm-30) cc_final: 0.5866 (tm-30) REVERT: A 358 THR cc_start: 0.8039 (m) cc_final: 0.7771 (m) REVERT: A 370 ARG cc_start: 0.8710 (tmm-80) cc_final: 0.8201 (ttp80) REVERT: B 296 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7360 (tpt-90) REVERT: B 413 GLU cc_start: 0.6524 (tm-30) cc_final: 0.5648 (tm-30) REVERT: B 414 ASP cc_start: 0.8296 (m-30) cc_final: 0.7881 (m-30) REVERT: C 232 ASP cc_start: 0.7638 (m-30) cc_final: 0.6920 (t0) REVERT: C 242 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7574 (mt-10) REVERT: C 269 GLN cc_start: 0.8605 (mm-40) cc_final: 0.8166 (mt0) REVERT: C 425 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8106 (pttm) REVERT: D 242 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7937 (mp0) REVERT: D 297 GLN cc_start: 0.7927 (tt0) cc_final: 0.7618 (mp10) REVERT: D 372 ILE cc_start: 0.9212 (mt) cc_final: 0.8916 (tt) REVERT: D 414 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7599 (t0) REVERT: E 246 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8250 (tm-30) REVERT: E 282 TYR cc_start: 0.8732 (m-80) cc_final: 0.8297 (m-10) REVERT: E 361 ASN cc_start: 0.7948 (m-40) cc_final: 0.7591 (t0) REVERT: E 420 MET cc_start: 0.8317 (ptp) cc_final: 0.8038 (ptm) REVERT: F 383 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8098 (mt-10) REVERT: G 246 GLN cc_start: 0.8339 (tt0) cc_final: 0.7947 (tt0) REVERT: G 256 ILE cc_start: 0.8994 (pt) cc_final: 0.8615 (mp) REVERT: G 381 ASP cc_start: 0.7399 (m-30) cc_final: 0.7123 (t0) REVERT: G 411 GLN cc_start: 0.8303 (mt0) cc_final: 0.7717 (mm-40) REVERT: G 424 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6317 (p0) REVERT: H 407 ASP cc_start: 0.7747 (p0) cc_final: 0.7452 (p0) REVERT: H 424 ASP cc_start: 0.8155 (m-30) cc_final: 0.7896 (t0) REVERT: I 283 SER cc_start: 0.9284 (m) cc_final: 0.8908 (p) REVERT: I 302 GLU cc_start: 0.7280 (pm20) cc_final: 0.7069 (mp0) REVERT: I 418 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.8213 (tp30) REVERT: J 269 GLN cc_start: 0.8752 (mp10) cc_final: 0.7799 (mm-40) REVERT: J 383 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7237 (mp0) REVERT: K 236 LYS cc_start: 0.8406 (mmtp) cc_final: 0.7765 (tmmt) REVERT: K 242 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8132 (mt-10) REVERT: L 276 GLU cc_start: 0.7967 (tt0) cc_final: 0.7667 (tt0) REVERT: M 360 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: M 428 ASP cc_start: 0.7190 (m-30) cc_final: 0.6481 (m-30) REVERT: N 410 LYS cc_start: 0.9093 (tppt) cc_final: 0.8575 (tppt) REVERT: O 232 ASP cc_start: 0.7575 (m-30) cc_final: 0.6900 (t0) REVERT: O 298 LEU cc_start: 0.8689 (tp) cc_final: 0.8409 (tp) REVERT: P 429 THR cc_start: 0.8621 (p) cc_final: 0.8413 (t) REVERT: Q 400 LYS cc_start: 0.6048 (OUTLIER) cc_final: 0.5562 (ptmm) REVERT: Q 418 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7641 (mm-30) REVERT: R 276 GLU cc_start: 0.8236 (tt0) cc_final: 0.7971 (tt0) REVERT: R 394 LYS cc_start: 0.8068 (ttmm) cc_final: 0.7835 (ptpp) REVERT: S 413 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7748 (tm-30) REVERT: T 280 GLU cc_start: 0.7209 (tt0) cc_final: 0.6935 (tt0) REVERT: T 283 SER cc_start: 0.9252 (m) cc_final: 0.8933 (p) REVERT: T 383 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8076 (mt-10) REVERT: U 250 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7439 (tm-30) REVERT: U 280 GLU cc_start: 0.7258 (tt0) cc_final: 0.6970 (tt0) REVERT: U 290 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8269 (mmtt) REVERT: U 363 THR cc_start: 0.9069 (m) cc_final: 0.8581 (p) REVERT: V 242 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7297 (mt-10) REVERT: V 275 LYS cc_start: 0.8521 (ptpp) cc_final: 0.7843 (ptpp) REVERT: V 377 MET cc_start: 0.8182 (mpp) cc_final: 0.7615 (mpp) REVERT: W 235 LEU cc_start: 0.9284 (mt) cc_final: 0.8891 (tp) REVERT: W 249 ILE cc_start: 0.9161 (tp) cc_final: 0.8954 (tp) REVERT: W 275 LYS cc_start: 0.9375 (mtmp) cc_final: 0.9065 (mttm) REVERT: W 394 LYS cc_start: 0.7073 (tttp) cc_final: 0.6664 (ptmm) REVERT: X 282 TYR cc_start: 0.8848 (m-80) cc_final: 0.8497 (m-10) REVERT: X 298 LEU cc_start: 0.8256 (tp) cc_final: 0.8051 (mt) REVERT: X 394 LYS cc_start: 0.7192 (mmmt) cc_final: 0.6577 (mtmt) REVERT: Y 230 LEU cc_start: 0.8755 (tp) cc_final: 0.8272 (tt) REVERT: Y 282 TYR cc_start: 0.8674 (m-80) cc_final: 0.8338 (m-10) REVERT: Y 366 TYR cc_start: 0.8739 (m-80) cc_final: 0.8384 (m-10) REVERT: Y 414 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8358 (t0) REVERT: Z 250 GLU cc_start: 0.8037 (pp20) cc_final: 0.7797 (pp20) REVERT: Z 362 GLU cc_start: 0.7665 (tt0) cc_final: 0.7376 (tt0) REVERT: Z 367 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7198 (mt-10) REVERT: a 275 LYS cc_start: 0.8468 (mttp) cc_final: 0.8169 (mttp) REVERT: a 303 GLN cc_start: 0.8046 (mp10) cc_final: 0.7844 (mp10) REVERT: a 413 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: b 242 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8136 (mp0) REVERT: b 246 GLN cc_start: 0.8417 (tt0) cc_final: 0.8185 (tt0) REVERT: b 362 GLU cc_start: 0.7033 (tt0) cc_final: 0.6757 (tt0) REVERT: b 386 SER cc_start: 0.8054 (m) cc_final: 0.7485 (t) REVERT: b 424 ASP cc_start: 0.7941 (p0) cc_final: 0.7737 (p0) REVERT: c 232 ASP cc_start: 0.7470 (m-30) cc_final: 0.7163 (p0) REVERT: c 246 GLN cc_start: 0.8199 (tt0) cc_final: 0.7948 (tt0) REVERT: c 281 HIS cc_start: 0.7126 (m170) cc_final: 0.6361 (m-70) REVERT: c 290 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7998 (ttmt) REVERT: e 265 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7847 (mm-40) REVERT: f 230 LEU cc_start: 0.8198 (pp) cc_final: 0.7877 (tt) REVERT: f 282 TYR cc_start: 0.9005 (m-80) cc_final: 0.8774 (m-10) REVERT: f 298 LEU cc_start: 0.8294 (mt) cc_final: 0.7173 (mt) REVERT: f 303 GLN cc_start: 0.7841 (mp10) cc_final: 0.7568 (mp10) REVERT: f 383 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7645 (mt-10) REVERT: g 407 ASP cc_start: 0.7090 (t0) cc_final: 0.6667 (t0) REVERT: h 275 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8551 (mttt) REVERT: h 437 PHE cc_start: 0.7971 (m-80) cc_final: 0.7567 (m-80) REVERT: h 438 SER cc_start: 0.7874 (m) cc_final: 0.7498 (p) outliers start: 274 outliers final: 142 residues processed: 1620 average time/residue: 0.2456 time to fit residues: 659.2495 Evaluate side-chains 1354 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1202 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 10 VAL Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain l residue 11 ILE Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 11 ILE Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain n residue 15 GLN Chi-restraints excluded: chain p residue 69 SER Chi-restraints excluded: chain q residue 71 HIS Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 415 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 266 VAL Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 239 ASN Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 424 ASP Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 246 GLN Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 281 HIS Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain M residue 246 GLN Chi-restraints excluded: chain M residue 390 VAL Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 371 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 292 THR Chi-restraints excluded: chain S residue 371 THR Chi-restraints excluded: chain S residue 385 LEU Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain S residue 435 SER Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain U residue 438 SER Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 256 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 414 ASP Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Z residue 372 ILE Chi-restraints excluded: chain Z residue 386 SER Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 242 GLU Chi-restraints excluded: chain b residue 267 THR Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 257 VAL Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 429 THR Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 253 LEU Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 267 THR Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 246 GLN Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 387 VAL Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 275 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 544 optimal weight: 9.9990 chunk 485 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 503 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 142 optimal weight: 0.0970 chunk 48 optimal weight: 8.9990 chunk 442 optimal weight: 10.0000 chunk 488 optimal weight: 10.0000 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: o 72 HIS ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 72 HIS ** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN C 234 GLN D 231 ASN D 277 GLN D 303 GLN D 378 ASN E 359 GLN ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 431 ASN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 GLN I 277 GLN K 231 ASN K 234 GLN K 277 GLN L 231 ASN L 378 ASN M 269 GLN ** M 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 431 ASN S 274 ASN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 378 ASN T 411 GLN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 ASN U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 408 GLN W 359 GLN X 265 GLN Y 281 HIS ** Z 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 231 ASN c 378 ASN d 303 GLN f 269 GLN f 431 ASN g 269 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.112600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093654 restraints weight = 80473.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096504 restraints weight = 38088.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098339 restraints weight = 23125.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099505 restraints weight = 16565.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100237 restraints weight = 13325.707| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 45170 Z= 0.229 Angle : 0.639 9.705 61015 Z= 0.339 Chirality : 0.043 0.191 7012 Planarity : 0.004 0.086 8251 Dihedral : 4.529 53.321 6207 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 6.49 % Allowed : 24.01 % Favored : 69.50 % 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: 1.64 (0.12), residues: 5613 helix: 3.31 (0.12), residues: 1530 sheet: 0.67 (0.11), residues: 2618 loop : -0.51 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 248 TYR 0.017 0.002 TYR U 282 PHE 0.021 0.002 PHE C 237 HIS 0.008 0.001 HIS s 72 Details of bonding type rmsd covalent geometry : bond 0.00510 (45170) covalent geometry : angle 0.63877 (61015) hydrogen bonds : bond 0.04051 ( 2703) hydrogen bonds : angle 4.44556 ( 7497) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1607 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 320 poor density : 1287 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 11 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.6831 (pt) REVERT: m 19 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.6161 (tmm) REVERT: q 72 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7830 (p-80) REVERT: A 242 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7042 (mt-10) REVERT: A 302 GLU cc_start: 0.7547 (tp30) cc_final: 0.7149 (tp30) REVERT: A 303 GLN cc_start: 0.6541 (tm-30) cc_final: 0.6261 (tm-30) REVERT: B 413 GLU cc_start: 0.6823 (tm-30) cc_final: 0.6482 (tm-30) REVERT: B 414 ASP cc_start: 0.8319 (m-30) cc_final: 0.7679 (m-30) REVERT: C 232 ASP cc_start: 0.7865 (m-30) cc_final: 0.7264 (t0) REVERT: C 242 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7594 (mt-10) REVERT: C 269 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8065 (mt0) REVERT: C 425 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8313 (pttm) REVERT: D 242 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7998 (mp0) REVERT: D 297 GLN cc_start: 0.8135 (tt0) cc_final: 0.7815 (mt0) REVERT: D 428 ASP cc_start: 0.7871 (m-30) cc_final: 0.7556 (m-30) REVERT: E 246 GLN cc_start: 0.8691 (tm-30) cc_final: 0.8426 (tm-30) REVERT: E 361 ASN cc_start: 0.8288 (m-40) cc_final: 0.7817 (m-40) REVERT: F 370 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8503 (ttm-80) REVERT: F 383 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8486 (mt-10) REVERT: F 409 MET cc_start: 0.8856 (mmm) cc_final: 0.8626 (mmp) REVERT: F 413 GLU cc_start: 0.7970 (pt0) cc_final: 0.7741 (pt0) REVERT: G 236 LYS cc_start: 0.8638 (mttt) cc_final: 0.8348 (ttpp) REVERT: G 240 ASP cc_start: 0.8493 (t0) cc_final: 0.8284 (t0) REVERT: G 256 ILE cc_start: 0.9177 (pt) cc_final: 0.8860 (mp) REVERT: G 367 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8017 (mm-30) REVERT: G 370 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8313 (ttp80) REVERT: G 381 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7211 (t70) REVERT: G 424 ASP cc_start: 0.7097 (p0) cc_final: 0.6859 (p0) REVERT: H 234 GLN cc_start: 0.8448 (mt0) cc_final: 0.8144 (mp10) REVERT: H 370 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8317 (ttm-80) REVERT: I 232 ASP cc_start: 0.7528 (m-30) cc_final: 0.7307 (t70) REVERT: I 283 SER cc_start: 0.9410 (m) cc_final: 0.9064 (p) REVERT: I 418 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8378 (tp30) REVERT: J 252 ILE cc_start: 0.9343 (tp) cc_final: 0.8956 (tp) REVERT: J 269 GLN cc_start: 0.9043 (mp10) cc_final: 0.8563 (mm-40) REVERT: J 290 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8546 (mmtp) REVERT: J 383 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7463 (mp0) REVERT: J 415 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7939 (mp) REVERT: J 420 MET cc_start: 0.8181 (ptm) cc_final: 0.7917 (ptt) REVERT: J 428 ASP cc_start: 0.8436 (m-30) cc_final: 0.8193 (m-30) REVERT: K 236 LYS cc_start: 0.8654 (mmtp) cc_final: 0.7935 (tmmt) REVERT: L 232 ASP cc_start: 0.8008 (t0) cc_final: 0.7732 (t0) REVERT: L 250 GLU cc_start: 0.8449 (tp30) cc_final: 0.7944 (tp30) REVERT: L 271 ASP cc_start: 0.8307 (m-30) cc_final: 0.8008 (m-30) REVERT: M 367 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8130 (mm-30) REVERT: M 416 THR cc_start: 0.8860 (m) cc_final: 0.8519 (p) REVERT: M 428 ASP cc_start: 0.7307 (m-30) cc_final: 0.6758 (m-30) REVERT: N 242 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8022 (mp0) REVERT: N 431 ASN cc_start: 0.8808 (t0) cc_final: 0.8364 (t0) REVERT: O 232 ASP cc_start: 0.7887 (m-30) cc_final: 0.7123 (t0) REVERT: O 298 LEU cc_start: 0.8761 (tp) cc_final: 0.8497 (tp) REVERT: O 387 VAL cc_start: 0.8886 (t) cc_final: 0.8652 (p) REVERT: P 235 LEU cc_start: 0.9191 (mt) cc_final: 0.8974 (mt) REVERT: Q 381 ASP cc_start: 0.7197 (OUTLIER) cc_final: 0.6701 (t70) REVERT: Q 383 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7410 (mp0) REVERT: R 276 GLU cc_start: 0.8315 (tt0) cc_final: 0.8044 (tt0) REVERT: R 394 LYS cc_start: 0.8206 (ttmm) cc_final: 0.7961 (pttt) REVERT: R 424 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7992 (t0) REVERT: S 254 SER cc_start: 0.8843 (t) cc_final: 0.8504 (m) REVERT: S 413 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7906 (tm-30) REVERT: T 244 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.7482 (ttp-110) REVERT: T 283 SER cc_start: 0.9331 (m) cc_final: 0.9058 (p) REVERT: U 236 LYS cc_start: 0.8904 (tppt) cc_final: 0.8372 (mtpt) REVERT: U 363 THR cc_start: 0.9251 (m) cc_final: 0.8706 (p) REVERT: U 413 GLU cc_start: 0.8881 (tm-30) cc_final: 0.8656 (tm-30) REVERT: U 431 ASN cc_start: 0.8657 (t0) cc_final: 0.8133 (t0) REVERT: V 242 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7387 (mt-10) REVERT: V 275 LYS cc_start: 0.8590 (ptpp) cc_final: 0.7694 (ptpp) REVERT: V 370 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7637 (ttm-80) REVERT: V 377 MET cc_start: 0.8343 (mpp) cc_final: 0.7675 (mpp) REVERT: W 302 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7519 (mp0) REVERT: W 418 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7218 (mm-30) REVERT: X 294 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.8168 (ttm-80) REVERT: Z 290 LYS cc_start: 0.8872 (mttp) cc_final: 0.8492 (mtmm) REVERT: Z 362 GLU cc_start: 0.7769 (tt0) cc_final: 0.7522 (tt0) REVERT: Z 367 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7385 (mt-10) REVERT: Z 370 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8033 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7945 (tm-30) REVERT: a 275 LYS cc_start: 0.8632 (mttp) cc_final: 0.8351 (mttp) REVERT: a 410 LYS cc_start: 0.8074 (tppt) cc_final: 0.7871 (tppt) REVERT: a 413 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8279 (tm-30) REVERT: b 362 GLU cc_start: 0.7098 (tt0) cc_final: 0.6874 (tt0) REVERT: b 386 SER cc_start: 0.8402 (m) cc_final: 0.7649 (t) REVERT: c 232 ASP cc_start: 0.7556 (m-30) cc_final: 0.7326 (p0) REVERT: c 246 GLN cc_start: 0.8275 (tt0) cc_final: 0.7908 (tp40) REVERT: c 279 GLU cc_start: 0.7528 (tt0) cc_final: 0.7269 (tt0) REVERT: c 290 LYS cc_start: 0.8329 (ttmt) cc_final: 0.8104 (ttmt) REVERT: c 437 PHE cc_start: 0.8311 (m-10) cc_final: 0.8067 (m-10) REVERT: d 418 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8515 (mm-30) REVERT: e 265 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8017 (mm-40) REVERT: f 230 LEU cc_start: 0.8173 (pp) cc_final: 0.7893 (tt) REVERT: f 303 GLN cc_start: 0.7841 (mp10) cc_final: 0.7491 (mp10) REVERT: g 261 ASN cc_start: 0.7714 (m-40) cc_final: 0.7409 (t0) REVERT: g 367 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8340 (mm-30) REVERT: g 370 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (tpp80) REVERT: g 405 THR cc_start: 0.7280 (p) cc_final: 0.6170 (m) REVERT: h 234 GLN cc_start: 0.7837 (mt0) cc_final: 0.7620 (mt0) REVERT: h 379 VAL cc_start: 0.9036 (t) cc_final: 0.8762 (p) outliers start: 320 outliers final: 194 residues processed: 1498 average time/residue: 0.2354 time to fit residues: 587.0404 Evaluate side-chains 1342 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 211 poor density : 1131 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 10 VAL Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain l residue 11 ILE Chi-restraints excluded: chain m residue 11 ILE Chi-restraints excluded: chain m residue 19 MET Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain n residue 15 GLN Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 71 HIS Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 412 ILE Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 295 SER Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 391 VAL Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 234 GLN Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 281 HIS Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 267 THR Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 292 THR Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 415 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 257 VAL Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 398 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 371 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 405 THR Chi-restraints excluded: chain Q residue 410 LYS Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 292 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 424 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 292 THR Chi-restraints excluded: chain S residue 371 THR Chi-restraints excluded: chain S residue 385 LEU Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain V residue 408 GLN Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 256 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ARG Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 295 SER Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 385 LEU Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 372 ILE Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain a residue 246 GLN Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 267 THR Chi-restraints excluded: chain b residue 402 LEU Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 252 ILE Chi-restraints excluded: chain c residue 253 LEU Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 257 VAL Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 429 THR Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 293 LEU Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 246 GLN Chi-restraints excluded: chain f residue 269 GLN Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 385 LEU Chi-restraints excluded: chain f residue 395 THR Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 431 ASN Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 267 THR Chi-restraints excluded: chain g residue 269 GLN Chi-restraints excluded: chain g residue 278 THR Chi-restraints excluded: chain g residue 363 THR Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 267 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 338 optimal weight: 7.9990 chunk 261 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 548 optimal weight: 4.9990 chunk 443 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN C 269 GLN D 303 GLN G 231 ASN G 234 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS J 281 HIS L 378 ASN ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 269 GLN ** M 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 303 GLN N 374 HIS N 434 ASN ** O 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 231 ASN R 234 GLN ** S 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 431 ASN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN X 269 GLN Y 431 ASN a 234 GLN a 263 HIS ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 246 GLN ** b 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 378 ASN b 434 ASN d 374 HIS f 269 GLN f 431 ASN g 234 GLN ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 378 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.093270 restraints weight = 81036.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.095931 restraints weight = 39413.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097597 restraints weight = 24332.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.098727 restraints weight = 17807.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099464 restraints weight = 14356.417| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 45170 Z= 0.199 Angle : 0.611 8.036 61015 Z= 0.321 Chirality : 0.042 0.176 7012 Planarity : 0.004 0.071 8251 Dihedral : 4.446 53.538 6207 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 6.17 % Allowed : 25.22 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.56 (0.11), residues: 5613 helix: 3.18 (0.12), residues: 1530 sheet: 0.65 (0.10), residues: 2618 loop : -0.53 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG U 417 TYR 0.019 0.001 TYR H 282 PHE 0.018 0.002 PHE f 272 HIS 0.005 0.001 HIS N 374 Details of bonding type rmsd covalent geometry : bond 0.00447 (45170) covalent geometry : angle 0.61055 (61015) hydrogen bonds : bond 0.03674 ( 2703) hydrogen bonds : angle 4.36525 ( 7497) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1534 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 304 poor density : 1230 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 71 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7539 (t70) REVERT: q 72 HIS cc_start: 0.8230 (OUTLIER) cc_final: 0.7493 (p-80) REVERT: A 242 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6868 (mt-10) REVERT: A 302 GLU cc_start: 0.7478 (tp30) cc_final: 0.7189 (tp30) REVERT: B 413 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6513 (tm-30) REVERT: B 414 ASP cc_start: 0.8180 (m-30) cc_final: 0.7466 (m-30) REVERT: C 232 ASP cc_start: 0.7675 (m-30) cc_final: 0.7235 (t0) REVERT: C 242 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7551 (mt-10) REVERT: C 269 GLN cc_start: 0.8562 (mm110) cc_final: 0.8060 (mt0) REVERT: C 425 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8371 (pttm) REVERT: C 431 ASN cc_start: 0.8272 (t0) cc_final: 0.7666 (t0) REVERT: D 242 GLU cc_start: 0.8286 (mt-10) cc_final: 0.8034 (mp0) REVERT: D 297 GLN cc_start: 0.7982 (tt0) cc_final: 0.7672 (mp10) REVERT: D 414 ASP cc_start: 0.8581 (t0) cc_final: 0.8322 (t0) REVERT: E 246 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8438 (tm-30) REVERT: F 294 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7914 (tpt170) REVERT: F 409 MET cc_start: 0.8736 (mmm) cc_final: 0.8445 (mmp) REVERT: F 413 GLU cc_start: 0.7943 (pt0) cc_final: 0.7742 (pt0) REVERT: G 236 LYS cc_start: 0.8584 (mttt) cc_final: 0.8330 (ttpp) REVERT: G 370 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8306 (ttp80) REVERT: G 381 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.7319 (t70) REVERT: G 411 GLN cc_start: 0.8221 (mt0) cc_final: 0.7796 (mm-40) REVERT: G 424 ASP cc_start: 0.7029 (p0) cc_final: 0.6813 (p0) REVERT: H 370 ARG cc_start: 0.8552 (OUTLIER) cc_final: 0.8298 (ttm-80) REVERT: I 280 GLU cc_start: 0.7662 (tt0) cc_final: 0.7334 (tt0) REVERT: I 283 SER cc_start: 0.9345 (m) cc_final: 0.9081 (p) REVERT: I 418 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8368 (tp30) REVERT: J 242 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7827 (mt-10) REVERT: J 249 ILE cc_start: 0.9353 (mt) cc_final: 0.9007 (tp) REVERT: J 252 ILE cc_start: 0.9360 (tp) cc_final: 0.9032 (tp) REVERT: J 290 LYS cc_start: 0.8803 (mmtm) cc_final: 0.8445 (mmtp) REVERT: J 415 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7967 (mp) REVERT: K 236 LYS cc_start: 0.8600 (mmtp) cc_final: 0.7925 (tmmt) REVERT: K 242 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8227 (mt-10) REVERT: L 232 ASP cc_start: 0.7844 (t0) cc_final: 0.7499 (t0) REVERT: L 250 GLU cc_start: 0.8372 (tp30) cc_final: 0.7855 (tp30) REVERT: L 272 PHE cc_start: 0.7735 (m-10) cc_final: 0.7486 (m-80) REVERT: L 302 GLU cc_start: 0.7670 (pm20) cc_final: 0.7162 (pm20) REVERT: M 367 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7968 (mm-30) REVERT: M 428 ASP cc_start: 0.6996 (m-30) cc_final: 0.6622 (m-30) REVERT: N 242 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7944 (mp0) REVERT: N 428 ASP cc_start: 0.8372 (m-30) cc_final: 0.7968 (m-30) REVERT: N 431 ASN cc_start: 0.8614 (t0) cc_final: 0.8311 (t0) REVERT: O 232 ASP cc_start: 0.7656 (m-30) cc_final: 0.6943 (t0) REVERT: O 292 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8496 (t) REVERT: P 418 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8358 (mm-30) REVERT: Q 263 HIS cc_start: 0.7323 (m-70) cc_final: 0.7107 (m-70) REVERT: Q 381 ASP cc_start: 0.7215 (OUTLIER) cc_final: 0.6986 (m-30) REVERT: Q 383 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7404 (mp0) REVERT: R 242 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8352 (mm-30) REVERT: R 276 GLU cc_start: 0.8133 (tt0) cc_final: 0.7921 (tt0) REVERT: S 280 GLU cc_start: 0.7273 (tt0) cc_final: 0.6875 (mt-10) REVERT: S 404 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8071 (mm) REVERT: T 244 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8145 (ttm-80) REVERT: U 236 LYS cc_start: 0.8993 (tppt) cc_final: 0.8494 (mtpt) REVERT: U 363 THR cc_start: 0.9255 (m) cc_final: 0.8779 (p) REVERT: U 367 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8105 (mt-10) REVERT: U 413 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8421 (tm-30) REVERT: U 422 PHE cc_start: 0.8541 (t80) cc_final: 0.8003 (t80) REVERT: U 431 ASN cc_start: 0.8547 (t0) cc_final: 0.8082 (t0) REVERT: V 242 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7323 (mt-10) REVERT: V 275 LYS cc_start: 0.8595 (ptpp) cc_final: 0.7886 (ptpp) REVERT: V 370 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7761 (ttm-80) REVERT: V 377 MET cc_start: 0.8294 (mpp) cc_final: 0.7892 (mpp) REVERT: V 418 GLU cc_start: 0.8278 (mm-30) cc_final: 0.8019 (mm-30) REVERT: W 302 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7334 (mp0) REVERT: W 410 LYS cc_start: 0.8315 (tptt) cc_final: 0.8007 (tptt) REVERT: W 418 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7312 (mm-30) REVERT: X 294 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.8107 (ttm-80) REVERT: X 381 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7745 (m-30) REVERT: Y 246 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8355 (tm-30) REVERT: Z 235 LEU cc_start: 0.8645 (mt) cc_final: 0.8420 (mt) REVERT: Z 250 GLU cc_start: 0.7938 (pp20) cc_final: 0.7658 (pp20) REVERT: Z 290 LYS cc_start: 0.8772 (mttp) cc_final: 0.8471 (mtmm) REVERT: Z 362 GLU cc_start: 0.7610 (tt0) cc_final: 0.7357 (tt0) REVERT: Z 413 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7987 (tm-30) REVERT: a 275 LYS cc_start: 0.8627 (mttp) cc_final: 0.8417 (mttp) REVERT: a 377 MET cc_start: 0.8724 (mmm) cc_final: 0.8434 (mmt) REVERT: a 413 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: b 386 SER cc_start: 0.8402 (m) cc_final: 0.7661 (t) REVERT: c 246 GLN cc_start: 0.8292 (tt0) cc_final: 0.8074 (tp40) REVERT: c 290 LYS cc_start: 0.8304 (ttmt) cc_final: 0.8048 (ttmt) REVERT: d 236 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8736 (ttpp) REVERT: e 265 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7884 (mm-40) REVERT: f 230 LEU cc_start: 0.8185 (pp) cc_final: 0.7945 (tt) REVERT: f 298 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8290 (tp) REVERT: f 303 GLN cc_start: 0.7886 (mp10) cc_final: 0.7645 (mp10) REVERT: f 383 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7396 (mt-10) REVERT: f 411 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8220 (mt0) REVERT: g 367 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8338 (mm-30) REVERT: h 379 VAL cc_start: 0.9024 (t) cc_final: 0.8788 (p) outliers start: 304 outliers final: 212 residues processed: 1421 average time/residue: 0.2364 time to fit residues: 561.0088 Evaluate side-chains 1366 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1137 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 10 VAL Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 71 HIS Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 294 ARG Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 245 ILE Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 266 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 385 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 287 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain J residue 435 SER Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 281 HIS Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 389 VAL Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 371 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 391 VAL Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 257 VAL Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 267 THR Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 369 ASP Chi-restraints excluded: chain N residue 425 LYS Chi-restraints excluded: chain O residue 230 LEU Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 292 THR Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 414 ASP Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain P residue 398 ASP Chi-restraints excluded: chain P residue 412 ILE Chi-restraints excluded: chain P residue 429 THR Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain Q residue 415 LEU Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 295 SER Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 289 SER Chi-restraints excluded: chain S residue 293 LEU Chi-restraints excluded: chain S residue 371 THR Chi-restraints excluded: chain S residue 385 LEU Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain S residue 405 THR Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain U residue 391 VAL Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 420 MET Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 249 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 256 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain X residue 294 ARG Chi-restraints excluded: chain X residue 381 ASP Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 287 ASP Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 232 ASP Chi-restraints excluded: chain Z residue 359 GLN Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 372 ILE Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 246 GLN Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 256 ILE Chi-restraints excluded: chain b residue 267 THR Chi-restraints excluded: chain b residue 402 LEU Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 429 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 429 THR Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 295 SER Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 242 GLU Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 293 LEU Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 385 LEU Chi-restraints excluded: chain f residue 391 VAL Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 431 ASN Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 256 ILE Chi-restraints excluded: chain g residue 267 THR Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 292 THR Chi-restraints excluded: chain h residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 249 optimal weight: 5.9990 chunk 312 optimal weight: 1.9990 chunk 421 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 190 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 440 optimal weight: 8.9990 chunk 18 optimal weight: 0.3980 chunk 444 optimal weight: 1.9990 chunk 327 optimal weight: 0.4980 chunk 23 optimal weight: 0.0170 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: n 13 GLN ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN F 392 ASN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS K 231 ASN ** K 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 269 GLN ** P 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 434 ASN T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN a 263 HIS ** b 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 269 GLN ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 231 ASN h 431 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.096073 restraints weight = 79191.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098900 restraints weight = 37839.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.100718 restraints weight = 23070.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101879 restraints weight = 16587.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.102599 restraints weight = 13312.846| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45170 Z= 0.117 Angle : 0.564 8.472 61015 Z= 0.294 Chirality : 0.040 0.176 7012 Planarity : 0.004 0.063 8251 Dihedral : 4.137 37.426 6204 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.15 % Allowed : 26.28 % Favored : 68.57 % 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: 1.63 (0.11), residues: 5613 helix: 3.18 (0.12), residues: 1530 sheet: 0.76 (0.10), residues: 2584 loop : -0.57 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 247 TYR 0.016 0.001 TYR H 282 PHE 0.020 0.001 PHE S 237 HIS 0.004 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00263 (45170) covalent geometry : angle 0.56378 (61015) hydrogen bonds : bond 0.03022 ( 2703) hydrogen bonds : angle 4.14393 ( 7497) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 1254 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 19 MET cc_start: 0.7336 (tmm) cc_final: 0.7096 (mmt) REVERT: q 72 HIS cc_start: 0.7991 (OUTLIER) cc_final: 0.7456 (p-80) REVERT: A 302 GLU cc_start: 0.7365 (tp30) cc_final: 0.7035 (tp30) REVERT: B 293 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8478 (mt) REVERT: B 413 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6519 (tm-30) REVERT: B 414 ASP cc_start: 0.8270 (m-30) cc_final: 0.7382 (m-30) REVERT: C 232 ASP cc_start: 0.7773 (m-30) cc_final: 0.7129 (t0) REVERT: C 269 GLN cc_start: 0.8528 (mm110) cc_final: 0.8022 (mt0) REVERT: C 425 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8341 (pttm) REVERT: C 431 ASN cc_start: 0.8321 (t0) cc_final: 0.7788 (t0) REVERT: D 242 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8101 (mp0) REVERT: D 297 GLN cc_start: 0.7952 (tt0) cc_final: 0.7615 (mp10) REVERT: D 372 ILE cc_start: 0.9241 (mt) cc_final: 0.8902 (tt) REVERT: D 414 ASP cc_start: 0.8680 (t0) cc_final: 0.8382 (t0) REVERT: D 428 ASP cc_start: 0.7596 (m-30) cc_final: 0.7355 (m-30) REVERT: E 246 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8375 (tm-30) REVERT: E 431 ASN cc_start: 0.7477 (m-40) cc_final: 0.7183 (m110) REVERT: F 370 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8589 (ttm-80) REVERT: F 409 MET cc_start: 0.8750 (mmm) cc_final: 0.8495 (mmp) REVERT: F 413 GLU cc_start: 0.8036 (pt0) cc_final: 0.7803 (pt0) REVERT: G 369 ASP cc_start: 0.8284 (m-30) cc_final: 0.8051 (m-30) REVERT: G 370 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8263 (ttp80) REVERT: G 381 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7033 (t0) REVERT: G 424 ASP cc_start: 0.7049 (p0) cc_final: 0.6825 (p0) REVERT: G 428 ASP cc_start: 0.7509 (m-30) cc_final: 0.7065 (m-30) REVERT: H 234 GLN cc_start: 0.8227 (mt0) cc_final: 0.7803 (mp10) REVERT: H 253 LEU cc_start: 0.8107 (mm) cc_final: 0.7849 (mm) REVERT: H 370 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8073 (ttm-80) REVERT: I 283 SER cc_start: 0.9382 (m) cc_final: 0.9056 (p) REVERT: I 418 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8336 (tp30) REVERT: J 247 ARG cc_start: 0.8349 (mtm180) cc_final: 0.8080 (ttm110) REVERT: J 249 ILE cc_start: 0.9289 (mt) cc_final: 0.8987 (tp) REVERT: J 269 GLN cc_start: 0.9292 (mp10) cc_final: 0.7981 (mm-40) REVERT: J 381 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7102 (t0) REVERT: J 383 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7846 (mp0) REVERT: J 415 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7845 (mp) REVERT: K 236 LYS cc_start: 0.8617 (mmtp) cc_final: 0.7871 (tmmt) REVERT: K 242 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8280 (mt-10) REVERT: K 303 GLN cc_start: 0.7570 (tm-30) cc_final: 0.6640 (tm-30) REVERT: L 232 ASP cc_start: 0.7920 (t0) cc_final: 0.7574 (t0) REVERT: L 234 GLN cc_start: 0.8232 (mt0) cc_final: 0.7892 (mt0) REVERT: L 250 GLU cc_start: 0.8434 (tp30) cc_final: 0.7873 (tp30) REVERT: L 302 GLU cc_start: 0.7672 (pm20) cc_final: 0.7060 (pm20) REVERT: M 367 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7722 (mt-10) REVERT: M 428 ASP cc_start: 0.6931 (m-30) cc_final: 0.6479 (m-30) REVERT: N 242 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7947 (mp0) REVERT: N 428 ASP cc_start: 0.8398 (m-30) cc_final: 0.7877 (m-30) REVERT: N 431 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8459 (t0) REVERT: O 232 ASP cc_start: 0.7680 (m-30) cc_final: 0.6854 (t0) REVERT: O 302 GLU cc_start: 0.7873 (pt0) cc_final: 0.7610 (pt0) REVERT: O 410 LYS cc_start: 0.8501 (tppt) cc_final: 0.8289 (tptt) REVERT: P 418 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8395 (mm-30) REVERT: Q 263 HIS cc_start: 0.7193 (m-70) cc_final: 0.6952 (m-70) REVERT: Q 370 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8389 (ttt90) REVERT: Q 381 ASP cc_start: 0.7372 (m-30) cc_final: 0.6666 (t70) REVERT: Q 383 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7400 (mp0) REVERT: R 242 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8452 (mm-30) REVERT: R 247 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7974 (tmm-80) REVERT: R 276 GLU cc_start: 0.8249 (tt0) cc_final: 0.7969 (tt0) REVERT: R 279 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7082 (mt-10) REVERT: R 424 ASP cc_start: 0.8238 (m-30) cc_final: 0.7328 (t0) REVERT: S 280 GLU cc_start: 0.7317 (tt0) cc_final: 0.7098 (mt-10) REVERT: S 404 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8240 (mm) REVERT: T 244 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8176 (ttm-80) REVERT: U 236 LYS cc_start: 0.9026 (tppt) cc_final: 0.8429 (mtpt) REVERT: U 302 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7213 (pt0) REVERT: U 363 THR cc_start: 0.9248 (m) cc_final: 0.8846 (p) REVERT: U 413 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8188 (tm-30) REVERT: U 431 ASN cc_start: 0.8472 (t0) cc_final: 0.7970 (t0) REVERT: V 242 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7526 (mt-10) REVERT: V 244 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8265 (ttp-110) REVERT: V 275 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7743 (ptpp) REVERT: V 367 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7620 (mt-10) REVERT: V 370 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7614 (ttm-80) REVERT: V 377 MET cc_start: 0.8300 (mpp) cc_final: 0.7482 (mpp) REVERT: V 418 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7854 (mm-30) REVERT: W 265 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8214 (mm-40) REVERT: W 302 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7289 (mp0) REVERT: W 410 LYS cc_start: 0.8415 (tptt) cc_final: 0.8171 (tptt) REVERT: X 230 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7884 (tt) REVERT: X 394 LYS cc_start: 0.7242 (mmmt) cc_final: 0.6569 (mttt) REVERT: Y 246 GLN cc_start: 0.8733 (tm-30) cc_final: 0.8455 (tm-30) REVERT: Y 381 ASP cc_start: 0.7670 (t70) cc_final: 0.7274 (t70) REVERT: Y 414 ASP cc_start: 0.8990 (t0) cc_final: 0.8749 (t0) REVERT: Y 418 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7908 (mm-30) REVERT: Z 290 LYS cc_start: 0.8788 (mttp) cc_final: 0.8456 (mtmm) REVERT: Z 362 GLU cc_start: 0.7665 (tt0) cc_final: 0.7402 (tt0) REVERT: Z 367 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7548 (mt-10) REVERT: Z 370 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7784 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7877 (tm-30) REVERT: a 377 MET cc_start: 0.8769 (mmm) cc_final: 0.8479 (mmt) REVERT: b 386 SER cc_start: 0.8272 (m) cc_final: 0.7529 (t) REVERT: c 232 ASP cc_start: 0.7516 (m-30) cc_final: 0.7065 (p0) REVERT: c 246 GLN cc_start: 0.8324 (tt0) cc_final: 0.8034 (tp40) REVERT: c 280 GLU cc_start: 0.7287 (mp0) cc_final: 0.7080 (mp0) REVERT: c 290 LYS cc_start: 0.8368 (ttmt) cc_final: 0.8095 (ttmt) REVERT: c 416 THR cc_start: 0.9413 (p) cc_final: 0.9165 (t) REVERT: c 429 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8001 (p) REVERT: c 431 ASN cc_start: 0.7672 (m110) cc_final: 0.7364 (m110) REVERT: d 236 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8591 (ttpp) REVERT: e 429 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8443 (p) REVERT: f 230 LEU cc_start: 0.8212 (pp) cc_final: 0.7904 (tt) REVERT: f 298 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8346 (tp) REVERT: f 303 GLN cc_start: 0.7849 (mp10) cc_final: 0.7573 (mp10) REVERT: g 261 ASN cc_start: 0.7591 (t0) cc_final: 0.7277 (t0) REVERT: g 370 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8125 (tpp80) REVERT: g 414 ASP cc_start: 0.8564 (m-30) cc_final: 0.8339 (m-30) REVERT: g 428 ASP cc_start: 0.7745 (m-30) cc_final: 0.7526 (m-30) REVERT: h 244 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7886 (mtp180) REVERT: h 379 VAL cc_start: 0.9034 (t) cc_final: 0.8757 (p) outliers start: 254 outliers final: 164 residues processed: 1413 average time/residue: 0.2602 time to fit residues: 609.3949 Evaluate side-chains 1319 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1134 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 10 VAL Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain q residue 73 ILE Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 370 ARG Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 381 ASP Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 417 ARG Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain N residue 254 SER Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 431 ASN Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 242 GLU Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 370 ARG Chi-restraints excluded: chain V residue 383 GLU Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 429 THR Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain W residue 381 ASP Chi-restraints excluded: chain X residue 230 LEU Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 423 SER Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain b residue 429 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 429 THR Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 298 LEU Chi-restraints excluded: chain f residue 391 VAL Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 413 GLU Chi-restraints excluded: chain f residue 428 ASP Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 415 LEU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 404 LEU Chi-restraints excluded: chain h residue 431 ASN Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 215 optimal weight: 0.8980 chunk 355 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 274 optimal weight: 0.0670 chunk 451 optimal weight: 7.9990 chunk 357 optimal weight: 0.6980 chunk 423 optimal weight: 0.6980 chunk 233 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 382 optimal weight: 4.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.2720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN D 269 GLN D 303 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS K 434 ASN L 434 ASN M 265 GLN M 269 GLN ** M 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 ASN N 234 GLN O 234 GLN O 277 GLN O 378 ASN P 261 ASN R 297 GLN R 434 ASN T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN ** Z 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 HIS a 359 GLN ** b 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 297 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.095944 restraints weight = 79955.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098575 restraints weight = 39344.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.100260 restraints weight = 24467.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.101350 restraints weight = 17832.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.102045 restraints weight = 14447.699| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 45170 Z= 0.126 Angle : 0.571 9.462 61015 Z= 0.296 Chirality : 0.040 0.172 7012 Planarity : 0.004 0.055 8251 Dihedral : 4.087 16.742 6202 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 5.17 % Allowed : 26.50 % Favored : 68.32 % 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: 1.60 (0.11), residues: 5613 helix: 3.07 (0.13), residues: 1530 sheet: 0.77 (0.10), residues: 2584 loop : -0.52 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG h 356 TYR 0.016 0.001 TYR H 282 PHE 0.021 0.001 PHE S 237 HIS 0.005 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00289 (45170) covalent geometry : angle 0.57100 (61015) hydrogen bonds : bond 0.03020 ( 2703) hydrogen bonds : angle 4.09668 ( 7497) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 255 poor density : 1217 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: q 72 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7396 (p-80) REVERT: A 242 GLU cc_start: 0.7261 (mt-10) cc_final: 0.7006 (mt-10) REVERT: A 302 GLU cc_start: 0.7359 (tp30) cc_final: 0.7093 (tp30) REVERT: B 293 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8467 (mt) REVERT: B 377 MET cc_start: 0.7512 (ptp) cc_final: 0.7107 (mtm) REVERT: B 414 ASP cc_start: 0.8141 (m-30) cc_final: 0.7274 (m-30) REVERT: C 232 ASP cc_start: 0.7563 (m-30) cc_final: 0.7076 (t0) REVERT: C 242 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7393 (mt-10) REVERT: C 250 GLU cc_start: 0.8309 (tt0) cc_final: 0.8101 (tm-30) REVERT: C 269 GLN cc_start: 0.8435 (mm110) cc_final: 0.7990 (mt0) REVERT: C 425 LYS cc_start: 0.8561 (mmmt) cc_final: 0.8287 (pttm) REVERT: C 431 ASN cc_start: 0.8304 (t0) cc_final: 0.7692 (t0) REVERT: D 242 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7971 (mp0) REVERT: D 269 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8404 (mm-40) REVERT: D 372 ILE cc_start: 0.9235 (mt) cc_final: 0.8909 (tt) REVERT: D 413 GLU cc_start: 0.8268 (pp20) cc_final: 0.7986 (tm-30) REVERT: D 414 ASP cc_start: 0.8598 (t0) cc_final: 0.8321 (t0) REVERT: D 428 ASP cc_start: 0.7459 (m-30) cc_final: 0.7141 (m-30) REVERT: E 246 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8338 (tm-30) REVERT: E 412 ILE cc_start: 0.9008 (mm) cc_final: 0.8801 (mt) REVERT: E 431 ASN cc_start: 0.7408 (m-40) cc_final: 0.7131 (m110) REVERT: F 409 MET cc_start: 0.8673 (mmm) cc_final: 0.8401 (mmp) REVERT: F 413 GLU cc_start: 0.8018 (pt0) cc_final: 0.7694 (pt0) REVERT: F 415 LEU cc_start: 0.9197 (mp) cc_final: 0.8910 (tt) REVERT: G 369 ASP cc_start: 0.8229 (m-30) cc_final: 0.8015 (m-30) REVERT: G 370 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8309 (ttp80) REVERT: G 381 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.6884 (t0) REVERT: G 424 ASP cc_start: 0.6830 (p0) cc_final: 0.6614 (p0) REVERT: H 234 GLN cc_start: 0.8069 (mt0) cc_final: 0.7627 (mp10) REVERT: H 370 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8287 (ttm-80) REVERT: I 283 SER cc_start: 0.9333 (m) cc_final: 0.9081 (p) REVERT: I 418 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8317 (tp30) REVERT: J 247 ARG cc_start: 0.8283 (mtm180) cc_final: 0.8035 (ttm110) REVERT: J 383 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7923 (mp0) REVERT: J 415 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8006 (mp) REVERT: K 236 LYS cc_start: 0.8590 (mmtp) cc_final: 0.7926 (tmmt) REVERT: K 242 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8102 (mt-10) REVERT: K 303 GLN cc_start: 0.7809 (tm-30) cc_final: 0.6883 (tm-30) REVERT: L 250 GLU cc_start: 0.8302 (tp30) cc_final: 0.7764 (tp30) REVERT: L 302 GLU cc_start: 0.7636 (pm20) cc_final: 0.7120 (pm20) REVERT: M 265 GLN cc_start: 0.7333 (mm-40) cc_final: 0.7047 (mm-40) REVERT: M 367 GLU cc_start: 0.8266 (mm-30) cc_final: 0.8014 (mm-30) REVERT: M 428 ASP cc_start: 0.6712 (m-30) cc_final: 0.6224 (m-30) REVERT: N 242 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7654 (pt0) REVERT: N 410 LYS cc_start: 0.9160 (tppt) cc_final: 0.8646 (tppt) REVERT: N 428 ASP cc_start: 0.8282 (m-30) cc_final: 0.7889 (m-30) REVERT: O 232 ASP cc_start: 0.7504 (m-30) cc_final: 0.6788 (t0) REVERT: O 376 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.8012 (ttmm) REVERT: P 235 LEU cc_start: 0.9095 (mt) cc_final: 0.8873 (tp) REVERT: P 265 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7939 (mm-40) REVERT: P 418 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8044 (mm-30) REVERT: Q 381 ASP cc_start: 0.7332 (m-30) cc_final: 0.6702 (t70) REVERT: Q 383 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7327 (mp0) REVERT: Q 394 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7987 (ptpp) REVERT: R 242 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8404 (mm-30) REVERT: R 247 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7967 (tmm-80) REVERT: R 276 GLU cc_start: 0.8182 (tt0) cc_final: 0.7908 (tt0) REVERT: R 424 ASP cc_start: 0.7941 (m-30) cc_final: 0.7670 (m-30) REVERT: S 267 THR cc_start: 0.7907 (t) cc_final: 0.7693 (m) REVERT: S 280 GLU cc_start: 0.7218 (tt0) cc_final: 0.6928 (mt-10) REVERT: S 404 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7964 (mm) REVERT: T 244 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7482 (ttp-110) REVERT: U 236 LYS cc_start: 0.9062 (tppt) cc_final: 0.8513 (mtpt) REVERT: U 282 TYR cc_start: 0.8636 (m-10) cc_final: 0.8361 (m-10) REVERT: U 363 THR cc_start: 0.9250 (m) cc_final: 0.8878 (p) REVERT: U 413 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8151 (tm-30) REVERT: U 431 ASN cc_start: 0.8311 (t0) cc_final: 0.7837 (t0) REVERT: V 240 ASP cc_start: 0.8089 (t0) cc_final: 0.7832 (t0) REVERT: V 242 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7290 (mt-10) REVERT: V 244 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8362 (ttp-110) REVERT: V 275 LYS cc_start: 0.8618 (ptpp) cc_final: 0.7954 (ptpp) REVERT: V 367 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7631 (mt-10) REVERT: V 376 LYS cc_start: 0.8515 (tppt) cc_final: 0.8277 (tppt) REVERT: V 377 MET cc_start: 0.8194 (mpp) cc_final: 0.7796 (mpp) REVERT: V 418 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7880 (mm-30) REVERT: W 302 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7362 (mp0) REVERT: W 394 LYS cc_start: 0.6456 (ptmm) cc_final: 0.5678 (tttp) REVERT: W 410 LYS cc_start: 0.8455 (tptt) cc_final: 0.8194 (tptt) REVERT: X 389 VAL cc_start: 0.8525 (t) cc_final: 0.8179 (m) REVERT: Z 290 LYS cc_start: 0.8671 (mttp) cc_final: 0.8393 (mtmm) REVERT: Z 362 GLU cc_start: 0.7533 (tt0) cc_final: 0.7261 (tt0) REVERT: Z 367 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7552 (mt-10) REVERT: Z 370 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7810 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7957 (tm-30) REVERT: a 377 MET cc_start: 0.8712 (mmm) cc_final: 0.8421 (mmt) REVERT: b 362 GLU cc_start: 0.7046 (tp30) cc_final: 0.6797 (tp30) REVERT: b 386 SER cc_start: 0.8156 (m) cc_final: 0.7466 (t) REVERT: c 280 GLU cc_start: 0.7470 (mp0) cc_final: 0.7128 (mp0) REVERT: c 410 LYS cc_start: 0.7510 (mttt) cc_final: 0.7130 (mttp) REVERT: c 431 ASN cc_start: 0.7662 (m110) cc_final: 0.7033 (m110) REVERT: d 236 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8572 (ttpp) REVERT: d 410 LYS cc_start: 0.8645 (tppp) cc_final: 0.8413 (tppt) REVERT: e 265 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7564 (mm-40) REVERT: e 429 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8483 (p) REVERT: f 230 LEU cc_start: 0.8047 (pp) cc_final: 0.7836 (tt) REVERT: f 370 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (ttp80) REVERT: f 428 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7091 (p0) REVERT: g 370 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8270 (tpp80) REVERT: g 428 ASP cc_start: 0.7692 (m-30) cc_final: 0.7437 (m-30) REVERT: h 244 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7869 (mtp180) REVERT: h 254 SER cc_start: 0.8897 (OUTLIER) cc_final: 0.8575 (p) REVERT: h 379 VAL cc_start: 0.9030 (t) cc_final: 0.8762 (p) outliers start: 255 outliers final: 186 residues processed: 1382 average time/residue: 0.2377 time to fit residues: 547.4262 Evaluate side-chains 1326 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1121 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain m residue 17 THR Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 289 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 289 SER Chi-restraints excluded: chain K residue 391 VAL Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 415 LEU Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 253 LEU Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain O residue 430 LEU Chi-restraints excluded: chain O residue 432 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 279 GLU Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 383 GLU Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 263 HIS Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 359 GLN Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 231 ASN Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 405 THR Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 267 THR Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 429 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 385 LEU Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 413 GLU Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 428 ASP Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 252 ILE Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 415 LEU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 404 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 212 optimal weight: 0.9990 chunk 529 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 479 optimal weight: 8.9990 chunk 237 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 316 optimal weight: 4.9990 chunk 419 optimal weight: 5.9990 chunk 544 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 ASN D 269 GLN D 303 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS L 234 GLN ** M 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 297 GLN T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN ** Z 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 263 HIS ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 285 ASN ** b 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 234 GLN f 269 GLN f 277 GLN ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 234 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093592 restraints weight = 80238.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096373 restraints weight = 38315.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.098151 restraints weight = 23312.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.099280 restraints weight = 16747.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.100006 restraints weight = 13460.011| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 45170 Z= 0.158 Angle : 0.596 10.368 61015 Z= 0.310 Chirality : 0.041 0.232 7012 Planarity : 0.004 0.056 8251 Dihedral : 4.177 16.964 6202 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 5.56 % Allowed : 26.38 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.11), residues: 5613 helix: 2.95 (0.13), residues: 1530 sheet: 0.74 (0.10), residues: 2584 loop : -0.53 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 244 TYR 0.013 0.001 TYR H 282 PHE 0.036 0.002 PHE O 237 HIS 0.006 0.001 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00362 (45170) covalent geometry : angle 0.59609 (61015) hydrogen bonds : bond 0.03260 ( 2703) hydrogen bonds : angle 4.16813 ( 7497) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 1168 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 19 MET cc_start: 0.7154 (mmt) cc_final: 0.6917 (mmp) REVERT: q 72 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.7313 (p-80) REVERT: A 242 GLU cc_start: 0.7292 (mt-10) cc_final: 0.7015 (mt-10) REVERT: A 411 GLN cc_start: 0.8341 (pt0) cc_final: 0.7776 (mt0) REVERT: B 271 ASP cc_start: 0.7409 (t0) cc_final: 0.7141 (t70) REVERT: B 293 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8539 (mt) REVERT: B 377 MET cc_start: 0.7644 (ptp) cc_final: 0.7273 (mtm) REVERT: B 383 GLU cc_start: 0.7703 (mp0) cc_final: 0.7161 (mp0) REVERT: B 413 GLU cc_start: 0.6661 (tm-30) cc_final: 0.6242 (tm-30) REVERT: B 414 ASP cc_start: 0.8095 (m-30) cc_final: 0.7398 (m-30) REVERT: C 232 ASP cc_start: 0.7791 (m-30) cc_final: 0.7143 (t0) REVERT: C 242 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7525 (mt-10) REVERT: C 250 GLU cc_start: 0.8546 (tt0) cc_final: 0.8221 (tm-30) REVERT: C 269 GLN cc_start: 0.8479 (mm110) cc_final: 0.7990 (mt0) REVERT: C 425 LYS cc_start: 0.8660 (mmmt) cc_final: 0.8379 (pttm) REVERT: D 242 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8044 (mp0) REVERT: D 372 ILE cc_start: 0.9203 (mt) cc_final: 0.8857 (tt) REVERT: D 428 ASP cc_start: 0.7563 (m-30) cc_final: 0.7116 (m-30) REVERT: E 246 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8381 (tm-30) REVERT: E 431 ASN cc_start: 0.7550 (m-40) cc_final: 0.7273 (m110) REVERT: F 236 LYS cc_start: 0.8516 (mptt) cc_final: 0.8139 (mptt) REVERT: F 377 MET cc_start: 0.7286 (pmm) cc_final: 0.6761 (pmm) REVERT: F 409 MET cc_start: 0.8747 (mmm) cc_final: 0.8532 (mmp) REVERT: F 413 GLU cc_start: 0.8000 (pt0) cc_final: 0.7736 (pt0) REVERT: G 370 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8307 (ttp80) REVERT: G 381 ASP cc_start: 0.7555 (OUTLIER) cc_final: 0.6914 (t0) REVERT: H 302 GLU cc_start: 0.7855 (tt0) cc_final: 0.7251 (tm-30) REVERT: H 370 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8345 (ttm-80) REVERT: I 269 GLN cc_start: 0.8591 (mp10) cc_final: 0.8358 (mp10) REVERT: I 283 SER cc_start: 0.9403 (m) cc_final: 0.9031 (p) REVERT: I 418 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8351 (tp30) REVERT: J 242 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7775 (mt-10) REVERT: J 247 ARG cc_start: 0.8353 (mtm180) cc_final: 0.8062 (ttm110) REVERT: J 383 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7708 (mp0) REVERT: J 415 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7935 (mp) REVERT: K 236 LYS cc_start: 0.8696 (mmtp) cc_final: 0.8031 (tmmt) REVERT: K 242 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8285 (mt-10) REVERT: K 303 GLN cc_start: 0.7827 (tm-30) cc_final: 0.6808 (tm-30) REVERT: L 232 ASP cc_start: 0.7904 (t0) cc_final: 0.7596 (t0) REVERT: L 250 GLU cc_start: 0.8411 (tp30) cc_final: 0.7863 (tp30) REVERT: L 302 GLU cc_start: 0.7716 (pm20) cc_final: 0.7091 (pm20) REVERT: L 410 LYS cc_start: 0.8308 (tptm) cc_final: 0.8101 (tptm) REVERT: L 414 ASP cc_start: 0.7473 (m-30) cc_final: 0.7138 (m-30) REVERT: M 242 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7337 (mp0) REVERT: M 265 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7843 (mm-40) REVERT: M 367 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8143 (mm-30) REVERT: M 428 ASP cc_start: 0.6724 (m-30) cc_final: 0.6079 (m-30) REVERT: N 242 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7706 (pt0) REVERT: O 232 ASP cc_start: 0.7770 (m-30) cc_final: 0.6793 (t0) REVERT: O 376 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.8035 (ttmm) REVERT: O 407 ASP cc_start: 0.7824 (m-30) cc_final: 0.7448 (t0) REVERT: O 418 GLU cc_start: 0.8567 (mm-30) cc_final: 0.7929 (mm-30) REVERT: P 235 LEU cc_start: 0.9149 (mt) cc_final: 0.8931 (tp) REVERT: P 265 GLN cc_start: 0.8379 (mm-40) cc_final: 0.8027 (mm-40) REVERT: P 369 ASP cc_start: 0.7790 (m-30) cc_final: 0.7472 (m-30) REVERT: P 418 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8115 (mm-30) REVERT: Q 381 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6867 (t70) REVERT: Q 383 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7327 (mp0) REVERT: Q 394 LYS cc_start: 0.8227 (ptpp) cc_final: 0.8019 (ptpp) REVERT: R 242 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8340 (mm-30) REVERT: R 276 GLU cc_start: 0.8289 (tt0) cc_final: 0.8049 (tt0) REVERT: R 370 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7459 (ttm-80) REVERT: R 383 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6854 (mt-10) REVERT: R 414 ASP cc_start: 0.7955 (t0) cc_final: 0.7717 (t0) REVERT: S 267 THR cc_start: 0.8071 (t) cc_final: 0.7553 (m) REVERT: S 280 GLU cc_start: 0.7333 (tt0) cc_final: 0.6945 (mt-10) REVERT: S 404 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.7982 (mm) REVERT: S 413 GLU cc_start: 0.8469 (tm-30) cc_final: 0.7974 (tm-30) REVERT: T 244 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7887 (ttp-110) REVERT: T 280 GLU cc_start: 0.7407 (tt0) cc_final: 0.7117 (tt0) REVERT: U 236 LYS cc_start: 0.9066 (tppt) cc_final: 0.8408 (mtpt) REVERT: U 282 TYR cc_start: 0.8782 (m-10) cc_final: 0.8457 (m-10) REVERT: U 363 THR cc_start: 0.9263 (m) cc_final: 0.8809 (p) REVERT: U 413 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8152 (tm-30) REVERT: U 431 ASN cc_start: 0.8518 (t0) cc_final: 0.7939 (t0) REVERT: V 240 ASP cc_start: 0.8258 (t0) cc_final: 0.7869 (t0) REVERT: V 242 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7410 (mt-10) REVERT: V 244 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.8395 (ttp-110) REVERT: V 275 LYS cc_start: 0.8629 (ptpp) cc_final: 0.7596 (ptpp) REVERT: V 276 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7415 (mm-30) REVERT: V 367 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7808 (mt-10) REVERT: V 377 MET cc_start: 0.8358 (mpp) cc_final: 0.7787 (mpp) REVERT: V 418 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7841 (mm-30) REVERT: W 271 ASP cc_start: 0.7266 (OUTLIER) cc_final: 0.6838 (m-30) REVERT: W 302 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7304 (mp0) REVERT: W 383 GLU cc_start: 0.7752 (pt0) cc_final: 0.7366 (pt0) REVERT: W 410 LYS cc_start: 0.8529 (tptt) cc_final: 0.8293 (tptt) REVERT: Y 366 TYR cc_start: 0.8889 (m-80) cc_final: 0.8553 (m-10) REVERT: Y 414 ASP cc_start: 0.8965 (t0) cc_final: 0.8669 (t0) REVERT: Z 290 LYS cc_start: 0.8842 (mttp) cc_final: 0.8492 (mtmm) REVERT: Z 362 GLU cc_start: 0.7666 (tt0) cc_final: 0.7397 (tt0) REVERT: Z 367 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7684 (mt-10) REVERT: Z 413 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8125 (tm-30) REVERT: a 377 MET cc_start: 0.8754 (mmm) cc_final: 0.8414 (mmt) REVERT: b 246 GLN cc_start: 0.8460 (tt0) cc_final: 0.8248 (tt0) REVERT: b 431 ASN cc_start: 0.7971 (m-40) cc_final: 0.7628 (m-40) REVERT: c 232 ASP cc_start: 0.6549 (p0) cc_final: 0.6348 (p0) REVERT: c 431 ASN cc_start: 0.7693 (m110) cc_final: 0.7237 (m110) REVERT: d 236 LYS cc_start: 0.8979 (ttpt) cc_final: 0.8653 (ttpp) REVERT: e 429 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8437 (p) REVERT: f 230 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7863 (tt) REVERT: f 370 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8305 (ttp80) REVERT: f 428 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7332 (p0) REVERT: g 261 ASN cc_start: 0.6861 (t0) cc_final: 0.6621 (t0) REVERT: g 370 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8293 (tpp80) REVERT: g 428 ASP cc_start: 0.7736 (m-30) cc_final: 0.7433 (m-30) REVERT: h 254 SER cc_start: 0.8954 (OUTLIER) cc_final: 0.8686 (p) REVERT: h 379 VAL cc_start: 0.9053 (t) cc_final: 0.8803 (p) outliers start: 274 outliers final: 200 residues processed: 1338 average time/residue: 0.2299 time to fit residues: 513.7902 Evaluate side-chains 1328 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1108 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 381 ASP Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 252 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 267 THR Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 402 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 252 ILE Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 413 GLU Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain O residue 402 LEU Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 269 GLN Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain P residue 432 VAL Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 232 ASP Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 263 HIS Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 230 LEU Chi-restraints excluded: chain Z residue 359 GLN Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 231 ASN Chi-restraints excluded: chain a residue 271 ASP Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 267 THR Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 429 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 293 LEU Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 432 VAL Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 230 LEU Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 413 GLU Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 428 ASP Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 267 THR Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 254 SER Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 404 LEU Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 45 optimal weight: 0.9980 chunk 336 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 316 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 429 optimal weight: 0.9990 chunk 320 optimal weight: 10.0000 chunk 238 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 GLN ** G 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 ASN H 374 HIS ** H 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 234 GLN M 297 GLN M 378 ASN O 378 ASN O 431 ASN R 297 GLN T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 ASN U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 434 ASN W 359 GLN Z 234 GLN a 263 HIS ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 378 ASN ** c 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 269 GLN ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 234 GLN f 269 GLN f 374 HIS ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094970 restraints weight = 80499.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097735 restraints weight = 38519.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.099511 restraints weight = 23455.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.100641 restraints weight = 16880.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101361 restraints weight = 13550.963| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 45170 Z= 0.121 Angle : 0.590 11.054 61015 Z= 0.304 Chirality : 0.040 0.185 7012 Planarity : 0.004 0.057 8251 Dihedral : 4.079 16.581 6202 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.89 % Allowed : 27.48 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.11), residues: 5613 helix: 2.93 (0.13), residues: 1530 sheet: 0.78 (0.10), residues: 2584 loop : -0.49 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 244 TYR 0.012 0.001 TYR H 282 PHE 0.030 0.001 PHE O 237 HIS 0.005 0.000 HIS E 281 Details of bonding type rmsd covalent geometry : bond 0.00282 (45170) covalent geometry : angle 0.58992 (61015) hydrogen bonds : bond 0.02954 ( 2703) hydrogen bonds : angle 4.08278 ( 7497) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1414 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 1173 time to evaluate : 1.947 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: m 19 MET cc_start: 0.7108 (mmt) cc_final: 0.6822 (mmp) REVERT: q 72 HIS cc_start: 0.7932 (OUTLIER) cc_final: 0.7262 (p-80) REVERT: A 242 GLU cc_start: 0.7304 (mt-10) cc_final: 0.7010 (mt-10) REVERT: A 302 GLU cc_start: 0.7210 (tp30) cc_final: 0.6902 (tp30) REVERT: B 271 ASP cc_start: 0.7265 (t0) cc_final: 0.6963 (t70) REVERT: B 293 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8531 (mt) REVERT: B 377 MET cc_start: 0.7579 (ptp) cc_final: 0.7357 (mtm) REVERT: B 383 GLU cc_start: 0.7708 (mp0) cc_final: 0.7189 (mp0) REVERT: B 414 ASP cc_start: 0.8081 (m-30) cc_final: 0.7614 (m-30) REVERT: C 232 ASP cc_start: 0.7792 (m-30) cc_final: 0.7123 (t0) REVERT: C 242 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7388 (mt-10) REVERT: C 250 GLU cc_start: 0.8367 (tt0) cc_final: 0.8007 (tm-30) REVERT: C 269 GLN cc_start: 0.8485 (mm110) cc_final: 0.8010 (mt0) REVERT: C 425 LYS cc_start: 0.8655 (mmmt) cc_final: 0.8368 (pttm) REVERT: D 242 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8099 (mp0) REVERT: D 372 ILE cc_start: 0.9175 (mt) cc_final: 0.8858 (tt) REVERT: D 413 GLU cc_start: 0.8542 (pp20) cc_final: 0.8282 (tm-30) REVERT: D 428 ASP cc_start: 0.7484 (m-30) cc_final: 0.6840 (m-30) REVERT: E 246 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8360 (tm-30) REVERT: E 431 ASN cc_start: 0.7575 (m-40) cc_final: 0.7228 (m110) REVERT: F 236 LYS cc_start: 0.8556 (mptt) cc_final: 0.8201 (mptt) REVERT: F 242 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6482 (mt-10) REVERT: F 413 GLU cc_start: 0.7972 (pt0) cc_final: 0.7763 (pt0) REVERT: G 369 ASP cc_start: 0.8318 (m-30) cc_final: 0.7965 (m-30) REVERT: G 370 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8271 (ttp80) REVERT: G 381 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6722 (t0) REVERT: H 234 GLN cc_start: 0.8299 (mt0) cc_final: 0.7862 (mp10) REVERT: H 302 GLU cc_start: 0.7839 (tt0) cc_final: 0.7425 (tm-30) REVERT: H 370 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8334 (ttm-80) REVERT: I 283 SER cc_start: 0.9385 (m) cc_final: 0.9007 (p) REVERT: I 418 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8363 (tp30) REVERT: J 242 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7768 (mt-10) REVERT: J 247 ARG cc_start: 0.8347 (mtm180) cc_final: 0.8058 (ttm110) REVERT: J 383 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7881 (mp0) REVERT: J 415 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7920 (mp) REVERT: K 236 LYS cc_start: 0.8668 (mmtp) cc_final: 0.8001 (tmmt) REVERT: K 242 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8244 (mt-10) REVERT: L 250 GLU cc_start: 0.8454 (tp30) cc_final: 0.7977 (tp30) REVERT: L 302 GLU cc_start: 0.7722 (pm20) cc_final: 0.7098 (pm20) REVERT: M 242 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7576 (mp0) REVERT: M 367 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8130 (mm-30) REVERT: M 428 ASP cc_start: 0.6682 (m-30) cc_final: 0.6074 (m-30) REVERT: N 242 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7654 (pt0) REVERT: O 376 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7928 (ttmm) REVERT: O 407 ASP cc_start: 0.7756 (m-30) cc_final: 0.7450 (t0) REVERT: O 418 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7960 (mm-30) REVERT: P 235 LEU cc_start: 0.9111 (mt) cc_final: 0.8904 (tp) REVERT: P 265 GLN cc_start: 0.8318 (mm-40) cc_final: 0.7994 (mm-40) REVERT: Q 381 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6432 (t70) REVERT: R 242 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8232 (mm-30) REVERT: R 247 ARG cc_start: 0.8358 (mtp-110) cc_final: 0.8045 (tmm-80) REVERT: R 276 GLU cc_start: 0.8306 (tt0) cc_final: 0.7740 (tt0) REVERT: R 370 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7516 (ttm-80) REVERT: R 383 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6726 (mt-10) REVERT: R 414 ASP cc_start: 0.7921 (t0) cc_final: 0.7588 (t0) REVERT: S 280 GLU cc_start: 0.7253 (tt0) cc_final: 0.6912 (mt-10) REVERT: S 404 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8053 (mm) REVERT: S 413 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8010 (tm-30) REVERT: T 244 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7510 (ttp-110) REVERT: T 280 GLU cc_start: 0.7435 (tt0) cc_final: 0.7134 (tt0) REVERT: U 236 LYS cc_start: 0.9047 (tppt) cc_final: 0.8386 (mtpt) REVERT: U 282 TYR cc_start: 0.8704 (m-10) cc_final: 0.8451 (m-10) REVERT: U 363 THR cc_start: 0.9261 (m) cc_final: 0.8881 (p) REVERT: U 413 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8192 (tm-30) REVERT: U 431 ASN cc_start: 0.8489 (t0) cc_final: 0.7920 (t0) REVERT: V 240 ASP cc_start: 0.8279 (t0) cc_final: 0.7908 (t0) REVERT: V 244 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8383 (ttp-110) REVERT: V 275 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8252 (ptpp) REVERT: V 367 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7799 (mt-10) REVERT: V 418 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7854 (mm-30) REVERT: W 271 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6752 (m-30) REVERT: W 302 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7340 (mp0) REVERT: W 383 GLU cc_start: 0.7701 (pt0) cc_final: 0.7222 (pt0) REVERT: W 394 LYS cc_start: 0.6809 (ptmm) cc_final: 0.6009 (tttp) REVERT: Y 246 GLN cc_start: 0.8528 (tm-30) cc_final: 0.7739 (tp40) REVERT: Y 410 LYS cc_start: 0.8326 (tmmt) cc_final: 0.7930 (pttm) REVERT: Z 290 LYS cc_start: 0.8795 (mttp) cc_final: 0.8370 (mtmm) REVERT: Z 362 GLU cc_start: 0.7643 (tt0) cc_final: 0.7377 (tt0) REVERT: Z 367 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7776 (mt-10) REVERT: Z 370 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7758 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8150 (tm-30) REVERT: a 377 MET cc_start: 0.8843 (mmm) cc_final: 0.8525 (mmt) REVERT: b 239 ASN cc_start: 0.8457 (t0) cc_final: 0.8130 (t0) REVERT: b 242 GLU cc_start: 0.8397 (mp0) cc_final: 0.8049 (mp0) REVERT: b 418 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7745 (mm-30) REVERT: c 410 LYS cc_start: 0.7498 (mttt) cc_final: 0.7269 (mttp) REVERT: c 431 ASN cc_start: 0.7622 (m110) cc_final: 0.7186 (m110) REVERT: d 236 LYS cc_start: 0.8957 (ttpt) cc_final: 0.8598 (ttpp) REVERT: d 410 LYS cc_start: 0.8735 (tppp) cc_final: 0.8505 (tppt) REVERT: e 240 ASP cc_start: 0.8317 (m-30) cc_final: 0.8038 (m-30) REVERT: e 275 LYS cc_start: 0.8333 (mttm) cc_final: 0.8099 (mtpt) REVERT: e 429 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8540 (p) REVERT: f 235 LEU cc_start: 0.9209 (mt) cc_final: 0.8935 (mt) REVERT: f 303 GLN cc_start: 0.7757 (mp10) cc_final: 0.7458 (mp10) REVERT: f 370 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8213 (ttp80) REVERT: f 428 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7368 (p0) REVERT: g 261 ASN cc_start: 0.6882 (t0) cc_final: 0.6658 (t0) REVERT: g 370 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8236 (tpp80) REVERT: g 383 GLU cc_start: 0.6960 (mp0) cc_final: 0.6639 (mp0) REVERT: g 428 ASP cc_start: 0.7743 (m-30) cc_final: 0.7432 (m-30) REVERT: h 244 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7787 (mtp180) REVERT: h 379 VAL cc_start: 0.9051 (t) cc_final: 0.8777 (p) outliers start: 241 outliers final: 177 residues processed: 1329 average time/residue: 0.2687 time to fit residues: 591.6118 Evaluate side-chains 1309 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 1112 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 389 VAL Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 231 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain S residue 415 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain U residue 387 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 383 GLU Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 420 MET Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 263 HIS Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 364 SER Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 231 ASN Chi-restraints excluded: chain a residue 271 ASP Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 429 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 269 GLN Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 290 LYS Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 413 GLU Chi-restraints excluded: chain f residue 415 LEU Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 428 ASP Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 404 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 71 optimal weight: 0.0980 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 333 optimal weight: 0.6980 chunk 135 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 326 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 ASN A 234 GLN B 378 ASN D 303 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 374 HIS I 269 GLN L 234 GLN T 378 ASN ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN a 263 HIS ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 269 GLN ** f 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.112532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094394 restraints weight = 80399.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097061 restraints weight = 39255.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.098781 restraints weight = 24173.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.099866 restraints weight = 17508.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100560 restraints weight = 14130.283| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.7273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 45170 Z= 0.140 Angle : 0.605 10.644 61015 Z= 0.313 Chirality : 0.041 0.184 7012 Planarity : 0.004 0.058 8251 Dihedral : 4.100 16.985 6202 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.63 % Allowed : 27.78 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.52 (0.11), residues: 5613 helix: 2.86 (0.13), residues: 1530 sheet: 0.77 (0.10), residues: 2584 loop : -0.47 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 248 TYR 0.018 0.001 TYR f 282 PHE 0.028 0.001 PHE O 237 HIS 0.006 0.001 HIS M 281 Details of bonding type rmsd covalent geometry : bond 0.00327 (45170) covalent geometry : angle 0.60502 (61015) hydrogen bonds : bond 0.03062 ( 2703) hydrogen bonds : angle 4.10297 ( 7497) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 228 poor density : 1129 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: m 19 MET cc_start: 0.6985 (mmt) cc_final: 0.6738 (mmp) REVERT: q 72 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7254 (p-80) REVERT: A 242 GLU cc_start: 0.7264 (mt-10) cc_final: 0.7004 (mt-10) REVERT: B 271 ASP cc_start: 0.7253 (t0) cc_final: 0.6973 (t70) REVERT: B 293 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8537 (mt) REVERT: B 377 MET cc_start: 0.7526 (ptp) cc_final: 0.7201 (mtm) REVERT: B 383 GLU cc_start: 0.7677 (mp0) cc_final: 0.7231 (mp0) REVERT: B 413 GLU cc_start: 0.7320 (tm-30) cc_final: 0.6710 (tm-30) REVERT: B 414 ASP cc_start: 0.8063 (m-30) cc_final: 0.7469 (m-30) REVERT: C 232 ASP cc_start: 0.7807 (m-30) cc_final: 0.7233 (t0) REVERT: C 242 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7367 (mt-10) REVERT: C 250 GLU cc_start: 0.8570 (tt0) cc_final: 0.8161 (tm-30) REVERT: C 269 GLN cc_start: 0.8465 (mm110) cc_final: 0.7981 (mt0) REVERT: C 425 LYS cc_start: 0.8652 (mmmt) cc_final: 0.8445 (pttm) REVERT: D 242 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7998 (mp0) REVERT: D 269 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8414 (mm110) REVERT: D 372 ILE cc_start: 0.9163 (mt) cc_final: 0.8822 (tt) REVERT: D 413 GLU cc_start: 0.8542 (pp20) cc_final: 0.8280 (tm-30) REVERT: E 246 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8359 (tm-30) REVERT: E 431 ASN cc_start: 0.7509 (m-40) cc_final: 0.7190 (m110) REVERT: F 236 LYS cc_start: 0.8531 (mptt) cc_final: 0.8197 (mptt) REVERT: F 377 MET cc_start: 0.7092 (pmm) cc_final: 0.6856 (pmm) REVERT: G 369 ASP cc_start: 0.8353 (m-30) cc_final: 0.7999 (m-30) REVERT: G 370 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8302 (ttp80) REVERT: G 381 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6828 (t0) REVERT: H 234 GLN cc_start: 0.8380 (mt0) cc_final: 0.7854 (mp10) REVERT: H 302 GLU cc_start: 0.7814 (tt0) cc_final: 0.7436 (tm-30) REVERT: H 370 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8397 (ttm-80) REVERT: I 418 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8328 (tp30) REVERT: I 428 ASP cc_start: 0.8752 (m-30) cc_final: 0.8286 (m-30) REVERT: J 242 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7740 (mt-10) REVERT: J 247 ARG cc_start: 0.8300 (mtm180) cc_final: 0.8033 (ttm110) REVERT: J 383 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7886 (mp0) REVERT: J 415 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7951 (mp) REVERT: K 236 LYS cc_start: 0.8674 (mmtp) cc_final: 0.8013 (tmmt) REVERT: K 242 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8217 (mt-10) REVERT: L 232 ASP cc_start: 0.7841 (t70) cc_final: 0.7511 (t0) REVERT: L 250 GLU cc_start: 0.8434 (tp30) cc_final: 0.7934 (tp30) REVERT: L 302 GLU cc_start: 0.7714 (pm20) cc_final: 0.7111 (pm20) REVERT: L 414 ASP cc_start: 0.7403 (m-30) cc_final: 0.7127 (m-30) REVERT: M 242 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7504 (mp0) REVERT: M 282 TYR cc_start: 0.8847 (m-80) cc_final: 0.8574 (m-80) REVERT: M 367 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8133 (mm-30) REVERT: N 242 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7683 (pt0) REVERT: O 376 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.8011 (ttmm) REVERT: O 418 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8089 (mm-30) REVERT: P 235 LEU cc_start: 0.9112 (mt) cc_final: 0.8899 (tp) REVERT: P 265 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8020 (mm-40) REVERT: P 418 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8348 (tp30) REVERT: Q 381 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.6507 (t70) REVERT: R 242 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8197 (mm-30) REVERT: R 247 ARG cc_start: 0.8344 (mtp-110) cc_final: 0.8043 (tmm-80) REVERT: R 370 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7528 (ttm-80) REVERT: R 383 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6674 (mt-10) REVERT: R 414 ASP cc_start: 0.7941 (t0) cc_final: 0.7566 (t0) REVERT: S 280 GLU cc_start: 0.7259 (tt0) cc_final: 0.6946 (mt-10) REVERT: S 404 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8047 (mm) REVERT: S 413 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8226 (tm-30) REVERT: T 244 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.7972 (ttp-110) REVERT: T 280 GLU cc_start: 0.7350 (tt0) cc_final: 0.7046 (tt0) REVERT: U 236 LYS cc_start: 0.9042 (tppt) cc_final: 0.8382 (mtpt) REVERT: U 248 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.8147 (ttm-80) REVERT: U 282 TYR cc_start: 0.8726 (m-10) cc_final: 0.8449 (m-10) REVERT: U 363 THR cc_start: 0.9266 (m) cc_final: 0.8872 (p) REVERT: U 413 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8168 (tm-30) REVERT: U 431 ASN cc_start: 0.8465 (t0) cc_final: 0.7913 (t0) REVERT: V 230 LEU cc_start: 0.8281 (tp) cc_final: 0.8037 (pt) REVERT: V 240 ASP cc_start: 0.8306 (t0) cc_final: 0.7939 (t0) REVERT: V 244 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8334 (ttp-110) REVERT: V 275 LYS cc_start: 0.8392 (ptpp) cc_final: 0.7871 (ptpp) REVERT: V 367 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7779 (mt-10) REVERT: V 376 LYS cc_start: 0.8508 (tppt) cc_final: 0.8140 (tptt) REVERT: V 418 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7849 (mm-30) REVERT: W 271 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6439 (p0) REVERT: W 302 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7368 (mp0) REVERT: W 394 LYS cc_start: 0.6777 (ptmm) cc_final: 0.5904 (tttp) REVERT: X 389 VAL cc_start: 0.8647 (t) cc_final: 0.8344 (m) REVERT: Y 410 LYS cc_start: 0.8255 (tmmt) cc_final: 0.7946 (pttm) REVERT: Z 290 LYS cc_start: 0.8769 (mttp) cc_final: 0.8425 (mtmm) REVERT: Z 362 GLU cc_start: 0.7647 (tt0) cc_final: 0.7393 (tt0) REVERT: Z 367 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7809 (mt-10) REVERT: Z 370 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7777 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8138 (tm-30) REVERT: a 276 GLU cc_start: 0.8307 (mp0) cc_final: 0.7479 (mt-10) REVERT: a 377 MET cc_start: 0.8813 (mmm) cc_final: 0.8468 (mmt) REVERT: b 418 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7818 (mm-30) REVERT: b 431 ASN cc_start: 0.7844 (m-40) cc_final: 0.7570 (m-40) REVERT: c 410 LYS cc_start: 0.7689 (mttt) cc_final: 0.7473 (mttp) REVERT: c 431 ASN cc_start: 0.7597 (m110) cc_final: 0.7146 (m110) REVERT: d 236 LYS cc_start: 0.9000 (ttpt) cc_final: 0.8701 (ttpp) REVERT: d 410 LYS cc_start: 0.8707 (tppp) cc_final: 0.8491 (tppt) REVERT: e 275 LYS cc_start: 0.8368 (mttm) cc_final: 0.8141 (mtpt) REVERT: f 370 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8118 (ttp80) REVERT: g 261 ASN cc_start: 0.7096 (t0) cc_final: 0.6871 (t0) REVERT: g 370 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8287 (tpp80) REVERT: g 383 GLU cc_start: 0.6936 (mp0) cc_final: 0.6662 (mp0) REVERT: g 428 ASP cc_start: 0.7626 (m-30) cc_final: 0.7355 (m-30) REVERT: h 244 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7816 (mtp180) REVERT: h 379 VAL cc_start: 0.9049 (t) cc_final: 0.8778 (p) outliers start: 228 outliers final: 189 residues processed: 1273 average time/residue: 0.2481 time to fit residues: 523.4868 Evaluate side-chains 1316 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 1109 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 281 HIS Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain M residue 293 LEU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 432 VAL Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 253 LEU Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 232 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 415 LEU Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain S residue 415 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 383 GLU Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 420 MET Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 263 HIS Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 385 LEU Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 231 ASN Chi-restraints excluded: chain a residue 271 ASP Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 386 SER Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 267 THR Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 404 LEU Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 315 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 533 optimal weight: 0.0970 chunk 135 optimal weight: 3.9990 chunk 253 optimal weight: 0.4980 chunk 506 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 338 optimal weight: 0.9990 chunk 3 optimal weight: 8.9990 chunk 354 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 GLN B 234 GLN C 277 GLN D 303 GLN E 277 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 269 GLN H 374 HIS I 269 GLN L 234 GLN ** R 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 392 ASN ** T 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 269 GLN ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 269 GLN ** f 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.111520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.093715 restraints weight = 81132.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.096303 restraints weight = 40022.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097956 restraints weight = 24772.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099031 restraints weight = 18027.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099715 restraints weight = 14545.742| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.7404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45170 Z= 0.158 Angle : 0.628 10.298 61015 Z= 0.325 Chirality : 0.041 0.189 7012 Planarity : 0.004 0.060 8251 Dihedral : 4.172 17.039 6202 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.46 % Allowed : 28.00 % Favored : 67.53 % 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: 1.48 (0.11), residues: 5613 helix: 2.77 (0.13), residues: 1530 sheet: 0.76 (0.10), residues: 2584 loop : -0.45 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 244 TYR 0.016 0.001 TYR f 282 PHE 0.031 0.002 PHE Z 272 HIS 0.006 0.001 HIS M 281 Details of bonding type rmsd covalent geometry : bond 0.00367 (45170) covalent geometry : angle 0.62781 (61015) hydrogen bonds : bond 0.03203 ( 2703) hydrogen bonds : angle 4.15427 ( 7497) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11226 Ramachandran restraints generated. 5613 Oldfield, 0 Emsley, 5613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1134 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: k 14 LEU cc_start: 0.8297 (mp) cc_final: 0.8088 (tt) REVERT: m 19 MET cc_start: 0.6819 (mmt) cc_final: 0.6609 (mmp) REVERT: q 72 HIS cc_start: 0.8091 (OUTLIER) cc_final: 0.7236 (p-80) REVERT: B 234 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: B 271 ASP cc_start: 0.7220 (t0) cc_final: 0.6977 (t70) REVERT: B 293 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8536 (mt) REVERT: B 377 MET cc_start: 0.7537 (ptp) cc_final: 0.7162 (mtm) REVERT: B 383 GLU cc_start: 0.7670 (mp0) cc_final: 0.7207 (mp0) REVERT: B 413 GLU cc_start: 0.7220 (tm-30) cc_final: 0.6898 (tm-30) REVERT: B 414 ASP cc_start: 0.7725 (m-30) cc_final: 0.7207 (m-30) REVERT: B 428 ASP cc_start: 0.6943 (m-30) cc_final: 0.6682 (m-30) REVERT: C 232 ASP cc_start: 0.7642 (m-30) cc_final: 0.7247 (t0) REVERT: C 242 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 250 GLU cc_start: 0.8433 (tt0) cc_final: 0.8150 (tm-30) REVERT: C 269 GLN cc_start: 0.8390 (mm110) cc_final: 0.7954 (mt0) REVERT: D 242 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7944 (mp0) REVERT: D 372 ILE cc_start: 0.9189 (mt) cc_final: 0.8857 (tt) REVERT: D 413 GLU cc_start: 0.8456 (pp20) cc_final: 0.8217 (tm-30) REVERT: D 428 ASP cc_start: 0.7411 (m-30) cc_final: 0.7098 (m-30) REVERT: E 246 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8368 (tm-30) REVERT: E 431 ASN cc_start: 0.7395 (m-40) cc_final: 0.7113 (m110) REVERT: F 377 MET cc_start: 0.7199 (pmm) cc_final: 0.6911 (pmm) REVERT: G 269 GLN cc_start: 0.8522 (mm-40) cc_final: 0.7667 (mp10) REVERT: G 370 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8330 (ttp80) REVERT: G 381 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7053 (t0) REVERT: H 230 LEU cc_start: 0.6801 (pt) cc_final: 0.6515 (mp) REVERT: H 234 GLN cc_start: 0.8374 (mt0) cc_final: 0.7879 (mp10) REVERT: H 302 GLU cc_start: 0.7741 (tt0) cc_final: 0.7461 (tm-30) REVERT: H 370 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8381 (ttm-80) REVERT: I 280 GLU cc_start: 0.7833 (tt0) cc_final: 0.7605 (tt0) REVERT: I 418 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8303 (tp30) REVERT: I 428 ASP cc_start: 0.8657 (m-30) cc_final: 0.8184 (m-30) REVERT: J 242 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7665 (mt-10) REVERT: J 247 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7976 (ttm110) REVERT: J 415 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7957 (mp) REVERT: K 236 LYS cc_start: 0.8678 (mmtp) cc_final: 0.8165 (tmmt) REVERT: K 242 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8108 (mt-10) REVERT: L 232 ASP cc_start: 0.7700 (t70) cc_final: 0.7313 (t0) REVERT: L 250 GLU cc_start: 0.8321 (tp30) cc_final: 0.7848 (tp30) REVERT: L 302 GLU cc_start: 0.7696 (pm20) cc_final: 0.7144 (pm20) REVERT: M 367 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8038 (mm-30) REVERT: M 377 MET cc_start: 0.7491 (mmt) cc_final: 0.7218 (mmt) REVERT: N 242 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7683 (pt0) REVERT: O 376 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8113 (ttmm) REVERT: O 418 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8258 (mm-30) REVERT: P 265 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8034 (mm-40) REVERT: P 362 GLU cc_start: 0.7719 (tt0) cc_final: 0.7420 (tt0) REVERT: Q 381 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.7128 (m-30) REVERT: R 242 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8180 (mm-30) REVERT: R 247 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.8004 (tmm-80) REVERT: R 279 GLU cc_start: 0.7504 (mp0) cc_final: 0.7296 (mp0) REVERT: R 370 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7542 (ttm-80) REVERT: R 383 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6673 (mt-10) REVERT: R 414 ASP cc_start: 0.7997 (t0) cc_final: 0.7566 (t0) REVERT: S 280 GLU cc_start: 0.7201 (tt0) cc_final: 0.6936 (mt-10) REVERT: S 358 THR cc_start: 0.8236 (m) cc_final: 0.7517 (p) REVERT: S 404 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8000 (mm) REVERT: S 413 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8248 (tm-30) REVERT: T 244 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7885 (ttp-110) REVERT: T 280 GLU cc_start: 0.7239 (tt0) cc_final: 0.6946 (tt0) REVERT: U 236 LYS cc_start: 0.9055 (tppt) cc_final: 0.8447 (mtpt) REVERT: U 248 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8113 (ttm-80) REVERT: U 282 TYR cc_start: 0.8688 (m-10) cc_final: 0.8472 (m-10) REVERT: U 363 THR cc_start: 0.9258 (m) cc_final: 0.8868 (p) REVERT: U 413 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8134 (tm-30) REVERT: U 431 ASN cc_start: 0.8421 (t0) cc_final: 0.7904 (t0) REVERT: V 230 LEU cc_start: 0.8295 (tp) cc_final: 0.8022 (pt) REVERT: V 240 ASP cc_start: 0.8216 (t0) cc_final: 0.7877 (t0) REVERT: V 244 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8367 (ttp-110) REVERT: V 367 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7894 (mt-10) REVERT: V 418 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7851 (mm-30) REVERT: W 271 ASP cc_start: 0.7179 (OUTLIER) cc_final: 0.6343 (p0) REVERT: W 302 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7430 (mp0) REVERT: W 394 LYS cc_start: 0.6657 (ptmm) cc_final: 0.5845 (tttp) REVERT: X 389 VAL cc_start: 0.8696 (t) cc_final: 0.8448 (m) REVERT: Y 410 LYS cc_start: 0.8276 (tmmt) cc_final: 0.7968 (ptpt) REVERT: Z 290 LYS cc_start: 0.8715 (mttp) cc_final: 0.8424 (mtmm) REVERT: Z 362 GLU cc_start: 0.7553 (tt0) cc_final: 0.7302 (tt0) REVERT: Z 367 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7858 (mt-10) REVERT: Z 370 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7837 (ttm-80) REVERT: Z 413 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8095 (tm-30) REVERT: a 269 GLN cc_start: 0.8817 (mm110) cc_final: 0.8431 (mm110) REVERT: b 246 GLN cc_start: 0.8406 (tt0) cc_final: 0.8199 (tt0) REVERT: b 431 ASN cc_start: 0.7850 (m-40) cc_final: 0.7558 (m-40) REVERT: c 410 LYS cc_start: 0.7751 (mttt) cc_final: 0.7522 (mttp) REVERT: c 431 ASN cc_start: 0.7475 (m110) cc_final: 0.7034 (m110) REVERT: d 234 GLN cc_start: 0.8653 (pt0) cc_final: 0.8400 (pt0) REVERT: d 236 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8682 (ttpp) REVERT: d 410 LYS cc_start: 0.8678 (tppp) cc_final: 0.8429 (tppt) REVERT: e 240 ASP cc_start: 0.8163 (m-30) cc_final: 0.7942 (m-30) REVERT: e 265 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7882 (mm-40) REVERT: e 275 LYS cc_start: 0.8364 (mttm) cc_final: 0.8137 (mtpt) REVERT: e 431 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.7068 (m110) REVERT: f 370 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8116 (ttp80) REVERT: f 400 LYS cc_start: 0.6449 (tmtt) cc_final: 0.6143 (tmtt) REVERT: f 428 ASP cc_start: 0.7965 (p0) cc_final: 0.7601 (p0) REVERT: g 261 ASN cc_start: 0.7224 (t0) cc_final: 0.7006 (t0) REVERT: g 370 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8327 (tpp80) REVERT: g 428 ASP cc_start: 0.7829 (m-30) cc_final: 0.7519 (m-30) REVERT: h 379 VAL cc_start: 0.9063 (t) cc_final: 0.8813 (p) outliers start: 220 outliers final: 185 residues processed: 1270 average time/residue: 0.2633 time to fit residues: 554.6087 Evaluate side-chains 1319 residues out of total 4928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1115 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain j residue 11 ILE Chi-restraints excluded: chain k residue 19 MET Chi-restraints excluded: chain m residue 15 GLN Chi-restraints excluded: chain n residue 11 ILE Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 72 HIS Chi-restraints excluded: chain r residue 65 LEU Chi-restraints excluded: chain s residue 66 THR Chi-restraints excluded: chain s residue 78 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 395 THR Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 256 ILE Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 409 MET Chi-restraints excluded: chain G residue 230 LEU Chi-restraints excluded: chain G residue 256 ILE Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 370 ARG Chi-restraints excluded: chain G residue 381 ASP Chi-restraints excluded: chain G residue 405 THR Chi-restraints excluded: chain G residue 407 ASP Chi-restraints excluded: chain H residue 253 LEU Chi-restraints excluded: chain H residue 256 ILE Chi-restraints excluded: chain H residue 257 VAL Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 370 ARG Chi-restraints excluded: chain H residue 379 VAL Chi-restraints excluded: chain H residue 395 THR Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 423 SER Chi-restraints excluded: chain I residue 243 SER Chi-restraints excluded: chain I residue 244 ARG Chi-restraints excluded: chain I residue 246 GLN Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 420 MET Chi-restraints excluded: chain I residue 423 SER Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 404 LEU Chi-restraints excluded: chain J residue 415 LEU Chi-restraints excluded: chain K residue 252 ILE Chi-restraints excluded: chain K residue 253 LEU Chi-restraints excluded: chain K residue 262 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 405 THR Chi-restraints excluded: chain K residue 408 GLN Chi-restraints excluded: chain L residue 242 GLU Chi-restraints excluded: chain L residue 246 GLN Chi-restraints excluded: chain L residue 256 ILE Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 415 LEU Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 409 MET Chi-restraints excluded: chain M residue 438 SER Chi-restraints excluded: chain N residue 278 THR Chi-restraints excluded: chain N residue 358 THR Chi-restraints excluded: chain N residue 395 THR Chi-restraints excluded: chain N residue 405 THR Chi-restraints excluded: chain N residue 435 SER Chi-restraints excluded: chain O residue 252 ILE Chi-restraints excluded: chain O residue 289 SER Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 390 VAL Chi-restraints excluded: chain P residue 231 ASN Chi-restraints excluded: chain P residue 252 ILE Chi-restraints excluded: chain P residue 292 THR Chi-restraints excluded: chain P residue 368 VAL Chi-restraints excluded: chain P residue 371 THR Chi-restraints excluded: chain P residue 395 THR Chi-restraints excluded: chain Q residue 253 LEU Chi-restraints excluded: chain Q residue 256 ILE Chi-restraints excluded: chain Q residue 278 THR Chi-restraints excluded: chain Q residue 292 THR Chi-restraints excluded: chain Q residue 381 ASP Chi-restraints excluded: chain Q residue 395 THR Chi-restraints excluded: chain Q residue 400 LYS Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 256 ILE Chi-restraints excluded: chain R residue 267 THR Chi-restraints excluded: chain R residue 370 ARG Chi-restraints excluded: chain R residue 405 THR Chi-restraints excluded: chain R residue 420 MET Chi-restraints excluded: chain R residue 428 ASP Chi-restraints excluded: chain S residue 230 LEU Chi-restraints excluded: chain S residue 256 ILE Chi-restraints excluded: chain S residue 404 LEU Chi-restraints excluded: chain T residue 235 LEU Chi-restraints excluded: chain T residue 244 ARG Chi-restraints excluded: chain T residue 253 LEU Chi-restraints excluded: chain T residue 358 THR Chi-restraints excluded: chain T residue 414 ASP Chi-restraints excluded: chain U residue 269 GLN Chi-restraints excluded: chain U residue 293 LEU Chi-restraints excluded: chain U residue 358 THR Chi-restraints excluded: chain U residue 379 VAL Chi-restraints excluded: chain V residue 244 ARG Chi-restraints excluded: chain V residue 246 GLN Chi-restraints excluded: chain V residue 253 LEU Chi-restraints excluded: chain V residue 263 HIS Chi-restraints excluded: chain V residue 358 THR Chi-restraints excluded: chain V residue 410 LYS Chi-restraints excluded: chain V residue 420 MET Chi-restraints excluded: chain W residue 252 ILE Chi-restraints excluded: chain W residue 267 THR Chi-restraints excluded: chain W residue 271 ASP Chi-restraints excluded: chain W residue 358 THR Chi-restraints excluded: chain W residue 372 ILE Chi-restraints excluded: chain X residue 267 THR Chi-restraints excluded: chain Y residue 240 ASP Chi-restraints excluded: chain Y residue 241 VAL Chi-restraints excluded: chain Y residue 263 HIS Chi-restraints excluded: chain Y residue 267 THR Chi-restraints excluded: chain Y residue 358 THR Chi-restraints excluded: chain Y residue 372 ILE Chi-restraints excluded: chain Y residue 379 VAL Chi-restraints excluded: chain Y residue 385 LEU Chi-restraints excluded: chain Y residue 415 LEU Chi-restraints excluded: chain Y residue 429 THR Chi-restraints excluded: chain Z residue 370 ARG Chi-restraints excluded: chain Z residue 377 MET Chi-restraints excluded: chain Z residue 391 VAL Chi-restraints excluded: chain Z residue 405 THR Chi-restraints excluded: chain Z residue 435 SER Chi-restraints excluded: chain a residue 231 ASN Chi-restraints excluded: chain a residue 271 ASP Chi-restraints excluded: chain a residue 372 ILE Chi-restraints excluded: chain a residue 413 GLU Chi-restraints excluded: chain a residue 429 THR Chi-restraints excluded: chain a residue 432 VAL Chi-restraints excluded: chain b residue 386 SER Chi-restraints excluded: chain b residue 405 THR Chi-restraints excluded: chain b residue 415 LEU Chi-restraints excluded: chain c residue 254 SER Chi-restraints excluded: chain c residue 267 THR Chi-restraints excluded: chain c residue 372 ILE Chi-restraints excluded: chain c residue 391 VAL Chi-restraints excluded: chain c residue 412 ILE Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Chi-restraints excluded: chain c residue 432 VAL Chi-restraints excluded: chain d residue 256 ILE Chi-restraints excluded: chain d residue 278 THR Chi-restraints excluded: chain d residue 363 THR Chi-restraints excluded: chain d residue 402 LEU Chi-restraints excluded: chain e residue 253 LEU Chi-restraints excluded: chain e residue 267 THR Chi-restraints excluded: chain e residue 368 VAL Chi-restraints excluded: chain e residue 402 LEU Chi-restraints excluded: chain e residue 405 THR Chi-restraints excluded: chain e residue 407 ASP Chi-restraints excluded: chain e residue 429 THR Chi-restraints excluded: chain e residue 431 ASN Chi-restraints excluded: chain f residue 232 ASP Chi-restraints excluded: chain f residue 256 ILE Chi-restraints excluded: chain f residue 267 THR Chi-restraints excluded: chain f residue 269 GLN Chi-restraints excluded: chain f residue 292 THR Chi-restraints excluded: chain f residue 370 ARG Chi-restraints excluded: chain f residue 402 LEU Chi-restraints excluded: chain f residue 418 GLU Chi-restraints excluded: chain f residue 432 VAL Chi-restraints excluded: chain g residue 253 LEU Chi-restraints excluded: chain g residue 267 THR Chi-restraints excluded: chain g residue 370 ARG Chi-restraints excluded: chain g residue 379 VAL Chi-restraints excluded: chain g residue 405 THR Chi-restraints excluded: chain g residue 413 GLU Chi-restraints excluded: chain g residue 429 THR Chi-restraints excluded: chain g residue 432 VAL Chi-restraints excluded: chain g residue 438 SER Chi-restraints excluded: chain h residue 244 ARG Chi-restraints excluded: chain h residue 253 LEU Chi-restraints excluded: chain h residue 256 ILE Chi-restraints excluded: chain h residue 435 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 262 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 462 optimal weight: 9.9990 chunk 211 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 284 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 274 optimal weight: 8.9990 chunk 478 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** p 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 GLN D 269 GLN D 303 GLN ** G 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 269 GLN ** L 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 392 ASN ** T 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 359 GLN ** a 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 378 ASN ** b 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 234 GLN ** f 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093504 restraints weight = 81616.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096126 restraints weight = 39683.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097823 restraints weight = 24431.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.098917 restraints weight = 17682.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099616 restraints weight = 14246.055| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.7427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.460 45170 Z= 0.283 Angle : 0.788 59.169 61015 Z= 0.449 Chirality : 0.043 0.698 7012 Planarity : 0.005 0.170 8251 Dihedral : 4.172 17.105 6202 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.34 % Allowed : 28.25 % Favored : 67.41 % Cbeta Deviations : 0.04 % 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: 1.48 (0.11), residues: 5613 helix: 2.76 (0.13), residues: 1530 sheet: 0.76 (0.10), residues: 2584 loop : -0.45 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 244 TYR 0.014 0.001 TYR Y 366 PHE 0.027 0.002 PHE Z 272 HIS 0.005 0.001 HIS M 281 Details of bonding type rmsd covalent geometry : bond 0.00600 (45170) covalent geometry : angle 0.78831 (61015) hydrogen bonds : bond 0.03226 ( 2703) hydrogen bonds : angle 4.15915 ( 7497) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10991.51 seconds wall clock time: 188 minutes 48.98 seconds (11328.98 seconds total)