Starting phenix.real_space_refine on Sun Feb 8 08:20:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.map" model { file = "/net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ngv_49394/02_2026/9ngv_49394.cif" } resolution = 3.04 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= 0.007 sd= 0.049 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 144 5.16 5 C 26604 2.51 5 N 7128 2.21 5 O 8190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42066 Number of models: 1 Model: "" Number of chains: 126 Chain: "Aa" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ab" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ac" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ad" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Ae" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Af" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Ag" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Ah" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ai" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Aj" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ak" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Al" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Am" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "An" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Ao" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ap" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Aq" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ar" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "As" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "At" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Au" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Av" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Aw" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ax" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ay" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Az" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Ba" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Bb" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Bc" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Bd" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Be" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Bf" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Bg" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Bh" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Bi" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Bj" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Bk" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Bl" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Bm" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Bn" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Bo" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Bp" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Bq" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Br" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Bs" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Bt" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Bu" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Bv" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Bw" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Bx" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "By" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Bz" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ca" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Cb" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Cc" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Cd" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Ce" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Cf" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cg" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ch" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Ci" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Cj" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Ck" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Cl" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Cm" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cn" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Co" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Cp" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Cq" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Cr" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Cs" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ct" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Cu" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Cv" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Cw" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Cx" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Cy" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Cz" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Da" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Db" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dc" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Dd" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "De" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Df" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Dg" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dh" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Di" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dj" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Dk" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Dl" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Dm" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Dn" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Do" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Dp" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dq" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Dr" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Ds" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Dt" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Du" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dv" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Dw" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Dx" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Dy" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Dz" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Ea" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Eb" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ec" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ed" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ee" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Ef" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Eg" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Eh" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Ei" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Ej" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Ek" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "El" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Em" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "En" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Eo" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Chain: "Ep" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 117 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Eq" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 61 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "Er" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 125 Classifications: {'peptide': 16} Modifications used: {'COO': 1} Link IDs: {'TRANS': 15} Chain: "Es" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Classifications: {'peptide': 5} Modifications used: {'COO': 1} Link IDs: {'TRANS': 4} Chain: "Et" Number of atoms: 484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 484 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Eu" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 276 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "Ev" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1238 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 15, 'TRANS': 144} Time building chain proxies: 10.90, per 1000 atoms: 0.26 Number of scatterers: 42066 At special positions: 0 Unit cell: (206.925, 206.925, 92.115, 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 144 16.00 O 8190 8.00 N 7128 7.00 C 26604 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: 3.60 Conformation dependent library (CDL) restraints added in 2.1 seconds 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10044 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 72 sheets defined 26.1% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'Aa' and resid 1 through 15 Processing helix chain 'Ab' and resid 3 through 7 Processing helix chain 'Af' and resid 792 through 814 removed outlier: 3.648A pdb=" N GLNAf 807 " --> pdb=" O THRAf 803 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 105 through 120 Processing helix chain 'Ag' and resid 123 through 143 removed outlier: 3.504A pdb=" N VALAg 128 " --> pdb=" O PROAg 124 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 2 through 15 Processing helix chain 'Ai' and resid 3 through 7 Processing helix chain 'Am' and resid 792 through 814 removed outlier: 3.703A pdb=" N GLNAm 807 " --> pdb=" O THRAm 803 " (cutoff:3.500A) Processing helix chain 'An' and resid 105 through 120 removed outlier: 3.503A pdb=" N TYRAn 120 " --> pdb=" O THRAn 116 " (cutoff:3.500A) Processing helix chain 'An' and resid 123 through 143 removed outlier: 3.503A pdb=" N VALAn 128 " --> pdb=" O PROAn 124 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 2 through 15 Processing helix chain 'Ap' and resid 3 through 7 Processing helix chain 'At' and resid 792 through 814 removed outlier: 3.711A pdb=" N GLNAt 807 " --> pdb=" O THRAt 803 " (cutoff:3.500A) Processing helix chain 'Au' and resid 105 through 120 removed outlier: 3.538A pdb=" N TYRAu 120 " --> pdb=" O THRAu 116 " (cutoff:3.500A) Processing helix chain 'Au' and resid 123 through 143 Processing helix chain 'Av' and resid 2 through 15 Processing helix chain 'Aw' and resid 3 through 7 Processing helix chain 'Ba' and resid 792 through 814 Processing helix chain 'Bb' and resid 105 through 120 Processing helix chain 'Bb' and resid 123 through 143 Processing helix chain 'Bc' and resid 2 through 15 Processing helix chain 'Bd' and resid 3 through 7 Processing helix chain 'Bh' and resid 792 through 814 removed outlier: 3.653A pdb=" N GLNBh 807 " --> pdb=" O THRBh 803 " (cutoff:3.500A) Processing helix chain 'Bi' and resid 105 through 120 Processing helix chain 'Bi' and resid 123 through 143 removed outlier: 3.501A pdb=" N VALBi 128 " --> pdb=" O PROBi 124 " (cutoff:3.500A) Processing helix chain 'Bj' and resid 2 through 15 Processing helix chain 'Bk' and resid 3 through 7 Processing helix chain 'Bo' and resid 792 through 814 removed outlier: 3.502A pdb=" N GLNBo 807 " --> pdb=" O THRBo 803 " (cutoff:3.500A) Processing helix chain 'Bp' and resid 105 through 120 Processing helix chain 'Bp' and resid 123 through 143 Processing helix chain 'Bq' and resid 2 through 15 Processing helix chain 'Br' and resid 3 through 7 Processing helix chain 'Bv' and resid 792 through 814 removed outlier: 3.562A pdb=" N GLNBv 807 " --> pdb=" O THRBv 803 " (cutoff:3.500A) Processing helix chain 'Bw' and resid 105 through 120 Processing helix chain 'Bw' and resid 123 through 143 removed outlier: 3.617A pdb=" N VALBw 128 " --> pdb=" O PROBw 124 " (cutoff:3.500A) Processing helix chain 'Bx' and resid 2 through 15 Processing helix chain 'By' and resid 3 through 7 Processing helix chain 'Cc' and resid 792 through 814 removed outlier: 3.519A pdb=" N GLNCc 807 " --> pdb=" O THRCc 803 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 105 through 120 Processing helix chain 'Cd' and resid 123 through 143 removed outlier: 3.521A pdb=" N VALCd 128 " --> pdb=" O PROCd 124 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 2 through 15 Processing helix chain 'Cf' and resid 3 through 7 Processing helix chain 'Cj' and resid 792 through 814 removed outlier: 3.646A pdb=" N GLNCj 807 " --> pdb=" O THRCj 803 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 105 through 120 Processing helix chain 'Ck' and resid 123 through 143 removed outlier: 3.608A pdb=" N VALCk 128 " --> pdb=" O PROCk 124 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 2 through 15 Processing helix chain 'Cm' and resid 3 through 7 Processing helix chain 'Cq' and resid 792 through 814 removed outlier: 3.634A pdb=" N GLNCq 807 " --> pdb=" O THRCq 803 " (cutoff:3.500A) Processing helix chain 'Cr' and resid 105 through 120 Processing helix chain 'Cr' and resid 123 through 143 removed outlier: 3.524A pdb=" N VALCr 128 " --> pdb=" O PROCr 124 " (cutoff:3.500A) Processing helix chain 'Cs' and resid 2 through 15 Processing helix chain 'Ct' and resid 3 through 7 Processing helix chain 'Cx' and resid 792 through 814 removed outlier: 3.691A pdb=" N GLNCx 807 " --> pdb=" O THRCx 803 " (cutoff:3.500A) Processing helix chain 'Cy' and resid 105 through 120 removed outlier: 3.521A pdb=" N TYRCy 120 " --> pdb=" O THRCy 116 " (cutoff:3.500A) Processing helix chain 'Cy' and resid 123 through 143 removed outlier: 3.580A pdb=" N VALCy 128 " --> pdb=" O PROCy 124 " (cutoff:3.500A) Processing helix chain 'Cz' and resid 2 through 15 Processing helix chain 'Da' and resid 3 through 7 Processing helix chain 'De' and resid 792 through 814 removed outlier: 3.722A pdb=" N GLNDe 807 " --> pdb=" O THRDe 803 " (cutoff:3.500A) Processing helix chain 'Df' and resid 105 through 120 removed outlier: 3.518A pdb=" N TYRDf 120 " --> pdb=" O THRDf 116 " (cutoff:3.500A) Processing helix chain 'Df' and resid 123 through 143 removed outlier: 3.501A pdb=" N VALDf 128 " --> pdb=" O PRODf 124 " (cutoff:3.500A) Processing helix chain 'Dg' and resid 2 through 15 Processing helix chain 'Dh' and resid 3 through 7 Processing helix chain 'Dl' and resid 792 through 814 Processing helix chain 'Dm' and resid 105 through 120 Processing helix chain 'Dm' and resid 123 through 143 Processing helix chain 'Dn' and resid 2 through 15 Processing helix chain 'Do' and resid 3 through 7 Processing helix chain 'Ds' and resid 792 through 814 removed outlier: 3.649A pdb=" N GLNDs 807 " --> pdb=" O THRDs 803 " (cutoff:3.500A) Processing helix chain 'Dt' and resid 105 through 120 Processing helix chain 'Dt' and resid 123 through 143 removed outlier: 3.501A pdb=" N VALDt 128 " --> pdb=" O PRODt 124 " (cutoff:3.500A) Processing helix chain 'Du' and resid 2 through 15 Processing helix chain 'Dv' and resid 3 through 7 Processing helix chain 'Dz' and resid 792 through 814 removed outlier: 3.533A pdb=" N GLNDz 807 " --> pdb=" O THRDz 803 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 105 through 120 Processing helix chain 'Ea' and resid 123 through 143 Processing helix chain 'Eb' and resid 2 through 15 Processing helix chain 'Ec' and resid 3 through 7 Processing helix chain 'Eg' and resid 792 through 814 Processing helix chain 'Eh' and resid 105 through 120 Processing helix chain 'Eh' and resid 123 through 143 Processing helix chain 'Ei' and resid 2 through 15 Processing helix chain 'Ej' and resid 3 through 7 Processing helix chain 'En' and resid 792 through 814 removed outlier: 3.512A pdb=" N GLNEn 807 " --> pdb=" O THREn 803 " (cutoff:3.500A) Processing helix chain 'Eo' and resid 105 through 120 Processing helix chain 'Eo' and resid 123 through 143 removed outlier: 3.514A pdb=" N VALEo 128 " --> pdb=" O PROEo 124 " (cutoff:3.500A) Processing helix chain 'Ep' and resid 2 through 15 Processing helix chain 'Eq' and resid 3 through 7 Processing helix chain 'Eu' and resid 792 through 814 removed outlier: 3.658A pdb=" N GLNEu 807 " --> pdb=" O THREu 803 " (cutoff:3.500A) Processing helix chain 'Ev' and resid 105 through 120 Processing helix chain 'Ev' and resid 123 through 143 removed outlier: 3.605A pdb=" N VALEv 128 " --> pdb=" O PROEv 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Ae' and resid 211 through 215 removed outlier: 5.240A pdb=" N ILEAe 212 " --> pdb=" O ILEAe 223 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILEAe 223 " --> pdb=" O ILEAe 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Ae' and resid 237 through 238 removed outlier: 6.524A pdb=" N LEUAe 255 " --> pdb=" O LYSAe 245 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILEAe 247 " --> pdb=" O ARGAe 253 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARGAe 253 " --> pdb=" O ILEAe 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Af' and resid 819 through 822 Processing sheet with id=AA4, first strand: chain 'Ag' and resid 150 through 158 removed outlier: 9.946A pdb=" N LYSAg 150 " --> pdb=" O ASPAg 249 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ARGAg 251 " --> pdb=" O LYSAg 150 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THRAg 152 " --> pdb=" O ARGAg 251 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASPAg 253 " --> pdb=" O THRAg 152 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N THRAg 154 " --> pdb=" O ASPAg 253 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ARGAg 255 " --> pdb=" O THRAg 154 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLNAg 156 " --> pdb=" O ARGAg 255 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VALAg 176 " --> pdb=" O VALAg 248 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYRAg 250 " --> pdb=" O VALAg 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Ag' and resid 168 through 171 removed outlier: 5.932A pdb=" N ILEAg 169 " --> pdb=" O ILEAg 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Al' and resid 211 through 215 removed outlier: 5.244A pdb=" N ILEAl 212 " --> pdb=" O ILEAl 223 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ILEAl 223 " --> pdb=" O ILEAl 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Al' and resid 237 through 238 removed outlier: 6.540A pdb=" N LEUAl 255 " --> pdb=" O LYSAl 245 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILEAl 247 " --> pdb=" O ARGAl 253 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARGAl 253 " --> pdb=" O ILEAl 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'An' and resid 150 through 158 removed outlier: 9.928A pdb=" N LYSAn 150 " --> pdb=" O ASPAn 249 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N ARGAn 251 " --> pdb=" O LYSAn 150 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THRAn 152 " --> pdb=" O ARGAn 251 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ASPAn 253 " --> pdb=" O THRAn 152 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N THRAn 154 " --> pdb=" O ASPAn 253 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ARGAn 255 " --> pdb=" O THRAn 154 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLNAn 156 " --> pdb=" O ARGAn 255 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VALAn 176 " --> pdb=" O TYRAn 250 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VALAn 252 " --> pdb=" O VALAn 176 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SERAn 178 " --> pdb=" O VALAn 252 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N LEUAn 254 " --> pdb=" O SERAn 178 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VALAn 180 " --> pdb=" O LEUAn 254 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VALAn 256 " --> pdb=" O VALAn 180 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEUAn 182 " --> pdb=" O VALAn 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'An' and resid 168 through 171 removed outlier: 5.916A pdb=" N ILEAn 169 " --> pdb=" O ILEAn 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'As' and resid 211 through 215 removed outlier: 5.275A pdb=" N ILEAs 212 " --> pdb=" O ILEAs 223 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ILEAs 223 " --> pdb=" O ILEAs 212 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'As' and resid 237 through 238 removed outlier: 6.516A pdb=" N LEUAs 255 " --> pdb=" O LYSAs 245 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILEAs 247 " --> pdb=" O ARGAs 253 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARGAs 253 " --> pdb=" O ILEAs 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Au' and resid 150 through 158 removed outlier: 9.822A pdb=" N LYSAu 150 " --> pdb=" O ASPAu 249 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ARGAu 251 " --> pdb=" O LYSAu 150 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THRAu 152 " --> pdb=" O ARGAu 251 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ASPAu 253 " --> pdb=" O THRAu 152 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N THRAu 154 " --> pdb=" O ASPAu 253 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ARGAu 255 " --> pdb=" O THRAu 154 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLNAu 156 " --> pdb=" O ARGAu 255 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VALAu 176 " --> pdb=" O VALAu 248 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYRAu 250 " --> pdb=" O VALAu 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Au' and resid 168 through 171 removed outlier: 5.912A pdb=" N ILEAu 169 " --> pdb=" O ILEAu 242 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Az' and resid 211 through 215 removed outlier: 6.721A pdb=" N TRPAz 221 " --> pdb=" O GLNAz 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Az' and resid 237 through 238 removed outlier: 6.546A pdb=" N LEUAz 255 " --> pdb=" O LYSAz 245 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ILEAz 247 " --> pdb=" O ARGAz 253 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARGAz 253 " --> pdb=" O ILEAz 247 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Bb' and resid 150 through 158 removed outlier: 9.900A pdb=" N LYSBb 150 " --> pdb=" O ASPBb 249 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N ARGBb 251 " --> pdb=" O LYSBb 150 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THRBb 152 " --> pdb=" O ARGBb 251 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ASPBb 253 " --> pdb=" O THRBb 152 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THRBb 154 " --> pdb=" O ASPBb 253 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ARGBb 255 " --> pdb=" O THRBb 154 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLNBb 156 " --> pdb=" O ARGBb 255 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N VALBb 176 " --> pdb=" O VALBb 248 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYRBb 250 " --> pdb=" O VALBb 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Bb' and resid 168 through 171 Processing sheet with id=AB9, first strand: chain 'Bg' and resid 211 through 215 removed outlier: 6.701A pdb=" N TRPBg 221 " --> pdb=" O GLNBg 213 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Bg' and resid 237 through 238 removed outlier: 6.513A pdb=" N LEUBg 255 " --> pdb=" O LYSBg 245 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILEBg 247 " --> pdb=" O ARGBg 253 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARGBg 253 " --> pdb=" O ILEBg 247 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Bi' and resid 150 through 158 removed outlier: 9.999A pdb=" N LYSBi 150 " --> pdb=" O ASPBi 249 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ARGBi 251 " --> pdb=" O LYSBi 150 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THRBi 152 " --> pdb=" O ARGBi 251 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ASPBi 253 " --> pdb=" O THRBi 152 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THRBi 154 " --> pdb=" O ASPBi 253 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ARGBi 255 " --> pdb=" O THRBi 154 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLNBi 156 " --> pdb=" O ARGBi 255 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VALBi 176 " --> pdb=" O TYRBi 250 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VALBi 252 " --> pdb=" O VALBi 176 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N SERBi 178 " --> pdb=" O VALBi 252 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEUBi 254 " --> pdb=" O SERBi 178 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VALBi 180 " --> pdb=" O LEUBi 254 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VALBi 256 " --> pdb=" O VALBi 180 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEUBi 182 " --> pdb=" O VALBi 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Bi' and resid 168 through 171 Processing sheet with id=AC4, first strand: chain 'Bn' and resid 211 through 215 removed outlier: 6.716A pdb=" N TRPBn 221 " --> pdb=" O GLNBn 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Bn' and resid 237 through 238 removed outlier: 6.531A pdb=" N LEUBn 255 " --> pdb=" O LYSBn 245 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ILEBn 247 " --> pdb=" O ARGBn 253 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ARGBn 253 " --> pdb=" O ILEBn 247 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Bp' and resid 150 through 158 removed outlier: 9.939A pdb=" N LYSBp 150 " --> pdb=" O ASPBp 249 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ARGBp 251 " --> pdb=" O LYSBp 150 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THRBp 152 " --> pdb=" O ARGBp 251 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ASPBp 253 " --> pdb=" O THRBp 152 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THRBp 154 " --> pdb=" O ASPBp 253 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ARGBp 255 " --> pdb=" O THRBp 154 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLNBp 156 " --> pdb=" O ARGBp 255 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VALBp 176 " --> pdb=" O TYRBp 250 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VALBp 252 " --> pdb=" O VALBp 176 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SERBp 178 " --> pdb=" O VALBp 252 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N LEUBp 254 " --> pdb=" O SERBp 178 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VALBp 180 " --> pdb=" O LEUBp 254 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VALBp 256 " --> pdb=" O VALBp 180 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEUBp 182 " --> pdb=" O VALBp 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Bp' and resid 168 through 171 Processing sheet with id=AC8, first strand: chain 'Bu' and resid 211 through 215 removed outlier: 5.212A pdb=" N ILEBu 212 " --> pdb=" O ILEBu 223 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ILEBu 223 " --> pdb=" O ILEBu 212 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Bu' and resid 237 through 238 removed outlier: 6.557A pdb=" N LEUBu 255 " --> pdb=" O LYSBu 245 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILEBu 247 " --> pdb=" O ARGBu 253 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARGBu 253 " --> pdb=" O ILEBu 247 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Bw' and resid 150 through 158 removed outlier: 9.996A pdb=" N LYSBw 150 " --> pdb=" O ASPBw 249 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N ARGBw 251 " --> pdb=" O LYSBw 150 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THRBw 152 " --> pdb=" O ARGBw 251 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ASPBw 253 " --> pdb=" O THRBw 152 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N THRBw 154 " --> pdb=" O ASPBw 253 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ARGBw 255 " --> pdb=" O THRBw 154 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N GLNBw 156 " --> pdb=" O ARGBw 255 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N VALBw 176 " --> pdb=" O VALBw 248 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N TYRBw 250 " --> pdb=" O VALBw 176 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Bw' and resid 168 through 171 Processing sheet with id=AD3, first strand: chain 'Cb' and resid 211 through 215 removed outlier: 6.691A pdb=" N TRPCb 221 " --> pdb=" O GLNCb 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Cb' and resid 237 through 238 removed outlier: 6.502A pdb=" N LEUCb 255 " --> pdb=" O LYSCb 245 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILECb 247 " --> pdb=" O ARGCb 253 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARGCb 253 " --> pdb=" O ILECb 247 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Cd' and resid 150 through 158 removed outlier: 9.967A pdb=" N LYSCd 150 " --> pdb=" O ASPCd 249 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N ARGCd 251 " --> pdb=" O LYSCd 150 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THRCd 152 " --> pdb=" O ARGCd 251 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ASPCd 253 " --> pdb=" O THRCd 152 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THRCd 154 " --> pdb=" O ASPCd 253 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ARGCd 255 " --> pdb=" O THRCd 154 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLNCd 156 " --> pdb=" O ARGCd 255 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VALCd 176 " --> pdb=" O TYRCd 250 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N VALCd 252 " --> pdb=" O VALCd 176 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SERCd 178 " --> pdb=" O VALCd 252 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEUCd 254 " --> pdb=" O SERCd 178 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VALCd 180 " --> pdb=" O LEUCd 254 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VALCd 256 " --> pdb=" O VALCd 180 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEUCd 182 " --> pdb=" O VALCd 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Cd' and resid 168 through 171 Processing sheet with id=AD7, first strand: chain 'Ci' and resid 211 through 215 removed outlier: 6.734A pdb=" N TRPCi 221 " --> pdb=" O GLNCi 213 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Ci' and resid 237 through 238 removed outlier: 6.519A pdb=" N LEUCi 255 " --> pdb=" O LYSCi 245 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ILECi 247 " --> pdb=" O ARGCi 253 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARGCi 253 " --> pdb=" O ILECi 247 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Ck' and resid 150 through 157 removed outlier: 9.928A pdb=" N LYSCk 150 " --> pdb=" O ASPCk 249 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ARGCk 251 " --> pdb=" O LYSCk 150 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THRCk 152 " --> pdb=" O ARGCk 251 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASPCk 253 " --> pdb=" O THRCk 152 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N THRCk 154 " --> pdb=" O ASPCk 253 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ARGCk 255 " --> pdb=" O THRCk 154 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLNCk 156 " --> pdb=" O ARGCk 255 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N VALCk 176 " --> pdb=" O VALCk 248 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N TYRCk 250 " --> pdb=" O VALCk 176 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Ck' and resid 168 through 171 Processing sheet with id=AE2, first strand: chain 'Cp' and resid 211 through 215 removed outlier: 5.224A pdb=" N ILECp 212 " --> pdb=" O ILECp 223 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ILECp 223 " --> pdb=" O ILECp 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Cp' and resid 237 through 238 removed outlier: 6.516A pdb=" N LEUCp 255 " --> pdb=" O LYSCp 245 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILECp 247 " --> pdb=" O ARGCp 253 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ARGCp 253 " --> pdb=" O ILECp 247 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Cr' and resid 150 through 158 removed outlier: 9.962A pdb=" N LYSCr 150 " --> pdb=" O ASPCr 249 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ARGCr 251 " --> pdb=" O LYSCr 150 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THRCr 152 " --> pdb=" O ARGCr 251 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ASPCr 253 " --> pdb=" O THRCr 152 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N THRCr 154 " --> pdb=" O ASPCr 253 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ARGCr 255 " --> pdb=" O THRCr 154 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLNCr 156 " --> pdb=" O ARGCr 255 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VALCr 176 " --> pdb=" O TYRCr 250 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VALCr 252 " --> pdb=" O VALCr 176 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SERCr 178 " --> pdb=" O VALCr 252 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEUCr 254 " --> pdb=" O SERCr 178 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VALCr 180 " --> pdb=" O LEUCr 254 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VALCr 256 " --> pdb=" O VALCr 180 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEUCr 182 " --> pdb=" O VALCr 256 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Cr' and resid 168 through 171 Processing sheet with id=AE6, first strand: chain 'Cw' and resid 211 through 215 removed outlier: 5.296A pdb=" N ILECw 212 " --> pdb=" O ILECw 223 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILECw 223 " --> pdb=" O ILECw 212 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Cw' and resid 237 through 238 removed outlier: 6.526A pdb=" N LEUCw 255 " --> pdb=" O LYSCw 245 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILECw 247 " --> pdb=" O ARGCw 253 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ARGCw 253 " --> pdb=" O ILECw 247 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Cy' and resid 150 through 157 removed outlier: 9.906A pdb=" N LYSCy 150 " --> pdb=" O ASPCy 249 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N ARGCy 251 " --> pdb=" O LYSCy 150 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THRCy 152 " --> pdb=" O ARGCy 251 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASPCy 253 " --> pdb=" O THRCy 152 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N THRCy 154 " --> pdb=" O ASPCy 253 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ARGCy 255 " --> pdb=" O THRCy 154 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLNCy 156 " --> pdb=" O ARGCy 255 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N VALCy 176 " --> pdb=" O VALCy 248 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N TYRCy 250 " --> pdb=" O VALCy 176 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Cy' and resid 168 through 171 removed outlier: 5.901A pdb=" N ILECy 169 " --> pdb=" O ILECy 242 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Dd' and resid 211 through 215 removed outlier: 5.295A pdb=" N ILEDd 212 " --> pdb=" O ILEDd 223 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILEDd 223 " --> pdb=" O ILEDd 212 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Dd' and resid 237 through 238 removed outlier: 6.555A pdb=" N LEUDd 255 " --> pdb=" O LYSDd 245 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILEDd 247 " --> pdb=" O ARGDd 253 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ARGDd 253 " --> pdb=" O ILEDd 247 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Df' and resid 150 through 158 removed outlier: 9.834A pdb=" N LYSDf 150 " --> pdb=" O ASPDf 249 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N ARGDf 251 " --> pdb=" O LYSDf 150 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THRDf 152 " --> pdb=" O ARGDf 251 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ASPDf 253 " --> pdb=" O THRDf 152 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THRDf 154 " --> pdb=" O ASPDf 253 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N ARGDf 255 " --> pdb=" O THRDf 154 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLNDf 156 " --> pdb=" O ARGDf 255 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N VALDf 176 " --> pdb=" O VALDf 248 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N TYRDf 250 " --> pdb=" O VALDf 176 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Df' and resid 168 through 171 removed outlier: 5.906A pdb=" N ILEDf 169 " --> pdb=" O ILEDf 242 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Dk' and resid 211 through 215 removed outlier: 6.691A pdb=" N TRPDk 221 " --> pdb=" O GLNDk 213 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Dk' and resid 237 through 238 removed outlier: 6.544A pdb=" N LEUDk 255 " --> pdb=" O LYSDk 245 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ILEDk 247 " --> pdb=" O ARGDk 253 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ARGDk 253 " --> pdb=" O ILEDk 247 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Dm' and resid 150 through 158 removed outlier: 9.897A pdb=" N LYSDm 150 " --> pdb=" O ASPDm 249 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N ARGDm 251 " --> pdb=" O LYSDm 150 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THRDm 152 " --> pdb=" O ARGDm 251 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ASPDm 253 " --> pdb=" O THRDm 152 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THRDm 154 " --> pdb=" O ASPDm 253 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ARGDm 255 " --> pdb=" O THRDm 154 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLNDm 156 " --> pdb=" O ARGDm 255 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N VALDm 176 " --> pdb=" O VALDm 248 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N TYRDm 250 " --> pdb=" O VALDm 176 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Dm' and resid 168 through 171 Processing sheet with id=AF9, first strand: chain 'Dr' and resid 211 through 215 removed outlier: 6.703A pdb=" N TRPDr 221 " --> pdb=" O GLNDr 213 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Dr' and resid 237 through 238 removed outlier: 6.517A pdb=" N LEUDr 255 " --> pdb=" O LYSDr 245 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILEDr 247 " --> pdb=" O ARGDr 253 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARGDr 253 " --> pdb=" O ILEDr 247 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Dt' and resid 150 through 158 removed outlier: 9.888A pdb=" N LYSDt 150 " --> pdb=" O ASPDt 249 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N ARGDt 251 " --> pdb=" O LYSDt 150 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THRDt 152 " --> pdb=" O ARGDt 251 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ASPDt 253 " --> pdb=" O THRDt 152 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THRDt 154 " --> pdb=" O ASPDt 253 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ARGDt 255 " --> pdb=" O THRDt 154 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLNDt 156 " --> pdb=" O ARGDt 255 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VALDt 176 " --> pdb=" O TYRDt 250 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N VALDt 252 " --> pdb=" O VALDt 176 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N SERDt 178 " --> pdb=" O VALDt 252 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEUDt 254 " --> pdb=" O SERDt 178 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VALDt 180 " --> pdb=" O LEUDt 254 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VALDt 256 " --> pdb=" O VALDt 180 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEUDt 182 " --> pdb=" O VALDt 256 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Dt' and resid 168 through 171 Processing sheet with id=AG4, first strand: chain 'Dy' and resid 211 through 215 removed outlier: 6.703A pdb=" N TRPDy 221 " --> pdb=" O GLNDy 213 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Dy' and resid 237 through 238 removed outlier: 6.534A pdb=" N LEUDy 255 " --> pdb=" O LYSDy 245 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILEDy 247 " --> pdb=" O ARGDy 253 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ARGDy 253 " --> pdb=" O ILEDy 247 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Ea' and resid 150 through 158 removed outlier: 9.928A pdb=" N LYSEa 150 " --> pdb=" O ASPEa 249 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ARGEa 251 " --> pdb=" O LYSEa 150 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THREa 152 " --> pdb=" O ARGEa 251 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ASPEa 253 " --> pdb=" O THREa 152 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THREa 154 " --> pdb=" O ASPEa 253 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ARGEa 255 " --> pdb=" O THREa 154 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLNEa 156 " --> pdb=" O ARGEa 255 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VALEa 176 " --> pdb=" O TYREa 250 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N VALEa 252 " --> pdb=" O VALEa 176 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N SEREa 178 " --> pdb=" O VALEa 252 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEUEa 254 " --> pdb=" O SEREa 178 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VALEa 180 " --> pdb=" O LEUEa 254 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VALEa 256 " --> pdb=" O VALEa 180 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEUEa 182 " --> pdb=" O VALEa 256 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Ea' and resid 168 through 171 Processing sheet with id=AG8, first strand: chain 'Ef' and resid 211 through 215 removed outlier: 5.185A pdb=" N ILEEf 212 " --> pdb=" O ILEEf 223 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILEEf 223 " --> pdb=" O ILEEf 212 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Ef' and resid 237 through 238 removed outlier: 6.560A pdb=" N LEUEf 255 " --> pdb=" O LYSEf 245 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILEEf 247 " --> pdb=" O ARGEf 253 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARGEf 253 " --> pdb=" O ILEEf 247 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Eh' and resid 150 through 158 removed outlier: 9.922A pdb=" N LYSEh 150 " --> pdb=" O ASPEh 249 " (cutoff:3.500A) removed outlier: 8.668A pdb=" N ARGEh 251 " --> pdb=" O LYSEh 150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THREh 152 " --> pdb=" O ARGEh 251 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N ASPEh 253 " --> pdb=" O THREh 152 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THREh 154 " --> pdb=" O ASPEh 253 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ARGEh 255 " --> pdb=" O THREh 154 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLNEh 156 " --> pdb=" O ARGEh 255 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N VALEh 176 " --> pdb=" O VALEh 248 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYREh 250 " --> pdb=" O VALEh 176 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Eh' and resid 168 through 171 Processing sheet with id=AH3, first strand: chain 'Em' and resid 211 through 215 removed outlier: 6.709A pdb=" N TRPEm 221 " --> pdb=" O GLNEm 213 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Em' and resid 237 through 238 removed outlier: 6.516A pdb=" N LEUEm 255 " --> pdb=" O LYSEm 245 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILEEm 247 " --> pdb=" O ARGEm 253 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ARGEm 253 " --> pdb=" O ILEEm 247 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Eo' and resid 150 through 157 removed outlier: 9.963A pdb=" N LYSEo 150 " --> pdb=" O ASPEo 249 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ARGEo 251 " --> pdb=" O LYSEo 150 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THREo 152 " --> pdb=" O ARGEo 251 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ASPEo 253 " --> pdb=" O THREo 152 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THREo 154 " --> pdb=" O ASPEo 253 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ARGEo 255 " --> pdb=" O THREo 154 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLNEo 156 " --> pdb=" O ARGEo 255 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N VALEo 176 " --> pdb=" O VALEo 248 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TYREo 250 " --> pdb=" O VALEo 176 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Eo' and resid 168 through 171 Processing sheet with id=AH7, first strand: chain 'Et' and resid 211 through 215 removed outlier: 6.742A pdb=" N TRPEt 221 " --> pdb=" O GLNEt 213 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Et' and resid 237 through 238 removed outlier: 6.543A pdb=" N LEUEt 255 " --> pdb=" O LYSEt 245 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILEEt 247 " --> pdb=" O ARGEt 253 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARGEt 253 " --> pdb=" O ILEEt 247 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Ev' and resid 150 through 158 removed outlier: 9.936A pdb=" N LYSEv 150 " --> pdb=" O ASPEv 249 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N ARGEv 251 " --> pdb=" O LYSEv 150 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THREv 152 " --> pdb=" O ARGEv 251 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ASPEv 253 " --> pdb=" O THREv 152 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THREv 154 " --> pdb=" O ASPEv 253 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ARGEv 255 " --> pdb=" O THREv 154 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLNEv 156 " --> pdb=" O ARGEv 255 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VALEv 176 " --> pdb=" O VALEv 248 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N TYREv 250 " --> pdb=" O VALEv 176 " (cutoff:3.500A) 1756 hydrogen bonds defined for protein. 4860 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: 11.35 Time building geometry restraints manager: 4.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13601 1.34 - 1.46: 9772 1.46 - 1.59: 19197 1.59 - 1.72: 0 1.72 - 1.84: 252 Bond restraints: 42822 Sorted by residual: bond pdb=" CB METEv 238 " pdb=" CG METEv 238 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.63e+00 bond pdb=" CA ASNAl 226 " pdb=" C ASNAl 226 " ideal model delta sigma weight residual 1.522 1.543 -0.021 1.37e-02 5.33e+03 2.27e+00 bond pdb=" CG1 ILEBp 215 " pdb=" CD1 ILEBp 215 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.04e+00 bond pdb=" CB SERAg 178 " pdb=" OG SERAg 178 " ideal model delta sigma weight residual 1.417 1.391 0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" SD METEv 238 " pdb=" CE METEv 238 " ideal model delta sigma weight residual 1.791 1.759 0.032 2.50e-02 1.60e+03 1.66e+00 ... (remaining 42817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 57727 2.58 - 5.16: 381 5.16 - 7.74: 3 7.74 - 10.32: 5 10.32 - 12.90: 6 Bond angle restraints: 58122 Sorted by residual: angle pdb=" CB METAn 115 " pdb=" CG METAn 115 " pdb=" SD METAn 115 " ideal model delta sigma weight residual 112.70 99.80 12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" CB METCy 115 " pdb=" CG METCy 115 " pdb=" SD METCy 115 " ideal model delta sigma weight residual 112.70 100.03 12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CB METBw 115 " pdb=" CG METBw 115 " pdb=" SD METBw 115 " ideal model delta sigma weight residual 112.70 100.31 12.39 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CB METDv 4 " pdb=" CG METDv 4 " pdb=" SD METDv 4 " ideal model delta sigma weight residual 112.70 123.86 -11.16 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CB METEh 115 " pdb=" CG METEh 115 " pdb=" SD METEh 115 " ideal model delta sigma weight residual 112.70 101.56 11.14 3.00e+00 1.11e-01 1.38e+01 ... (remaining 58117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 22241 17.81 - 35.62: 2754 35.62 - 53.44: 746 53.44 - 71.25: 83 71.25 - 89.06: 60 Dihedral angle restraints: 25884 sinusoidal: 10242 harmonic: 15642 Sorted by residual: dihedral pdb=" CA ASPAg 207 " pdb=" C ASPAg 207 " pdb=" N LYSAg 208 " pdb=" CA LYSAg 208 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASPDt 207 " pdb=" C ASPDt 207 " pdb=" N LYSDt 208 " pdb=" CA LYSDt 208 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ASPBi 207 " pdb=" C ASPBi 207 " pdb=" N LYSBi 208 " pdb=" CA LYSBi 208 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 25881 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3713 0.028 - 0.056: 1923 0.056 - 0.084: 543 0.084 - 0.112: 379 0.112 - 0.140: 102 Chirality restraints: 6660 Sorted by residual: chirality pdb=" CA ILEBn 216 " pdb=" N ILEBn 216 " pdb=" C ILEBn 216 " pdb=" CB ILEBn 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILEEf 216 " pdb=" N ILEEf 216 " pdb=" C ILEEf 216 " pdb=" CB ILEEf 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILEDd 216 " pdb=" N ILEDd 216 " pdb=" C ILEDd 216 " pdb=" CB ILEDd 216 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 6657 not shown) Planarity restraints: 7470 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARGBg 233 " 0.153 9.50e-02 1.11e+02 6.90e-02 3.51e+00 pdb=" NE ARGBg 233 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARGBg 233 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARGBg 233 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARGBg 233 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SERAl 225 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.65e+00 pdb=" C SERAl 225 " 0.028 2.00e-02 2.50e+03 pdb=" O SERAl 225 " -0.011 2.00e-02 2.50e+03 pdb=" N ASNAl 226 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASNAl 226 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ASNAl 226 " 0.027 2.00e-02 2.50e+03 pdb=" O ASNAl 226 " -0.010 2.00e-02 2.50e+03 pdb=" N GLYAl 227 " -0.009 2.00e-02 2.50e+03 ... (remaining 7467 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 22389 3.00 - 3.48: 42085 3.48 - 3.95: 70648 3.95 - 4.43: 83766 4.43 - 4.90: 136541 Nonbonded interactions: 355429 Sorted by model distance: nonbonded pdb=" O ASPCb 268 " pdb=" OD1 ASPCb 268 " model vdw 2.528 3.040 nonbonded pdb=" O PROAg 188 " pdb=" ND2 ASNAg 262 " model vdw 2.568 3.120 nonbonded pdb=" NE2 GLNBo 796 " pdb=" OD1 ASPBo 800 " model vdw 2.574 3.120 nonbonded pdb=" O PROCr 188 " pdb=" ND2 ASNCr 262 " model vdw 2.577 3.120 nonbonded pdb=" C SERCi 249 " pdb=" OG SERCi 249 " model vdw 2.586 2.616 ... (remaining 355424 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 'Aa' selection = chain 'Ah' selection = chain 'Ao' selection = chain 'Av' selection = chain 'Bc' selection = chain 'Bj' selection = chain 'Bq' selection = chain 'Bx' selection = chain 'Ce' selection = chain 'Cl' selection = chain 'Cs' selection = chain 'Cz' selection = chain 'Dg' selection = chain 'Dn' selection = chain 'Du' selection = chain 'Eb' selection = chain 'Ei' selection = chain 'Ep' } ncs_group { reference = chain 'Ab' selection = chain 'Ai' selection = chain 'Ap' selection = chain 'Aw' selection = chain 'Bd' selection = chain 'Bk' selection = chain 'Br' selection = chain 'By' selection = chain 'Cf' selection = chain 'Cm' selection = chain 'Ct' selection = chain 'Da' selection = chain 'Dh' selection = chain 'Do' selection = chain 'Dv' selection = chain 'Ec' selection = chain 'Ej' selection = chain 'Eq' } ncs_group { reference = chain 'Ac' selection = chain 'Aj' selection = chain 'Aq' selection = chain 'Ax' selection = chain 'Be' selection = chain 'Bl' selection = chain 'Bs' selection = chain 'Bz' selection = chain 'Cg' selection = chain 'Cn' selection = chain 'Cu' selection = chain 'Db' selection = chain 'Di' selection = chain 'Dp' selection = chain 'Dw' selection = chain 'Ed' selection = chain 'Ek' selection = chain 'Er' } ncs_group { reference = chain 'Ad' selection = chain 'Ak' selection = chain 'Ar' selection = chain 'Ay' selection = chain 'Bf' selection = chain 'Bm' selection = chain 'Bt' selection = chain 'Ca' selection = chain 'Ch' selection = chain 'Co' selection = chain 'Cv' selection = chain 'Dc' selection = chain 'Dj' selection = chain 'Dq' selection = chain 'Dx' selection = chain 'Ee' selection = chain 'El' selection = chain 'Es' } ncs_group { reference = chain 'Ae' selection = chain 'Al' selection = chain 'As' selection = chain 'Az' selection = chain 'Bg' selection = chain 'Bn' selection = chain 'Bu' selection = chain 'Cb' selection = chain 'Ci' selection = chain 'Cp' selection = chain 'Cw' selection = chain 'Dd' selection = chain 'Dk' selection = chain 'Dr' selection = chain 'Dy' selection = chain 'Ef' selection = chain 'Em' selection = chain 'Et' } ncs_group { reference = chain 'Af' selection = chain 'Am' selection = chain 'At' selection = chain 'Ba' selection = chain 'Bh' selection = chain 'Bo' selection = chain 'Bv' selection = chain 'Cc' selection = chain 'Cj' selection = chain 'Cq' selection = chain 'Cx' selection = chain 'De' selection = chain 'Dl' selection = chain 'Ds' selection = chain 'Dz' selection = chain 'Eg' selection = chain 'En' selection = chain 'Eu' } ncs_group { reference = chain 'Ag' selection = chain 'An' selection = chain 'Au' selection = chain 'Bb' selection = chain 'Bi' selection = chain 'Bp' selection = chain 'Bw' selection = chain 'Cd' selection = chain 'Ck' selection = chain 'Cr' selection = chain 'Cy' selection = chain 'Df' selection = chain 'Dm' selection = chain 'Dt' selection = chain 'Ea' selection = chain 'Eh' selection = chain 'Eo' selection = chain 'Ev' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.020 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 43.860 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.570 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: 0.000 Load rotamer database and sin/cos tables:1.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.003 0.056 42822 Z= 0.122 Angle : 0.530 12.901 58122 Z= 0.276 Chirality : 0.042 0.140 6660 Planarity : 0.004 0.069 7470 Dihedral : 16.822 89.059 15840 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.85 % Allowed : 21.92 % Favored : 75.23 % 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 are not related in a simple way. whole: -0.01 (0.11), residues: 5202 helix: 1.35 (0.13), residues: 1314 sheet: -0.69 (0.14), residues: 1314 loop : -0.24 (0.12), residues: 2574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARGBg 233 TYR 0.023 0.001 TYRBb 194 PHE 0.010 0.001 PHECa 2 TRP 0.009 0.001 TRPAg 206 HIS 0.006 0.001 HISAh 12 Details of bonding type rmsd covalent geometry : bond 0.00265 (42822) covalent geometry : angle 0.53039 (58122) hydrogen bonds : bond 0.13135 ( 1756) hydrogen bonds : angle 5.96882 ( 4860) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 730 time to evaluate : 1.760 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: Ab 5 ILE cc_start: 0.4734 (OUTLIER) cc_final: 0.3865 (mp) REVERT: Ae 263 LYS cc_start: 0.8329 (mttt) cc_final: 0.7906 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8248 (t0) cc_final: 0.7630 (t0) REVERT: Ag 110 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6917 (tptm) REVERT: Ag 219 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8870 (mtpt) REVERT: Al 210 TYR cc_start: 0.8279 (m-80) cc_final: 0.8046 (m-80) REVERT: Al 237 LYS cc_start: 0.8008 (mmtt) cc_final: 0.7653 (mmtp) REVERT: Al 263 LYS cc_start: 0.8099 (mtpm) cc_final: 0.7263 (mtmm) REVERT: Al 268 ASP cc_start: 0.8641 (t0) cc_final: 0.8173 (t0) REVERT: An 170 ARG cc_start: 0.8739 (mpp80) cc_final: 0.8375 (mtm180) REVERT: Aq 4 ILE cc_start: 0.1330 (OUTLIER) cc_final: 0.0992 (mp) REVERT: As 263 LYS cc_start: 0.8044 (mttt) cc_final: 0.7795 (mtmm) REVERT: As 268 ASP cc_start: 0.8543 (t0) cc_final: 0.8180 (t0) REVERT: Au 170 ARG cc_start: 0.8961 (mpp80) cc_final: 0.8570 (mtm180) REVERT: Az 209 ILE cc_start: 0.8992 (mm) cc_final: 0.8729 (mm) REVERT: Az 237 LYS cc_start: 0.8278 (mmtt) cc_final: 0.7891 (mmtp) REVERT: Az 268 ASP cc_start: 0.8264 (t0) cc_final: 0.7659 (t0) REVERT: Bb 210 SER cc_start: 0.8804 (p) cc_final: 0.8322 (p) REVERT: Bb 214 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8670 (mmm) REVERT: Bb 219 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8502 (mtpt) REVERT: Bg 209 ILE cc_start: 0.8328 (mt) cc_final: 0.8101 (mm) REVERT: Bg 237 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7778 (mmtm) REVERT: Bg 243 MET cc_start: 0.7663 (ttp) cc_final: 0.7410 (ttp) REVERT: Bg 263 LYS cc_start: 0.8079 (mtpm) cc_final: 0.7586 (mtmm) REVERT: Bg 268 ASP cc_start: 0.8367 (t0) cc_final: 0.7902 (t0) REVERT: Bi 170 ARG cc_start: 0.8960 (mpp80) cc_final: 0.8495 (mtm180) REVERT: Bi 219 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8681 (mttt) REVERT: Bn 243 MET cc_start: 0.7602 (ttp) cc_final: 0.7335 (ttm) REVERT: Bn 263 LYS cc_start: 0.8128 (mttt) cc_final: 0.7641 (mtmt) REVERT: Bn 268 ASP cc_start: 0.8193 (t0) cc_final: 0.7774 (t0) REVERT: Bo 822 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8176 (tp30) REVERT: Bp 242 ILE cc_start: 0.8731 (mt) cc_final: 0.8377 (mt) REVERT: Bu 263 LYS cc_start: 0.8188 (mttt) cc_final: 0.7850 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8578 (t0) cc_final: 0.8053 (t0) REVERT: Cb 263 LYS cc_start: 0.8045 (mttt) cc_final: 0.7672 (mtmm) REVERT: Cd 170 ARG cc_start: 0.9028 (mpp80) cc_final: 0.8796 (mtm180) REVERT: Cd 210 SER cc_start: 0.8353 (p) cc_final: 0.8068 (p) REVERT: Cd 238 MET cc_start: 0.8738 (mmm) cc_final: 0.7816 (mmt) REVERT: Cd 241 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7834 (mt) REVERT: Cf 4 MET cc_start: 0.5602 (mmt) cc_final: 0.4856 (tpt) REVERT: Cg 4 ILE cc_start: 0.2007 (OUTLIER) cc_final: 0.1158 (mp) REVERT: Ci 268 ASP cc_start: 0.8545 (t0) cc_final: 0.8014 (t0) REVERT: Cj 791 GLN cc_start: 0.5745 (tt0) cc_final: 0.5311 (mp10) REVERT: Ck 160 LEU cc_start: 0.7671 (mt) cc_final: 0.7283 (mp) REVERT: Ck 210 SER cc_start: 0.8578 (p) cc_final: 0.8253 (p) REVERT: Cp 263 LYS cc_start: 0.8316 (mttt) cc_final: 0.7854 (mtmm) REVERT: Cp 268 ASP cc_start: 0.8048 (t0) cc_final: 0.7513 (t0) REVERT: Cr 116 THR cc_start: 0.7963 (t) cc_final: 0.7539 (p) REVERT: Cr 219 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8886 (mtpt) REVERT: Cr 240 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8590 (t) REVERT: Cr 242 ILE cc_start: 0.8421 (mt) cc_final: 0.8092 (mt) REVERT: Cu 4 ILE cc_start: 0.0834 (OUTLIER) cc_final: 0.0396 (mp) REVERT: Cw 210 TYR cc_start: 0.8486 (m-80) cc_final: 0.8090 (m-80) REVERT: Cw 237 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7658 (mmtp) REVERT: Cw 268 ASP cc_start: 0.8671 (t0) cc_final: 0.8277 (t0) REVERT: Cy 170 ARG cc_start: 0.8756 (mpp80) cc_final: 0.8394 (mtm180) REVERT: Db 4 ILE cc_start: 0.1484 (OUTLIER) cc_final: 0.0672 (pt) REVERT: Dd 263 LYS cc_start: 0.8086 (mttt) cc_final: 0.7855 (mtmm) REVERT: Dd 267 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: Dd 268 ASP cc_start: 0.8505 (t0) cc_final: 0.8161 (t0) REVERT: Df 170 ARG cc_start: 0.8969 (mpp80) cc_final: 0.8567 (mtm180) REVERT: Df 214 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8238 (mmm) REVERT: Dk 209 ILE cc_start: 0.8993 (mm) cc_final: 0.8735 (mm) REVERT: Dk 237 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7901 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8279 (t0) cc_final: 0.7671 (t0) REVERT: Dm 115 MET cc_start: 0.7781 (tmt) cc_final: 0.7011 (tmt) REVERT: Dm 210 SER cc_start: 0.8848 (p) cc_final: 0.8394 (p) REVERT: Dm 219 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8544 (mtpt) REVERT: Dp 4 ILE cc_start: 0.1682 (OUTLIER) cc_final: 0.1430 (mp) REVERT: Dr 209 ILE cc_start: 0.8304 (mt) cc_final: 0.7938 (mm) REVERT: Dr 237 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7857 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8361 (t0) cc_final: 0.7912 (t0) REVERT: Dt 110 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6277 (mttt) REVERT: Dt 170 ARG cc_start: 0.8967 (mpp80) cc_final: 0.8497 (mtm180) REVERT: Dt 219 LYS cc_start: 0.8974 (OUTLIER) cc_final: 0.8675 (mttt) REVERT: Dt 240 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8287 (t) REVERT: Dy 243 MET cc_start: 0.7539 (ttp) cc_final: 0.7258 (ttm) REVERT: Dy 263 LYS cc_start: 0.8085 (mttt) cc_final: 0.7556 (mtmt) REVERT: Dy 268 ASP cc_start: 0.8125 (t0) cc_final: 0.7693 (t0) REVERT: Dz 795 GLN cc_start: 0.8155 (mp10) cc_final: 0.7555 (mp10) REVERT: Ef 263 LYS cc_start: 0.8192 (mttt) cc_final: 0.7917 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8571 (t0) cc_final: 0.8047 (t0) REVERT: Eh 155 SER cc_start: 0.8527 (t) cc_final: 0.7915 (p) REVERT: Eh 214 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8204 (mtm) REVERT: Em 263 LYS cc_start: 0.8051 (mttt) cc_final: 0.7774 (mtmm) REVERT: Em 267 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7834 (pm20) REVERT: Em 268 ASP cc_start: 0.8243 (t0) cc_final: 0.7835 (t0) REVERT: En 801 MET cc_start: 0.8666 (mtp) cc_final: 0.8379 (mtp) REVERT: Eo 210 SER cc_start: 0.8365 (p) cc_final: 0.8079 (p) REVERT: Eo 238 MET cc_start: 0.8532 (mmm) cc_final: 0.7587 (mmt) REVERT: Eo 241 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7696 (mt) REVERT: Eq 4 MET cc_start: 0.6429 (mmt) cc_final: 0.5483 (tpt) REVERT: Er 4 ILE cc_start: 0.1323 (OUTLIER) cc_final: 0.0406 (mp) REVERT: Et 268 ASP cc_start: 0.8594 (t0) cc_final: 0.8069 (t0) REVERT: Ev 160 LEU cc_start: 0.7648 (mt) cc_final: 0.7241 (mp) REVERT: Ev 239 LEU cc_start: 0.7926 (mp) cc_final: 0.7645 (mt) outliers start: 131 outliers final: 90 residues processed: 830 average time/residue: 0.2517 time to fit residues: 345.8360 Evaluate side-chains 828 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 713 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 3 ASP Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 3 SER Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 110 LYS Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 179 LEU Chi-restraints excluded: chain Ag residue 219 LYS Chi-restraints excluded: chain Ag residue 262 ASN Chi-restraints excluded: chain Aj residue 3 SER Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 10 THR Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain Ao residue 3 ASP Chi-restraints excluded: chain Ap residue 5 ILE Chi-restraints excluded: chain Aq residue 3 SER Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain At residue 814 GLN Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ba residue 814 GLN Chi-restraints excluded: chain Bb residue 209 THR Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bc residue 3 ASP Chi-restraints excluded: chain Be residue 3 SER Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 219 LYS Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bs residue 3 SER Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bz residue 3 SER Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Ce residue 3 ASP Chi-restraints excluded: chain Cg residue 3 SER Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 10 THR Chi-restraints excluded: chain Ci residue 213 GLN Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Cl residue 3 ASP Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 3 SER Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 179 LEU Chi-restraints excluded: chain Cr residue 219 LYS Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 262 ASN Chi-restraints excluded: chain Cs residue 3 ASP Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 10 THR Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 3 ASP Chi-restraints excluded: chain Da residue 5 ILE Chi-restraints excluded: chain Db residue 3 SER Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 10 THR Chi-restraints excluded: chain Dd residue 267 GLU Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 214 MET Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 10 THR Chi-restraints excluded: chain Dl residue 814 GLN Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 219 LYS Chi-restraints excluded: chain Dn residue 3 ASP Chi-restraints excluded: chain Dp residue 3 SER Chi-restraints excluded: chain Dp residue 4 ILE Chi-restraints excluded: chain Dp residue 7 THR Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 219 LYS Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dw residue 3 SER Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ed residue 3 SER Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 214 MET Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Ej residue 4 MET Chi-restraints excluded: chain Ej residue 5 ILE Chi-restraints excluded: chain Ek residue 3 SER Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Em residue 267 GLU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 215 ILE Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Er residue 3 SER Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Et residue 213 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 0.0670 chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0060 chunk 207 optimal weight: 0.8980 chunk 470 optimal weight: 0.8980 overall best weight: 0.7736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: An 123 ASN At 796 GLN Bb 126 GLN Bi 123 ASN Bp 123 ASN Bw 126 GLN Ci 213 GLN Df 262 ASN ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 126 GLN Dt 123 ASN Ea 123 ASN Eo 123 ASN Et 213 GLN ** Ev 234 ASN ** 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 = 0.3754 r_free = 0.3754 target = 0.160917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.126845 restraints weight = 45337.425| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.49 r_work: 0.3261 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.0563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 42822 Z= 0.142 Angle : 0.497 7.468 58122 Z= 0.253 Chirality : 0.042 0.145 6660 Planarity : 0.004 0.039 7470 Dihedral : 6.807 80.366 6124 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.49 % Allowed : 21.85 % Favored : 74.66 % 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 are not related in a simple way. whole: 0.24 (0.11), residues: 5202 helix: 1.63 (0.13), residues: 1332 sheet: -0.42 (0.15), residues: 1170 loop : -0.24 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGBg 233 TYR 0.017 0.001 TYRDm 194 PHE 0.010 0.001 PHEEf 264 TRP 0.005 0.001 TRPAs 221 HIS 0.004 0.001 HISAh 12 Details of bonding type rmsd covalent geometry : bond 0.00340 (42822) covalent geometry : angle 0.49714 (58122) hydrogen bonds : bond 0.03949 ( 1756) hydrogen bonds : angle 4.75482 ( 4860) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 728 time to evaluate : 1.613 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: Ab 5 ILE cc_start: 0.4915 (OUTLIER) cc_final: 0.3977 (mp) REVERT: Ae 263 LYS cc_start: 0.8485 (mttt) cc_final: 0.8085 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8275 (t0) cc_final: 0.7653 (t0) REVERT: Ag 214 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8547 (mpp) REVERT: Al 210 TYR cc_start: 0.8539 (m-80) cc_final: 0.8265 (m-80) REVERT: Al 237 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7820 (mmtp) REVERT: Al 263 LYS cc_start: 0.8294 (mtpm) cc_final: 0.7666 (mtmm) REVERT: Al 268 ASP cc_start: 0.8506 (t0) cc_final: 0.8120 (t0) REVERT: An 170 ARG cc_start: 0.8783 (mpp80) cc_final: 0.8447 (mtm180) REVERT: An 214 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8164 (mtt) REVERT: As 237 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8107 (mmtm) REVERT: As 263 LYS cc_start: 0.8176 (mttt) cc_final: 0.7899 (mtmm) REVERT: As 268 ASP cc_start: 0.8468 (t0) cc_final: 0.8149 (t0) REVERT: Au 115 MET cc_start: 0.8099 (tmt) cc_final: 0.7451 (tmt) REVERT: Au 170 ARG cc_start: 0.8937 (mpp80) cc_final: 0.8567 (mtm180) REVERT: Az 209 ILE cc_start: 0.9125 (mm) cc_final: 0.8896 (mm) REVERT: Az 237 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7942 (mmtp) REVERT: Az 268 ASP cc_start: 0.8383 (t0) cc_final: 0.7763 (t0) REVERT: Bb 110 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7016 (tptm) REVERT: Bb 210 SER cc_start: 0.8722 (p) cc_final: 0.8355 (p) REVERT: Bb 214 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.8317 (mtp) REVERT: Be 10 THR cc_start: 0.6216 (OUTLIER) cc_final: 0.6015 (m) REVERT: Bg 237 LYS cc_start: 0.8151 (mmtt) cc_final: 0.7756 (mmtm) REVERT: Bg 263 LYS cc_start: 0.8468 (mtpm) cc_final: 0.7987 (mtmm) REVERT: Bg 268 ASP cc_start: 0.8326 (t0) cc_final: 0.7886 (t0) REVERT: Bh 814 GLN cc_start: 0.8323 (mm-40) cc_final: 0.8004 (tp-100) REVERT: Bi 110 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6332 (ptpt) REVERT: Bi 170 ARG cc_start: 0.8935 (mpp80) cc_final: 0.8542 (mtm180) REVERT: Bi 240 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8448 (t) REVERT: Bk 5 ILE cc_start: 0.6069 (OUTLIER) cc_final: 0.5558 (mp) REVERT: Bn 237 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8075 (mmmt) REVERT: Bn 243 MET cc_start: 0.7707 (ttp) cc_final: 0.7387 (ttm) REVERT: Bn 263 LYS cc_start: 0.8318 (mttt) cc_final: 0.8006 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8257 (t0) cc_final: 0.7833 (t0) REVERT: Bo 822 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8202 (tp30) REVERT: Bp 118 ASN cc_start: 0.7868 (m-40) cc_final: 0.7525 (m-40) REVERT: Bp 214 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7526 (mmm) REVERT: Bp 242 ILE cc_start: 0.8833 (mt) cc_final: 0.8536 (mt) REVERT: Bq 12 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.5276 (t70) REVERT: Bu 263 LYS cc_start: 0.8221 (mttt) cc_final: 0.7838 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8478 (t0) cc_final: 0.8032 (t0) REVERT: Bw 110 LYS cc_start: 0.7456 (OUTLIER) cc_final: 0.6764 (ptpt) REVERT: Bw 184 SER cc_start: 0.7625 (m) cc_final: 0.7411 (m) REVERT: Bw 241 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7913 (mt) REVERT: By 5 ILE cc_start: 0.5568 (OUTLIER) cc_final: 0.5005 (mp) REVERT: Bz 4 ILE cc_start: 0.1298 (OUTLIER) cc_final: 0.0856 (mp) REVERT: Cb 237 LYS cc_start: 0.7829 (mmtt) cc_final: 0.7358 (mmtt) REVERT: Cb 263 LYS cc_start: 0.8123 (mttt) cc_final: 0.7692 (mtmm) REVERT: Cd 210 SER cc_start: 0.8536 (p) cc_final: 0.8262 (p) REVERT: Cd 238 MET cc_start: 0.8764 (mmm) cc_final: 0.7769 (mmt) REVERT: Cd 241 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8033 (mt) REVERT: Cf 4 MET cc_start: 0.6256 (mmt) cc_final: 0.5570 (tpt) REVERT: Ci 268 ASP cc_start: 0.8547 (t0) cc_final: 0.8084 (t0) REVERT: Cj 791 GLN cc_start: 0.5780 (tt0) cc_final: 0.5295 (mp10) REVERT: Cj 814 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.6979 (ptpt) REVERT: Ck 160 LEU cc_start: 0.7813 (mt) cc_final: 0.7422 (mp) REVERT: Ck 210 SER cc_start: 0.8729 (p) cc_final: 0.8423 (p) REVERT: Cp 251 GLN cc_start: 0.7935 (mt0) cc_final: 0.7316 (mp10) REVERT: Cp 263 LYS cc_start: 0.8464 (mttt) cc_final: 0.8064 (mtmm) REVERT: Cp 268 ASP cc_start: 0.8065 (t0) cc_final: 0.7546 (t0) REVERT: Cr 242 ILE cc_start: 0.8662 (mt) cc_final: 0.8376 (mt) REVERT: Ct 5 ILE cc_start: 0.6092 (OUTLIER) cc_final: 0.5153 (mp) REVERT: Cw 210 TYR cc_start: 0.8546 (m-80) cc_final: 0.8195 (m-80) REVERT: Cw 237 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7815 (mmtp) REVERT: Cw 268 ASP cc_start: 0.8623 (t0) cc_final: 0.8052 (t0) REVERT: Cy 214 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.8124 (mtt) REVERT: Cz 12 HIS cc_start: 0.6688 (OUTLIER) cc_final: 0.5259 (t70) REVERT: Dd 237 LYS cc_start: 0.8488 (mmtt) cc_final: 0.8216 (mmtm) REVERT: Dd 263 LYS cc_start: 0.8148 (mttt) cc_final: 0.7846 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8432 (t0) cc_final: 0.8020 (t0) REVERT: Df 115 MET cc_start: 0.7986 (tmt) cc_final: 0.7380 (tmt) REVERT: Df 214 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.7610 (mmt) REVERT: Dk 209 ILE cc_start: 0.9117 (mm) cc_final: 0.8877 (mm) REVERT: Dk 237 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7924 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8369 (t0) cc_final: 0.7745 (t0) REVERT: Dl 820 TYR cc_start: 0.8935 (t80) cc_final: 0.8723 (t80) REVERT: Dm 210 SER cc_start: 0.8788 (p) cc_final: 0.8404 (p) REVERT: Dr 237 LYS cc_start: 0.8264 (mmtt) cc_final: 0.7916 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8297 (t0) cc_final: 0.7866 (t0) REVERT: Ds 814 GLN cc_start: 0.8448 (mm-40) cc_final: 0.8118 (tp-100) REVERT: Dt 110 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6605 (mttt) REVERT: Dt 170 ARG cc_start: 0.8947 (mpp80) cc_final: 0.8585 (mtm180) REVERT: Dt 240 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8412 (t) REVERT: Dy 237 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8088 (mmmt) REVERT: Dy 243 MET cc_start: 0.7789 (ttp) cc_final: 0.7456 (ttm) REVERT: Dy 263 LYS cc_start: 0.8299 (mttt) cc_final: 0.7986 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8229 (t0) cc_final: 0.7809 (t0) REVERT: Dz 795 GLN cc_start: 0.8097 (mp10) cc_final: 0.7341 (mp10) REVERT: Ea 118 ASN cc_start: 0.7904 (m-40) cc_final: 0.7526 (m-40) REVERT: Ea 242 ILE cc_start: 0.8803 (mt) cc_final: 0.8466 (mt) REVERT: Eb 12 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.5247 (t70) REVERT: Ef 263 LYS cc_start: 0.8237 (mttt) cc_final: 0.7855 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8529 (t0) cc_final: 0.7935 (t0) REVERT: Eh 110 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6861 (tptm) REVERT: Eh 214 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.7609 (mmt) REVERT: Eh 241 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.7916 (mt) REVERT: Ej 4 MET cc_start: 0.5368 (tpt) cc_final: 0.4931 (tpt) REVERT: Ek 4 ILE cc_start: 0.0884 (OUTLIER) cc_final: 0.0618 (mp) REVERT: Em 237 LYS cc_start: 0.7870 (mmtt) cc_final: 0.7394 (mmtt) REVERT: Em 263 LYS cc_start: 0.8121 (mttt) cc_final: 0.7692 (mtmm) REVERT: Em 268 ASP cc_start: 0.8198 (t0) cc_final: 0.7750 (t0) REVERT: En 801 MET cc_start: 0.8622 (mtp) cc_final: 0.8418 (mtp) REVERT: Eo 210 SER cc_start: 0.8582 (p) cc_final: 0.8280 (p) REVERT: Eo 238 MET cc_start: 0.8679 (mmm) cc_final: 0.7689 (mmt) REVERT: Eo 241 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7960 (mt) REVERT: Eo 255 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7534 (mpt180) REVERT: Eq 4 MET cc_start: 0.6610 (mmt) cc_final: 0.5719 (tpt) REVERT: Et 268 ASP cc_start: 0.8565 (t0) cc_final: 0.8097 (t0) REVERT: Eu 814 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: Ev 160 LEU cc_start: 0.7787 (mt) cc_final: 0.7378 (mp) outliers start: 160 outliers final: 79 residues processed: 848 average time/residue: 0.2501 time to fit residues: 350.1941 Evaluate side-chains 821 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 709 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 179 LEU Chi-restraints excluded: chain Ag residue 209 THR Chi-restraints excluded: chain Ag residue 214 MET Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain At residue 814 GLN Chi-restraints excluded: chain Au residue 128 VAL Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Ba residue 814 GLN Chi-restraints excluded: chain Bb residue 110 LYS Chi-restraints excluded: chain Bb residue 128 VAL Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 10 THR Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bk residue 5 ILE Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bp residue 128 VAL Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bu residue 226 ASN Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Cb residue 260 GLN Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 179 LEU Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain De residue 814 GLN Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 214 MET Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Dl residue 814 GLN Chi-restraints excluded: chain Dm residue 128 VAL Chi-restraints excluded: chain Dm residue 215 ILE Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Ea residue 128 VAL Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eg residue 817 THR Chi-restraints excluded: chain Eh residue 110 LYS Chi-restraints excluded: chain Eh residue 128 VAL Chi-restraints excluded: chain Eh residue 165 THR Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 214 MET Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Eo residue 255 ARG Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 67 optimal weight: 0.9990 chunk 319 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 422 optimal weight: 1.9990 chunk 439 optimal weight: 3.9990 chunk 296 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 342 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ag 123 ASN Au 126 GLN Cc 814 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 123 ASN Cr 123 ASN Cy 126 GLN Df 126 GLN ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eh 123 ASN En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.159594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126638 restraints weight = 45478.720| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.44 r_work: 0.3251 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 42822 Z= 0.161 Angle : 0.506 6.188 58122 Z= 0.254 Chirality : 0.043 0.144 6660 Planarity : 0.004 0.040 7470 Dihedral : 5.842 80.452 5994 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.40 % Allowed : 20.98 % Favored : 74.62 % 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 are not related in a simple way. whole: 0.25 (0.11), residues: 5202 helix: 1.75 (0.13), residues: 1332 sheet: -0.54 (0.15), residues: 1188 loop : -0.23 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAs 233 TYR 0.013 0.001 TYRCr 194 PHE 0.013 0.001 PHEEf 264 TRP 0.007 0.001 TRPAn 206 HIS 0.004 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00396 (42822) covalent geometry : angle 0.50639 (58122) hydrogen bonds : bond 0.03750 ( 1756) hydrogen bonds : angle 4.64638 ( 4860) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 732 time to evaluate : 1.438 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: Ab 5 ILE cc_start: 0.4949 (OUTLIER) cc_final: 0.4032 (mp) REVERT: Ae 263 LYS cc_start: 0.8485 (mttt) cc_final: 0.8084 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8100 (t0) cc_final: 0.7537 (t0) REVERT: Ag 115 MET cc_start: 0.8294 (tmm) cc_final: 0.7267 (tmm) REVERT: Al 210 TYR cc_start: 0.8495 (m-80) cc_final: 0.8137 (m-80) REVERT: Al 237 LYS cc_start: 0.8126 (mmtt) cc_final: 0.7755 (mmtp) REVERT: Al 263 LYS cc_start: 0.8314 (mtpm) cc_final: 0.7683 (mtmm) REVERT: Al 268 ASP cc_start: 0.8581 (t0) cc_final: 0.7895 (t0) REVERT: An 214 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8182 (mtt) REVERT: Ao 12 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.5419 (t70) REVERT: Aq 13 LYS cc_start: 0.6131 (OUTLIER) cc_final: 0.5447 (mmtm) REVERT: As 237 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8093 (mmtm) REVERT: As 263 LYS cc_start: 0.8167 (mttt) cc_final: 0.7850 (mtmm) REVERT: As 268 ASP cc_start: 0.8450 (t0) cc_final: 0.8016 (t0) REVERT: At 814 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8270 (tp-100) REVERT: Ax 13 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5332 (mmtm) REVERT: Az 209 ILE cc_start: 0.9090 (mm) cc_final: 0.8835 (mm) REVERT: Az 237 LYS cc_start: 0.8316 (mmtt) cc_final: 0.7973 (mmtp) REVERT: Az 268 ASP cc_start: 0.8370 (t0) cc_final: 0.7709 (t0) REVERT: Ba 814 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8187 (tp40) REVERT: Bb 110 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7095 (tptm) REVERT: Bb 210 SER cc_start: 0.8741 (p) cc_final: 0.8374 (p) REVERT: Bb 214 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8373 (mtp) REVERT: Bg 237 LYS cc_start: 0.8290 (mmtt) cc_final: 0.7914 (mmtm) REVERT: Bg 263 LYS cc_start: 0.8446 (mtpm) cc_final: 0.7971 (mtmm) REVERT: Bg 268 ASP cc_start: 0.8335 (t0) cc_final: 0.7876 (t0) REVERT: Bh 814 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8096 (tp40) REVERT: Bi 170 ARG cc_start: 0.8953 (mpp80) cc_final: 0.8526 (mtm180) REVERT: Bj 12 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.5458 (t70) REVERT: Bn 237 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8060 (mmmt) REVERT: Bn 243 MET cc_start: 0.7705 (ttp) cc_final: 0.7393 (ttm) REVERT: Bn 263 LYS cc_start: 0.8336 (mttt) cc_final: 0.7996 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8345 (t0) cc_final: 0.7788 (t0) REVERT: Bo 822 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8293 (tp30) REVERT: Bp 118 ASN cc_start: 0.7794 (m-40) cc_final: 0.7490 (m-40) REVERT: Bp 214 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7592 (mmm) REVERT: Bp 242 ILE cc_start: 0.8880 (mt) cc_final: 0.8600 (mt) REVERT: Bq 12 HIS cc_start: 0.6806 (OUTLIER) cc_final: 0.5267 (t70) REVERT: Bs 13 LYS cc_start: 0.6590 (OUTLIER) cc_final: 0.6245 (mmtm) REVERT: Bu 253 ARG cc_start: 0.7896 (mtm180) cc_final: 0.7624 (mtm110) REVERT: Bu 263 LYS cc_start: 0.8259 (mttt) cc_final: 0.7843 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8490 (t0) cc_final: 0.8019 (t0) REVERT: Bw 110 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6929 (tptm) REVERT: Bw 241 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.7872 (mt) REVERT: Bx 6 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6579 (mm) REVERT: Bx 12 HIS cc_start: 0.6906 (OUTLIER) cc_final: 0.6317 (t70) REVERT: By 5 ILE cc_start: 0.5783 (OUTLIER) cc_final: 0.5218 (mp) REVERT: Bz 4 ILE cc_start: 0.1194 (OUTLIER) cc_final: 0.0834 (mp) REVERT: Cb 237 LYS cc_start: 0.7821 (mmtt) cc_final: 0.7356 (mmtt) REVERT: Cb 263 LYS cc_start: 0.8090 (mttt) cc_final: 0.7654 (mtmm) REVERT: Cd 115 MET cc_start: 0.8325 (tmm) cc_final: 0.7920 (tmm) REVERT: Cd 210 SER cc_start: 0.8548 (p) cc_final: 0.8271 (p) REVERT: Cd 219 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8688 (mtpt) REVERT: Cd 238 MET cc_start: 0.8624 (mmm) cc_final: 0.7764 (mmt) REVERT: Cf 4 MET cc_start: 0.6264 (mmt) cc_final: 0.5580 (tpt) REVERT: Cg 13 LYS cc_start: 0.6247 (OUTLIER) cc_final: 0.5356 (mmtm) REVERT: Ci 226 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7773 (p0) REVERT: Ci 237 LYS cc_start: 0.8299 (mptt) cc_final: 0.7502 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8577 (t0) cc_final: 0.8103 (t0) REVERT: Cj 791 GLN cc_start: 0.5878 (tt0) cc_final: 0.5430 (mp10) REVERT: Cj 814 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7934 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.6867 (ptpt) REVERT: Ck 115 MET cc_start: 0.8487 (tmm) cc_final: 0.8096 (tmm) REVERT: Ck 210 SER cc_start: 0.8752 (p) cc_final: 0.8447 (p) REVERT: Cp 237 LYS cc_start: 0.8024 (mmtt) cc_final: 0.7769 (mmtt) REVERT: Cp 263 LYS cc_start: 0.8470 (mttt) cc_final: 0.8062 (mtmm) REVERT: Cp 268 ASP cc_start: 0.8068 (t0) cc_final: 0.7508 (t0) REVERT: Cr 242 ILE cc_start: 0.8675 (mt) cc_final: 0.8383 (mt) REVERT: Ct 5 ILE cc_start: 0.6176 (OUTLIER) cc_final: 0.5360 (mp) REVERT: Cu 4 ILE cc_start: 0.0012 (OUTLIER) cc_final: -0.0319 (mp) REVERT: Cu 13 LYS cc_start: 0.6043 (OUTLIER) cc_final: 0.5262 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8540 (m-80) cc_final: 0.8172 (m-80) REVERT: Cw 237 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7740 (mmtp) REVERT: Cw 268 ASP cc_start: 0.8618 (t0) cc_final: 0.8150 (t0) REVERT: Cy 214 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8119 (mtt) REVERT: Cz 12 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.5693 (t70) REVERT: Db 13 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5344 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8126 (mmtm) REVERT: Dd 251 GLN cc_start: 0.8212 (mt0) cc_final: 0.7852 (mt0) REVERT: Dd 263 LYS cc_start: 0.8112 (mttt) cc_final: 0.7765 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8475 (t0) cc_final: 0.8009 (t0) REVERT: Df 110 LYS cc_start: 0.7157 (OUTLIER) cc_final: 0.6696 (tptm) REVERT: Df 214 MET cc_start: 0.8905 (mmt) cc_final: 0.8264 (mpp) REVERT: Di 13 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5392 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9078 (mm) cc_final: 0.8825 (mm) REVERT: Dk 237 LYS cc_start: 0.8311 (mmtt) cc_final: 0.7977 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8364 (t0) cc_final: 0.7708 (t0) REVERT: Dl 814 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8366 (tp-100) REVERT: Dm 110 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7016 (tptm) REVERT: Dm 210 SER cc_start: 0.8811 (p) cc_final: 0.8417 (p) REVERT: Dr 209 ILE cc_start: 0.8616 (mm) cc_final: 0.8379 (mm) REVERT: Dr 237 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7825 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8293 (t0) cc_final: 0.7859 (t0) REVERT: Ds 814 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8130 (tp40) REVERT: Dt 110 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.6566 (mttt) REVERT: Dt 170 ARG cc_start: 0.8967 (mpp80) cc_final: 0.8557 (mtm180) REVERT: Dy 237 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8085 (mmmt) REVERT: Dy 243 MET cc_start: 0.7743 (ttp) cc_final: 0.7437 (ttm) REVERT: Dy 263 LYS cc_start: 0.8321 (mttt) cc_final: 0.8001 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8308 (t0) cc_final: 0.7745 (t0) REVERT: Dz 795 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7699 (mp10) REVERT: Ea 118 ASN cc_start: 0.7869 (m-40) cc_final: 0.7536 (m-40) REVERT: Ea 240 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8687 (t) REVERT: Ea 242 ILE cc_start: 0.8848 (mt) cc_final: 0.8508 (mt) REVERT: Eb 12 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.5423 (t70) REVERT: Ed 13 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6346 (mmtm) REVERT: Ef 226 ASN cc_start: 0.8340 (OUTLIER) cc_final: 0.7931 (p0) REVERT: Ef 253 ARG cc_start: 0.7902 (mtm180) cc_final: 0.7685 (mtm110) REVERT: Ef 263 LYS cc_start: 0.8260 (mttt) cc_final: 0.7837 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8537 (t0) cc_final: 0.7903 (t0) REVERT: Eh 110 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6967 (tptm) REVERT: Eh 214 MET cc_start: 0.8752 (mmt) cc_final: 0.8212 (mpp) REVERT: Eh 241 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.7916 (mt) REVERT: Ej 4 MET cc_start: 0.5574 (tpt) cc_final: 0.5084 (tpt) REVERT: Ek 4 ILE cc_start: 0.1427 (OUTLIER) cc_final: 0.1004 (mp) REVERT: Ek 13 LYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5634 (mmtm) REVERT: Em 237 LYS cc_start: 0.7850 (mmtt) cc_final: 0.7382 (mmtt) REVERT: Em 263 LYS cc_start: 0.8127 (mttt) cc_final: 0.7688 (mtmm) REVERT: Em 268 ASP cc_start: 0.8149 (t0) cc_final: 0.7680 (t0) REVERT: Eo 182 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.7734 (mt) REVERT: Eo 210 SER cc_start: 0.8601 (p) cc_final: 0.8287 (p) REVERT: Eo 219 LYS cc_start: 0.9026 (mtpt) cc_final: 0.8640 (mtpt) REVERT: Eo 238 MET cc_start: 0.8717 (mmm) cc_final: 0.7719 (mmt) REVERT: Eq 4 MET cc_start: 0.6186 (mmt) cc_final: 0.5369 (tpt) REVERT: Er 13 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5422 (mmtm) REVERT: Et 226 ASN cc_start: 0.8224 (OUTLIER) cc_final: 0.7720 (p0) REVERT: Et 237 LYS cc_start: 0.8308 (mptt) cc_final: 0.7464 (mmtt) REVERT: Et 268 ASP cc_start: 0.8581 (t0) cc_final: 0.8118 (t0) REVERT: Eu 814 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7895 (tm-30) outliers start: 202 outliers final: 104 residues processed: 886 average time/residue: 0.2531 time to fit residues: 368.4123 Evaluate side-chains 874 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 722 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 3 ASP Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 218 THR Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain At residue 814 GLN Chi-restraints excluded: chain Au residue 128 VAL Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Ba residue 814 GLN Chi-restraints excluded: chain Bb residue 110 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 218 THR Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 4 MET Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bp residue 128 VAL Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 3 ASP Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Cb residue 260 GLN Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 226 ASN Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 214 MET Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 218 THR Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain De residue 814 GLN Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 218 THR Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dl residue 814 GLN Chi-restraints excluded: chain Dm residue 110 LYS Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 218 THR Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dp residue 7 THR Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dp residue 13 LYS Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 204 ILE Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 226 ASN Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 110 LYS Chi-restraints excluded: chain Eh residue 128 VAL Chi-restraints excluded: chain Eh residue 165 THR Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain Em residue 260 GLN Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 226 ASN Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 227 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 311 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 479 optimal weight: 2.9990 chunk 450 optimal weight: 0.8980 chunk 218 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** As 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Az 251 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.160823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.127480 restraints weight = 45058.854| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.43 r_work: 0.3266 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 42822 Z= 0.140 Angle : 0.482 6.691 58122 Z= 0.242 Chirality : 0.042 0.142 6660 Planarity : 0.004 0.034 7470 Dihedral : 5.620 80.979 5976 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.51 % Allowed : 21.07 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.11), residues: 5202 helix: 1.91 (0.13), residues: 1332 sheet: -0.41 (0.15), residues: 1170 loop : -0.15 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGAs 233 TYR 0.013 0.001 TYRDm 194 PHE 0.011 0.001 PHEBf 2 TRP 0.006 0.001 TRPAn 206 HIS 0.003 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00341 (42822) covalent geometry : angle 0.48152 (58122) hydrogen bonds : bond 0.03447 ( 1756) hydrogen bonds : angle 4.55570 ( 4860) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 745 time to evaluate : 1.557 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: Ab 5 ILE cc_start: 0.4909 (OUTLIER) cc_final: 0.3984 (mp) REVERT: Ae 237 LYS cc_start: 0.8020 (mmtt) cc_final: 0.7404 (mmtt) REVERT: Ae 263 LYS cc_start: 0.8348 (mttt) cc_final: 0.7946 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8105 (t0) cc_final: 0.7531 (t0) REVERT: Aj 13 LYS cc_start: 0.5986 (OUTLIER) cc_final: 0.5388 (mmtm) REVERT: Al 210 TYR cc_start: 0.8489 (m-80) cc_final: 0.8137 (m-80) REVERT: Al 237 LYS cc_start: 0.8132 (mmtt) cc_final: 0.7760 (mmtp) REVERT: Al 263 LYS cc_start: 0.8315 (mtpm) cc_final: 0.7704 (mtmm) REVERT: Al 268 ASP cc_start: 0.8545 (t0) cc_final: 0.7940 (t0) REVERT: An 115 MET cc_start: 0.8712 (tmm) cc_final: 0.7773 (tmm) REVERT: An 170 ARG cc_start: 0.8783 (mpp80) cc_final: 0.8460 (mtm180) REVERT: An 214 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8116 (mtt) REVERT: Aq 13 LYS cc_start: 0.6167 (OUTLIER) cc_final: 0.5469 (mmtm) REVERT: As 237 LYS cc_start: 0.8516 (mmtt) cc_final: 0.8091 (mmtm) REVERT: As 263 LYS cc_start: 0.8152 (mttt) cc_final: 0.7855 (mtmm) REVERT: As 268 ASP cc_start: 0.8334 (t0) cc_final: 0.7888 (t0) REVERT: At 814 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8313 (tp-100) REVERT: Ax 13 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5334 (mmtm) REVERT: Az 209 ILE cc_start: 0.9074 (mm) cc_final: 0.8804 (mm) REVERT: Az 237 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7962 (mmtp) REVERT: Az 268 ASP cc_start: 0.8307 (t0) cc_final: 0.7745 (t0) REVERT: Ba 820 TYR cc_start: 0.8921 (t80) cc_final: 0.8254 (t80) REVERT: Bb 210 SER cc_start: 0.8717 (p) cc_final: 0.8353 (p) REVERT: Bb 214 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: Bb 219 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8693 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7959 (mmtm) REVERT: Bg 243 MET cc_start: 0.7855 (ttp) cc_final: 0.7588 (ttp) REVERT: Bg 268 ASP cc_start: 0.8330 (t0) cc_final: 0.7911 (t0) REVERT: Bh 814 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8192 (tp40) REVERT: Bi 170 ARG cc_start: 0.8919 (mpp80) cc_final: 0.8466 (mtm180) REVERT: Bj 12 HIS cc_start: 0.6868 (OUTLIER) cc_final: 0.5469 (t70) REVERT: Bl 13 LYS cc_start: 0.5497 (OUTLIER) cc_final: 0.5118 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8325 (mmtt) cc_final: 0.8053 (mmmt) REVERT: Bn 243 MET cc_start: 0.7744 (ttp) cc_final: 0.7471 (ttm) REVERT: Bn 263 LYS cc_start: 0.8320 (mttt) cc_final: 0.7992 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8336 (t0) cc_final: 0.7769 (t0) REVERT: Bo 822 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8327 (tp30) REVERT: Bp 118 ASN cc_start: 0.7832 (m-40) cc_final: 0.7507 (m-40) REVERT: Bp 214 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.7644 (mmm) REVERT: Bp 242 ILE cc_start: 0.8863 (mt) cc_final: 0.8579 (mt) REVERT: Bq 12 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.5233 (t70) REVERT: Bs 13 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.6256 (mmtm) REVERT: Bu 253 ARG cc_start: 0.7905 (mtm180) cc_final: 0.7684 (mtm110) REVERT: Bu 263 LYS cc_start: 0.8251 (mttt) cc_final: 0.7854 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8453 (t0) cc_final: 0.8002 (t0) REVERT: Bw 110 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7085 (ptpt) REVERT: Bw 222 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8401 (m110) REVERT: Bw 241 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.7887 (mt) REVERT: Bx 6 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6627 (mm) REVERT: Bx 12 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6198 (t70) REVERT: Bz 4 ILE cc_start: 0.1329 (OUTLIER) cc_final: 0.0940 (mp) REVERT: Bz 13 LYS cc_start: 0.5969 (OUTLIER) cc_final: 0.5573 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7819 (mmtt) cc_final: 0.7367 (mmtt) REVERT: Cb 263 LYS cc_start: 0.8116 (mttt) cc_final: 0.7712 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8322 (t0) cc_final: 0.8042 (t0) REVERT: Cd 115 MET cc_start: 0.8267 (tmm) cc_final: 0.8052 (tmm) REVERT: Cd 210 SER cc_start: 0.8515 (p) cc_final: 0.8247 (p) REVERT: Cd 214 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7885 (mtt) REVERT: Cd 219 LYS cc_start: 0.9021 (mtpt) cc_final: 0.8744 (mtpt) REVERT: Cd 238 MET cc_start: 0.8579 (mmm) cc_final: 0.7720 (mmt) REVERT: Cd 240 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8619 (t) REVERT: Cd 241 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.7985 (mt) REVERT: Cd 255 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7573 (mpt180) REVERT: Cf 4 MET cc_start: 0.6250 (mmt) cc_final: 0.5585 (tpt) REVERT: Cg 4 ILE cc_start: 0.0758 (OUTLIER) cc_final: 0.0384 (mp) REVERT: Cg 13 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5393 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8282 (mptt) cc_final: 0.7494 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8576 (t0) cc_final: 0.8078 (t0) REVERT: Cj 791 GLN cc_start: 0.5567 (tt0) cc_final: 0.5181 (mp10) REVERT: Cj 814 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7551 (OUTLIER) cc_final: 0.6830 (ptpt) REVERT: Ck 160 LEU cc_start: 0.7803 (mt) cc_final: 0.7431 (mp) REVERT: Ck 210 SER cc_start: 0.8754 (p) cc_final: 0.8441 (p) REVERT: Cp 237 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7393 (mmtt) REVERT: Cp 263 LYS cc_start: 0.8475 (mttt) cc_final: 0.8091 (mtmm) REVERT: Cp 268 ASP cc_start: 0.8072 (t0) cc_final: 0.7506 (t0) REVERT: Cr 242 ILE cc_start: 0.8675 (mt) cc_final: 0.8385 (mt) REVERT: Ct 5 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5290 (mp) REVERT: Cu 4 ILE cc_start: 0.0282 (OUTLIER) cc_final: -0.0087 (mp) REVERT: Cw 210 TYR cc_start: 0.8540 (m-80) cc_final: 0.8184 (m-80) REVERT: Cw 237 LYS cc_start: 0.8106 (mmtt) cc_final: 0.7735 (mmtp) REVERT: Cw 268 ASP cc_start: 0.8599 (t0) cc_final: 0.8138 (t0) REVERT: Cy 214 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8159 (mtt) REVERT: Cz 12 HIS cc_start: 0.7007 (OUTLIER) cc_final: 0.5662 (t70) REVERT: Db 13 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5346 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8119 (mmtm) REVERT: Dd 263 LYS cc_start: 0.7981 (mttt) cc_final: 0.7749 (mtmm) REVERT: Dd 267 GLU cc_start: 0.8045 (pm20) cc_final: 0.7795 (pm20) REVERT: Dd 268 ASP cc_start: 0.8445 (t0) cc_final: 0.7933 (t0) REVERT: De 814 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8320 (tp-100) REVERT: Df 110 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7007 (tptm) REVERT: Df 214 MET cc_start: 0.8797 (mmt) cc_final: 0.8316 (mpp) REVERT: Di 13 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5407 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9067 (mm) cc_final: 0.8790 (mm) REVERT: Dk 237 LYS cc_start: 0.8309 (mmtt) cc_final: 0.7975 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8302 (t0) cc_final: 0.7715 (t0) REVERT: Dm 110 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7160 (tptm) REVERT: Dm 210 SER cc_start: 0.8777 (p) cc_final: 0.8386 (p) REVERT: Dr 237 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7812 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8293 (t0) cc_final: 0.7878 (t0) REVERT: Ds 814 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8204 (tp-100) REVERT: Dt 110 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.6694 (mttt) REVERT: Dt 170 ARG cc_start: 0.8937 (mpp80) cc_final: 0.8579 (mtm180) REVERT: Dy 237 LYS cc_start: 0.8350 (mmtt) cc_final: 0.8090 (mmmt) REVERT: Dy 243 MET cc_start: 0.7765 (ttp) cc_final: 0.7482 (ttm) REVERT: Dy 263 LYS cc_start: 0.8317 (mttt) cc_final: 0.8016 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8320 (t0) cc_final: 0.7748 (t0) REVERT: Dz 795 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7776 (mp10) REVERT: Ea 118 ASN cc_start: 0.7859 (m-40) cc_final: 0.7525 (m-40) REVERT: Ea 240 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8633 (t) REVERT: Ea 242 ILE cc_start: 0.8821 (mt) cc_final: 0.8461 (mt) REVERT: Eb 12 HIS cc_start: 0.6865 (OUTLIER) cc_final: 0.5373 (t70) REVERT: Ed 13 LYS cc_start: 0.6542 (OUTLIER) cc_final: 0.6295 (mmtm) REVERT: Ef 253 ARG cc_start: 0.7934 (mtm180) cc_final: 0.7707 (mtm110) REVERT: Ef 263 LYS cc_start: 0.8268 (mttt) cc_final: 0.7864 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8535 (t0) cc_final: 0.7888 (t0) REVERT: Eh 110 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7015 (tptm) REVERT: Eh 222 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8370 (m110) REVERT: Eh 241 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.7999 (mt) REVERT: Ei 6 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6635 (mm) REVERT: Ei 12 HIS cc_start: 0.7066 (OUTLIER) cc_final: 0.6271 (t70) REVERT: Ek 4 ILE cc_start: 0.1528 (OUTLIER) cc_final: 0.1167 (mp) REVERT: Ek 13 LYS cc_start: 0.6066 (OUTLIER) cc_final: 0.5633 (mmtm) REVERT: Em 237 LYS cc_start: 0.7851 (mmtt) cc_final: 0.7399 (mmtt) REVERT: Em 253 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7433 (mtm110) REVERT: Em 263 LYS cc_start: 0.8122 (mttt) cc_final: 0.7701 (mtmm) REVERT: Em 268 ASP cc_start: 0.8119 (t0) cc_final: 0.7653 (t0) REVERT: Eo 116 THR cc_start: 0.8645 (t) cc_final: 0.8308 (p) REVERT: Eo 210 SER cc_start: 0.8634 (p) cc_final: 0.8367 (p) REVERT: Eo 219 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8694 (mtpt) REVERT: Eo 238 MET cc_start: 0.8724 (mmm) cc_final: 0.7764 (mmt) REVERT: Eo 241 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.7947 (mt) REVERT: Eq 4 MET cc_start: 0.6304 (mmt) cc_final: 0.5489 (tpt) REVERT: Er 4 ILE cc_start: 0.1102 (OUTLIER) cc_final: 0.0765 (mp) REVERT: Er 13 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5516 (mmtm) REVERT: Et 237 LYS cc_start: 0.8312 (mptt) cc_final: 0.7473 (mmtt) REVERT: Et 268 ASP cc_start: 0.8576 (t0) cc_final: 0.8084 (t0) REVERT: Eu 814 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: Ev 160 LEU cc_start: 0.7795 (mt) cc_final: 0.7409 (mp) outliers start: 207 outliers final: 116 residues processed: 900 average time/residue: 0.2436 time to fit residues: 358.2625 Evaluate side-chains 900 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 730 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain At residue 814 GLN Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 252 VAL Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 4 MET Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 3 ASP Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 260 GLN Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 240 THR Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cd residue 255 ARG Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 7 THR Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain De residue 814 GLN Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 218 THR Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 110 LYS Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 215 ILE Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dp residue 7 THR Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dp residue 13 LYS Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 110 LYS Chi-restraints excluded: chain Eh residue 165 THR Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain Em residue 260 GLN Chi-restraints excluded: chain Em residue 267 GLU Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 115 MET Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 314 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 211 optimal weight: 0.6980 chunk 397 optimal weight: 0.7980 chunk 285 optimal weight: 0.7980 chunk 273 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 319 optimal weight: 0.9990 chunk 388 optimal weight: 2.9990 chunk 416 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.159112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125957 restraints weight = 45429.390| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.49 r_work: 0.3250 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 42822 Z= 0.145 Angle : 0.490 7.122 58122 Z= 0.245 Chirality : 0.042 0.143 6660 Planarity : 0.004 0.036 7470 Dihedral : 5.440 81.337 5970 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.88 % Allowed : 20.72 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.11), residues: 5202 helix: 1.97 (0.13), residues: 1332 sheet: -0.50 (0.14), residues: 1206 loop : -0.14 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGDd 233 TYR 0.013 0.001 TYRDm 194 PHE 0.011 0.001 PHEEf 264 TRP 0.007 0.001 TRPAn 206 HIS 0.003 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00355 (42822) covalent geometry : angle 0.49024 (58122) hydrogen bonds : bond 0.03410 ( 1756) hydrogen bonds : angle 4.52929 ( 4860) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 976 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 224 poor density : 752 time to evaluate : 1.652 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: Ab 5 ILE cc_start: 0.4984 (OUTLIER) cc_final: 0.4013 (mp) REVERT: Ae 237 LYS cc_start: 0.8022 (mmtt) cc_final: 0.7433 (mmtt) REVERT: Ae 263 LYS cc_start: 0.8423 (mttt) cc_final: 0.7975 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8121 (t0) cc_final: 0.7547 (t0) REVERT: Ag 182 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7842 (mt) REVERT: Aj 13 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5397 (mmtm) REVERT: Al 210 TYR cc_start: 0.8623 (m-80) cc_final: 0.8280 (m-80) REVERT: Al 237 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7762 (mmtp) REVERT: Al 263 LYS cc_start: 0.8328 (mtpm) cc_final: 0.7743 (mtmm) REVERT: Al 268 ASP cc_start: 0.8546 (t0) cc_final: 0.7952 (t0) REVERT: An 115 MET cc_start: 0.8878 (tmm) cc_final: 0.7897 (tmm) REVERT: An 214 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8151 (mtt) REVERT: Ao 12 HIS cc_start: 0.6795 (OUTLIER) cc_final: 0.5309 (t70) REVERT: Aq 4 ILE cc_start: 0.1013 (OUTLIER) cc_final: 0.0648 (mp) REVERT: Aq 13 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.5658 (mmtm) REVERT: As 237 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8091 (mmtm) REVERT: As 263 LYS cc_start: 0.8184 (mttt) cc_final: 0.7943 (mtmm) REVERT: As 268 ASP cc_start: 0.8342 (t0) cc_final: 0.7839 (t0) REVERT: At 814 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8340 (tp-100) REVERT: Av 12 HIS cc_start: 0.6807 (OUTLIER) cc_final: 0.6428 (t70) REVERT: Ax 13 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5342 (mmtm) REVERT: Az 209 ILE cc_start: 0.9073 (mm) cc_final: 0.8860 (mm) REVERT: Az 237 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7961 (mmtp) REVERT: Az 268 ASP cc_start: 0.8328 (t0) cc_final: 0.7767 (t0) REVERT: Ba 820 TYR cc_start: 0.8935 (t80) cc_final: 0.8280 (t80) REVERT: Bb 210 SER cc_start: 0.8713 (p) cc_final: 0.8357 (p) REVERT: Bb 214 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8319 (mtp) REVERT: Bb 219 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8738 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7852 (mmtm) REVERT: Bg 243 MET cc_start: 0.7887 (ttp) cc_final: 0.7589 (ttp) REVERT: Bg 268 ASP cc_start: 0.8342 (t0) cc_final: 0.7920 (t0) REVERT: Bh 814 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8245 (tp-100) REVERT: Bi 170 ARG cc_start: 0.8930 (mpp80) cc_final: 0.8570 (mtm180) REVERT: Bj 12 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.5579 (t70) REVERT: Bk 5 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5542 (mp) REVERT: Bl 13 LYS cc_start: 0.5589 (OUTLIER) cc_final: 0.5150 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8083 (mmmt) REVERT: Bn 243 MET cc_start: 0.7794 (ttp) cc_final: 0.7541 (ttm) REVERT: Bn 263 LYS cc_start: 0.8351 (mttt) cc_final: 0.8047 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8315 (t0) cc_final: 0.7719 (t0) REVERT: Bo 822 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8182 (tp30) REVERT: Bp 118 ASN cc_start: 0.7862 (m-40) cc_final: 0.7549 (m-40) REVERT: Bp 214 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7676 (mmm) REVERT: Bp 242 ILE cc_start: 0.8886 (mt) cc_final: 0.8605 (mt) REVERT: Bq 12 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.5485 (t70) REVERT: Bs 13 LYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6260 (mmtm) REVERT: Bu 263 LYS cc_start: 0.8289 (mttt) cc_final: 0.7928 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8435 (t0) cc_final: 0.8017 (t0) REVERT: Bw 110 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.7191 (ptpt) REVERT: Bw 222 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8425 (m110) REVERT: Bw 241 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.7932 (mt) REVERT: Bx 6 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6716 (mm) REVERT: Bx 12 HIS cc_start: 0.6835 (OUTLIER) cc_final: 0.6302 (t70) REVERT: By 5 ILE cc_start: 0.5728 (OUTLIER) cc_final: 0.5117 (mp) REVERT: Bz 4 ILE cc_start: 0.1538 (OUTLIER) cc_final: 0.1151 (mp) REVERT: Bz 13 LYS cc_start: 0.5991 (OUTLIER) cc_final: 0.5583 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7405 (mmtt) REVERT: Cb 263 LYS cc_start: 0.8166 (mttt) cc_final: 0.7806 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8323 (t0) cc_final: 0.7869 (t0) REVERT: Cd 115 MET cc_start: 0.8420 (tmm) cc_final: 0.8176 (tmm) REVERT: Cd 210 SER cc_start: 0.8519 (p) cc_final: 0.8262 (p) REVERT: Cd 214 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7891 (mtt) REVERT: Cd 219 LYS cc_start: 0.9003 (mtpt) cc_final: 0.8787 (mtpt) REVERT: Cd 238 MET cc_start: 0.8566 (mmm) cc_final: 0.7747 (mmt) REVERT: Cd 241 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8032 (mt) REVERT: Cd 255 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7532 (mpt180) REVERT: Cf 4 MET cc_start: 0.6322 (mmt) cc_final: 0.5607 (tpt) REVERT: Cg 4 ILE cc_start: 0.0729 (OUTLIER) cc_final: 0.0284 (mp) REVERT: Cg 13 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5392 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8321 (mptt) cc_final: 0.7554 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8589 (t0) cc_final: 0.8102 (t0) REVERT: Cj 791 GLN cc_start: 0.5773 (tt0) cc_final: 0.5320 (mp10) REVERT: Cj 814 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8010 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.6917 (ptpt) REVERT: Ck 115 MET cc_start: 0.8530 (tmm) cc_final: 0.8173 (tmm) REVERT: Ck 160 LEU cc_start: 0.7816 (mt) cc_final: 0.7446 (mp) REVERT: Ck 210 SER cc_start: 0.8723 (p) cc_final: 0.8396 (p) REVERT: Cp 237 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7444 (mmtt) REVERT: Cp 263 LYS cc_start: 0.8368 (mttt) cc_final: 0.7904 (mtmm) REVERT: Cp 268 ASP cc_start: 0.8076 (t0) cc_final: 0.7515 (t0) REVERT: Cr 242 ILE cc_start: 0.8708 (mt) cc_final: 0.8423 (mt) REVERT: Ct 5 ILE cc_start: 0.6292 (OUTLIER) cc_final: 0.5412 (mp) REVERT: Cu 4 ILE cc_start: 0.0751 (OUTLIER) cc_final: 0.0388 (mp) REVERT: Cu 13 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5222 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8566 (m-80) cc_final: 0.8230 (m-80) REVERT: Cw 237 LYS cc_start: 0.8136 (mmtt) cc_final: 0.7785 (mmtp) REVERT: Cw 263 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7774 (mttm) REVERT: Cw 268 ASP cc_start: 0.8558 (t0) cc_final: 0.8097 (t0) REVERT: Cy 115 MET cc_start: 0.8988 (tmm) cc_final: 0.7863 (tmm) REVERT: Cy 214 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: Cz 12 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.5599 (t70) REVERT: Db 4 ILE cc_start: 0.1195 (OUTLIER) cc_final: 0.0845 (mp) REVERT: Db 13 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5401 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8532 (mmtt) cc_final: 0.8129 (mmtm) REVERT: Dd 263 LYS cc_start: 0.8056 (mttt) cc_final: 0.7854 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8442 (t0) cc_final: 0.7934 (t0) REVERT: De 814 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8379 (tp-100) REVERT: Df 110 LYS cc_start: 0.7521 (OUTLIER) cc_final: 0.7131 (tptm) REVERT: Df 115 MET cc_start: 0.8593 (tmm) cc_final: 0.8237 (tmm) REVERT: Df 214 MET cc_start: 0.8806 (mmt) cc_final: 0.8379 (mpp) REVERT: Di 13 LYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5507 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9056 (mm) cc_final: 0.8832 (mm) REVERT: Dk 237 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7920 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8322 (t0) cc_final: 0.7770 (t0) REVERT: Dm 210 SER cc_start: 0.8766 (p) cc_final: 0.8396 (p) REVERT: Dr 237 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7825 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8315 (t0) cc_final: 0.7910 (t0) REVERT: Ds 814 GLN cc_start: 0.8582 (mm-40) cc_final: 0.8303 (tp-100) REVERT: Dt 110 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6828 (mttt) REVERT: Dt 170 ARG cc_start: 0.8997 (mpp80) cc_final: 0.8649 (mtm180) REVERT: Dy 237 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8107 (mmmt) REVERT: Dy 243 MET cc_start: 0.7821 (ttp) cc_final: 0.7552 (ttm) REVERT: Dy 263 LYS cc_start: 0.8334 (mttt) cc_final: 0.8056 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8327 (t0) cc_final: 0.7746 (t0) REVERT: Dz 795 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: Ea 118 ASN cc_start: 0.7872 (m-40) cc_final: 0.7537 (m-40) REVERT: Ea 240 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8670 (t) REVERT: Ea 242 ILE cc_start: 0.8846 (mt) cc_final: 0.8544 (mt) REVERT: Eb 12 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.5284 (t70) REVERT: Ec 4 MET cc_start: 0.6339 (mmt) cc_final: 0.5391 (tpt) REVERT: Ed 13 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6365 (mmtm) REVERT: Ef 263 LYS cc_start: 0.8296 (mttt) cc_final: 0.7931 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8542 (t0) cc_final: 0.7937 (t0) REVERT: Eh 110 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7139 (tptm) REVERT: Eh 241 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8029 (mt) REVERT: Ei 6 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6684 (mm) REVERT: Ei 12 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6314 (t70) REVERT: Ek 4 ILE cc_start: 0.1526 (OUTLIER) cc_final: 0.1081 (mp) REVERT: Ek 13 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5632 (mmtm) REVERT: Em 237 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7435 (mmtt) REVERT: Em 253 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7668 (mtm110) REVERT: Em 263 LYS cc_start: 0.8166 (mttt) cc_final: 0.7780 (mtmm) REVERT: Em 268 ASP cc_start: 0.8131 (t0) cc_final: 0.7670 (t0) REVERT: Eo 182 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.7769 (mt) REVERT: Eo 210 SER cc_start: 0.8659 (p) cc_final: 0.8388 (p) REVERT: Eo 219 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8767 (mtpt) REVERT: Eo 238 MET cc_start: 0.8666 (mmm) cc_final: 0.7767 (mmp) REVERT: Eo 241 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8046 (mt) REVERT: Eq 4 MET cc_start: 0.6423 (mmt) cc_final: 0.5590 (tpt) REVERT: Er 4 ILE cc_start: 0.1299 (OUTLIER) cc_final: 0.0923 (mp) REVERT: Er 13 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5520 (mmtm) REVERT: Et 226 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7842 (p0) REVERT: Et 237 LYS cc_start: 0.8323 (mptt) cc_final: 0.7507 (mmtt) REVERT: Et 268 ASP cc_start: 0.8574 (t0) cc_final: 0.8091 (t0) REVERT: Eu 814 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: Ev 141 LYS cc_start: 0.8593 (ttpt) cc_final: 0.8301 (tttp) REVERT: Ev 160 LEU cc_start: 0.7818 (mt) cc_final: 0.7442 (mp) REVERT: Ev 231 ARG cc_start: 0.7711 (mmt180) cc_final: 0.7487 (mmt180) outliers start: 224 outliers final: 132 residues processed: 922 average time/residue: 0.2520 time to fit residues: 378.9954 Evaluate side-chains 932 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 739 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 3 ASP Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ah residue 3 ASP Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 10 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain At residue 814 GLN Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 252 VAL Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 165 THR Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 4 MET Chi-restraints excluded: chain Bk residue 5 ILE Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 3 ASP Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 260 GLN Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 218 THR Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cd residue 255 ARG Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 7 THR Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain De residue 814 GLN Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 218 THR Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 252 VAL Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 10 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 7 THR Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 110 LYS Chi-restraints excluded: chain Eh residue 165 THR Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain Em residue 260 GLN Chi-restraints excluded: chain Em residue 267 GLU Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 218 THR Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 226 ASN Chi-restraints excluded: chain Et residue 249 SER Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 115 MET Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 223 optimal weight: 3.9990 chunk 393 optimal weight: 0.0970 chunk 309 optimal weight: 2.9990 chunk 402 optimal weight: 0.0770 chunk 447 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 208 optimal weight: 3.9990 chunk 417 optimal weight: 4.9990 chunk 345 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 367 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ae 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Bg 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bw 245 GLN Cc 814 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.168549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133222 restraints weight = 44730.940| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.62 r_work: 0.3395 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 42822 Z= 0.105 Angle : 0.454 6.814 58122 Z= 0.229 Chirality : 0.041 0.141 6660 Planarity : 0.004 0.043 7470 Dihedral : 5.252 80.784 5970 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.20 % Allowed : 21.37 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.11), residues: 5202 helix: 2.15 (0.13), residues: 1332 sheet: -0.37 (0.15), residues: 1170 loop : -0.00 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGAe 253 TYR 0.013 0.001 TYRDm 194 PHE 0.011 0.001 PHEDt 112 TRP 0.004 0.001 TRPDd 221 HIS 0.002 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00249 (42822) covalent geometry : angle 0.45390 (58122) hydrogen bonds : bond 0.03166 ( 1756) hydrogen bonds : angle 4.42247 ( 4860) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 748 time to evaluate : 1.547 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: Ab 5 ILE cc_start: 0.4682 (OUTLIER) cc_final: 0.3888 (mp) REVERT: Ae 237 LYS cc_start: 0.7969 (mmtt) cc_final: 0.7711 (mmtt) REVERT: Ae 263 LYS cc_start: 0.8170 (mttt) cc_final: 0.7480 (mtmm) REVERT: Ae 268 ASP cc_start: 0.7995 (t0) cc_final: 0.7349 (t0) REVERT: Ag 182 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7572 (mt) REVERT: Ah 12 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.5938 (t-90) REVERT: Aj 13 LYS cc_start: 0.5760 (OUTLIER) cc_final: 0.5263 (mmtm) REVERT: Al 210 TYR cc_start: 0.8328 (m-80) cc_final: 0.7972 (m-80) REVERT: Al 237 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7613 (mmtp) REVERT: Al 263 LYS cc_start: 0.8151 (mtpm) cc_final: 0.7413 (mtmm) REVERT: Al 268 ASP cc_start: 0.8534 (t0) cc_final: 0.7932 (t0) REVERT: An 115 MET cc_start: 0.8632 (tmm) cc_final: 0.7648 (tmm) REVERT: An 170 ARG cc_start: 0.8848 (mpp80) cc_final: 0.8497 (mtm180) REVERT: An 214 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8107 (mtt) REVERT: Ao 12 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.5342 (t70) REVERT: Aq 4 ILE cc_start: 0.1050 (OUTLIER) cc_final: 0.0824 (mp) REVERT: Aq 13 LYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5531 (mmtm) REVERT: As 237 LYS cc_start: 0.8410 (mmtt) cc_final: 0.7996 (mmtm) REVERT: As 263 LYS cc_start: 0.8020 (mttt) cc_final: 0.7571 (mtmm) REVERT: As 268 ASP cc_start: 0.8427 (t0) cc_final: 0.7892 (t0) REVERT: Av 12 HIS cc_start: 0.6315 (OUTLIER) cc_final: 0.5984 (t70) REVERT: Ax 13 LYS cc_start: 0.5947 (OUTLIER) cc_final: 0.5321 (mmtm) REVERT: Az 209 ILE cc_start: 0.9046 (mm) cc_final: 0.8803 (mm) REVERT: Az 237 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7945 (mmtp) REVERT: Az 268 ASP cc_start: 0.8150 (t0) cc_final: 0.7549 (t0) REVERT: Ba 820 TYR cc_start: 0.8843 (t80) cc_final: 0.8161 (t80) REVERT: Bb 210 SER cc_start: 0.8699 (p) cc_final: 0.8291 (p) REVERT: Bb 214 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8150 (mtp) REVERT: Bb 219 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8527 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7919 (mmtm) REVERT: Bg 243 MET cc_start: 0.7637 (ttp) cc_final: 0.7280 (ttp) REVERT: Bg 268 ASP cc_start: 0.8266 (t0) cc_final: 0.7759 (t0) REVERT: Bh 814 GLN cc_start: 0.8287 (mm-40) cc_final: 0.8008 (tp-100) REVERT: Bh 822 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8328 (mm-30) REVERT: Bi 110 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6077 (ptpt) REVERT: Bi 170 ARG cc_start: 0.8915 (mpp80) cc_final: 0.8570 (mtm180) REVERT: Bi 240 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8206 (t) REVERT: Bj 12 HIS cc_start: 0.6397 (OUTLIER) cc_final: 0.5100 (t70) REVERT: Bl 13 LYS cc_start: 0.5573 (OUTLIER) cc_final: 0.5187 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8299 (mmtt) cc_final: 0.7992 (mmmt) REVERT: Bn 243 MET cc_start: 0.7561 (ttp) cc_final: 0.7280 (ttm) REVERT: Bn 263 LYS cc_start: 0.8202 (mttt) cc_final: 0.7744 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8220 (t0) cc_final: 0.7578 (t0) REVERT: Bo 822 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: Bp 214 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7405 (mmm) REVERT: Bp 242 ILE cc_start: 0.8644 (mt) cc_final: 0.8333 (mt) REVERT: Bq 12 HIS cc_start: 0.6518 (OUTLIER) cc_final: 0.5008 (t70) REVERT: Bs 13 LYS cc_start: 0.6408 (OUTLIER) cc_final: 0.6187 (mmtm) REVERT: Bu 253 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7434 (ptm-80) REVERT: Bu 263 LYS cc_start: 0.7872 (mttt) cc_final: 0.7510 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8401 (t0) cc_final: 0.7863 (t0) REVERT: Bw 110 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6746 (ptpt) REVERT: Bw 222 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8217 (m110) REVERT: Bw 241 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7727 (mt) REVERT: Bx 6 LEU cc_start: 0.6370 (OUTLIER) cc_final: 0.6076 (mm) REVERT: Bz 4 ILE cc_start: 0.0797 (OUTLIER) cc_final: 0.0503 (mp) REVERT: Bz 13 LYS cc_start: 0.5837 (OUTLIER) cc_final: 0.5519 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7787 (mmtt) cc_final: 0.7290 (mmtt) REVERT: Cb 253 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7206 (mtm110) REVERT: Cb 263 LYS cc_start: 0.7952 (mttt) cc_final: 0.7369 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8190 (t0) cc_final: 0.7936 (t0) REVERT: Cd 210 SER cc_start: 0.8457 (p) cc_final: 0.8134 (p) REVERT: Cd 214 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7612 (mtt) REVERT: Cd 238 MET cc_start: 0.8495 (mmm) cc_final: 0.7785 (mmt) REVERT: Cd 241 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7782 (mt) REVERT: Cf 4 MET cc_start: 0.6174 (mmt) cc_final: 0.5482 (tpt) REVERT: Cg 4 ILE cc_start: 0.0138 (OUTLIER) cc_final: -0.0168 (mp) REVERT: Cg 13 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5360 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8204 (mptt) cc_final: 0.7323 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8539 (t0) cc_final: 0.7949 (t0) REVERT: Cj 791 GLN cc_start: 0.5575 (tt0) cc_final: 0.5098 (mp10) REVERT: Cj 814 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6430 (ptpt) REVERT: Ck 160 LEU cc_start: 0.7732 (mt) cc_final: 0.7371 (mp) REVERT: Ck 210 SER cc_start: 0.8639 (p) cc_final: 0.8248 (p) REVERT: Cp 237 LYS cc_start: 0.7987 (mmtt) cc_final: 0.7735 (mmtt) REVERT: Cp 253 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7630 (mtm110) REVERT: Cp 263 LYS cc_start: 0.8172 (mttt) cc_final: 0.7497 (mtmm) REVERT: Cp 268 ASP cc_start: 0.7955 (t0) cc_final: 0.7317 (t0) REVERT: Cr 214 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8283 (mpp) REVERT: Cr 242 ILE cc_start: 0.8536 (mt) cc_final: 0.8244 (mt) REVERT: Ct 5 ILE cc_start: 0.5910 (OUTLIER) cc_final: 0.5112 (mp) REVERT: Cu 4 ILE cc_start: 0.0086 (OUTLIER) cc_final: -0.0152 (mp) REVERT: Cu 13 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5207 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8365 (m-80) cc_final: 0.7962 (m-80) REVERT: Cw 237 LYS cc_start: 0.8007 (mmtt) cc_final: 0.7634 (mmtp) REVERT: Cw 263 LYS cc_start: 0.8034 (mmmt) cc_final: 0.7185 (mtmm) REVERT: Cw 268 ASP cc_start: 0.8572 (t0) cc_final: 0.8064 (t0) REVERT: Cx 816 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: Cy 115 MET cc_start: 0.8698 (tmm) cc_final: 0.7565 (tmm) REVERT: Cy 170 ARG cc_start: 0.8871 (mpp80) cc_final: 0.8490 (mtm180) REVERT: Cy 182 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7309 (mt) REVERT: Cy 214 MET cc_start: 0.8845 (OUTLIER) cc_final: 0.8089 (mtt) REVERT: Cz 12 HIS cc_start: 0.6514 (OUTLIER) cc_final: 0.5251 (t70) REVERT: Db 4 ILE cc_start: 0.0891 (OUTLIER) cc_final: 0.0671 (mp) REVERT: Db 13 LYS cc_start: 0.5805 (OUTLIER) cc_final: 0.5216 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8304 (mmtt) cc_final: 0.7956 (mmtm) REVERT: Dd 263 LYS cc_start: 0.8015 (mttt) cc_final: 0.7559 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8397 (t0) cc_final: 0.7855 (t0) REVERT: Df 110 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6677 (tptm) REVERT: Df 214 MET cc_start: 0.8745 (mmt) cc_final: 0.8247 (mpp) REVERT: Di 13 LYS cc_start: 0.6024 (OUTLIER) cc_final: 0.5378 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9023 (mm) cc_final: 0.8767 (mm) REVERT: Dk 237 LYS cc_start: 0.8280 (mmtt) cc_final: 0.7913 (mmtp) REVERT: Dk 268 ASP cc_start: 0.8136 (t0) cc_final: 0.7544 (t0) REVERT: Dm 182 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7738 (mt) REVERT: Dm 210 SER cc_start: 0.8712 (p) cc_final: 0.8283 (p) REVERT: Dm 214 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8237 (mtt) REVERT: Dp 13 LYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5812 (mptt) REVERT: Dr 237 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7765 (mmtm) REVERT: Dr 268 ASP cc_start: 0.8239 (t0) cc_final: 0.7757 (t0) REVERT: Ds 814 GLN cc_start: 0.8344 (mm-40) cc_final: 0.8076 (tp-100) REVERT: Dt 110 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6300 (mttt) REVERT: Dt 170 ARG cc_start: 0.8974 (mpp80) cc_final: 0.8636 (mtm180) REVERT: Dt 240 THR cc_start: 0.8606 (OUTLIER) cc_final: 0.8258 (t) REVERT: Dy 237 LYS cc_start: 0.8338 (mmtt) cc_final: 0.8027 (mmmt) REVERT: Dy 243 MET cc_start: 0.7577 (ttp) cc_final: 0.7310 (ttm) REVERT: Dy 263 LYS cc_start: 0.8183 (mttt) cc_final: 0.7741 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8240 (t0) cc_final: 0.7623 (t0) REVERT: Dz 795 GLN cc_start: 0.7780 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: Ea 160 LEU cc_start: 0.7931 (mt) cc_final: 0.7630 (mt) REVERT: Ea 240 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8557 (t) REVERT: Eb 12 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.4794 (t70) REVERT: Ec 4 MET cc_start: 0.5881 (mmt) cc_final: 0.4891 (tpt) REVERT: Ef 263 LYS cc_start: 0.7903 (mttt) cc_final: 0.7582 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8438 (t0) cc_final: 0.8005 (t0) REVERT: Eh 110 LYS cc_start: 0.6951 (OUTLIER) cc_final: 0.6583 (tptm) REVERT: Eh 222 ASN cc_start: 0.8703 (OUTLIER) cc_final: 0.8204 (m110) REVERT: Eh 241 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7833 (mt) REVERT: Ei 6 LEU cc_start: 0.6305 (OUTLIER) cc_final: 0.6041 (mm) REVERT: Ei 12 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.5981 (t70) REVERT: Ek 4 ILE cc_start: 0.1230 (OUTLIER) cc_final: 0.0963 (mp) REVERT: Ek 13 LYS cc_start: 0.6042 (OUTLIER) cc_final: 0.5678 (mmtm) REVERT: Em 237 LYS cc_start: 0.7807 (mmtt) cc_final: 0.7303 (mmtt) REVERT: Em 253 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7321 (mtm110) REVERT: Em 263 LYS cc_start: 0.7945 (mttt) cc_final: 0.7355 (mtmm) REVERT: Em 268 ASP cc_start: 0.8025 (t0) cc_final: 0.7530 (t0) REVERT: Eo 182 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7360 (mt) REVERT: Eo 210 SER cc_start: 0.8494 (p) cc_final: 0.8197 (p) REVERT: Eo 219 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8542 (mtpt) REVERT: Eo 238 MET cc_start: 0.8565 (mmm) cc_final: 0.7714 (mmt) REVERT: Eo 241 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.7713 (mt) REVERT: Eq 4 MET cc_start: 0.6237 (mmt) cc_final: 0.5590 (tpt) REVERT: Er 4 ILE cc_start: 0.0786 (OUTLIER) cc_final: 0.0536 (mp) REVERT: Er 13 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5405 (mmtm) REVERT: Et 237 LYS cc_start: 0.8196 (mptt) cc_final: 0.7284 (mmtt) REVERT: Et 268 ASP cc_start: 0.8538 (t0) cc_final: 0.7961 (t0) REVERT: Eu 814 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7764 (tm-30) REVERT: Ev 160 LEU cc_start: 0.7729 (mt) cc_final: 0.7335 (mp) REVERT: Ev 231 ARG cc_start: 0.7752 (mmt180) cc_final: 0.7525 (mmt180) outliers start: 193 outliers final: 111 residues processed: 889 average time/residue: 0.2514 time to fit residues: 363.8171 Evaluate side-chains 913 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 737 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 179 LEU Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ah residue 12 HIS Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Al residue 267 GLU Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain As residue 267 GLU Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bn residue 267 GLU Chi-restraints excluded: chain Bo residue 822 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 214 MET Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cx residue 816 GLU Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 182 LEU Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 168 VAL Chi-restraints excluded: chain Dm residue 182 LEU Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 214 MET Chi-restraints excluded: chain Dm residue 215 ILE Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dp residue 13 LYS Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dw residue 13 LYS Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 110 LYS Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ej residue 4 MET Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain Em residue 267 GLU Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 413 optimal weight: 3.9990 chunk 356 optimal weight: 0.9990 chunk 344 optimal weight: 0.0980 chunk 464 optimal weight: 0.8980 chunk 433 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 305 optimal weight: 5.9990 chunk 453 optimal weight: 4.9990 chunk 288 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** As 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** At 814 GLN ** Bg 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 814 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** De 814 GLN ** Dk 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.166847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.131115 restraints weight = 44640.891| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.65 r_work: 0.3383 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 42822 Z= 0.138 Angle : 0.480 7.731 58122 Z= 0.239 Chirality : 0.042 0.143 6660 Planarity : 0.004 0.050 7470 Dihedral : 5.159 80.954 5965 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.71 % Allowed : 20.78 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.11), residues: 5202 helix: 2.14 (0.13), residues: 1332 sheet: -0.46 (0.14), residues: 1206 loop : -0.04 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARGCb 233 TYR 0.013 0.001 TYRDm 194 PHE 0.011 0.001 PHEEf 264 TRP 0.007 0.001 TRPAn 206 HIS 0.002 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00338 (42822) covalent geometry : angle 0.47981 (58122) hydrogen bonds : bond 0.03271 ( 1756) hydrogen bonds : angle 4.42353 ( 4860) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 753 time to evaluate : 1.555 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: Ab 5 ILE cc_start: 0.4781 (OUTLIER) cc_final: 0.3956 (mp) REVERT: Ae 237 LYS cc_start: 0.7989 (mmtt) cc_final: 0.7774 (mmtt) REVERT: Ae 250 LEU cc_start: 0.7183 (mt) cc_final: 0.6787 (mp) REVERT: Ae 263 LYS cc_start: 0.8171 (mttt) cc_final: 0.7492 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8008 (t0) cc_final: 0.7353 (t0) REVERT: Ag 182 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7620 (mt) REVERT: Ah 12 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.6063 (t-90) REVERT: Aj 13 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5262 (mmtm) REVERT: Al 210 TYR cc_start: 0.8454 (m-80) cc_final: 0.8043 (m-80) REVERT: Al 237 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7598 (mmtp) REVERT: Al 268 ASP cc_start: 0.8527 (t0) cc_final: 0.7793 (t0) REVERT: An 115 MET cc_start: 0.8618 (tmm) cc_final: 0.7727 (tmm) REVERT: An 214 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: Ao 12 HIS cc_start: 0.6873 (OUTLIER) cc_final: 0.5419 (t70) REVERT: Aq 4 ILE cc_start: 0.1102 (OUTLIER) cc_final: 0.0850 (mp) REVERT: Aq 13 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5670 (mmtm) REVERT: As 237 LYS cc_start: 0.8423 (mmtt) cc_final: 0.7973 (mmtm) REVERT: As 263 LYS cc_start: 0.8033 (mttt) cc_final: 0.7593 (mtmm) REVERT: As 268 ASP cc_start: 0.8443 (t0) cc_final: 0.7900 (t0) REVERT: Av 12 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.6053 (t70) REVERT: Ax 13 LYS cc_start: 0.5989 (OUTLIER) cc_final: 0.5340 (mmtm) REVERT: Az 209 ILE cc_start: 0.9047 (mm) cc_final: 0.8806 (mm) REVERT: Az 237 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7897 (mmtp) REVERT: Az 268 ASP cc_start: 0.8159 (t0) cc_final: 0.7552 (t0) REVERT: Ba 820 TYR cc_start: 0.8854 (t80) cc_final: 0.8179 (t80) REVERT: Bb 182 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7760 (mt) REVERT: Bb 210 SER cc_start: 0.8723 (p) cc_final: 0.8325 (p) REVERT: Bb 214 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: Bb 219 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8525 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8145 (mmtt) cc_final: 0.7798 (mmtm) REVERT: Bg 243 MET cc_start: 0.7629 (ttp) cc_final: 0.7254 (ttp) REVERT: Bg 253 ARG cc_start: 0.8036 (mtm180) cc_final: 0.7787 (mtm110) REVERT: Bg 268 ASP cc_start: 0.8272 (t0) cc_final: 0.7753 (t0) REVERT: Bh 814 GLN cc_start: 0.8306 (mm-40) cc_final: 0.8027 (tp-100) REVERT: Bh 822 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8335 (mm-30) REVERT: Bi 110 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6088 (ptpt) REVERT: Bi 170 ARG cc_start: 0.8934 (mpp80) cc_final: 0.8601 (mtm180) REVERT: Bi 240 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8220 (t) REVERT: Bj 12 HIS cc_start: 0.6513 (OUTLIER) cc_final: 0.5264 (t70) REVERT: Bk 5 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5481 (mp) REVERT: Bl 13 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5424 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8306 (mmtt) cc_final: 0.8005 (mmmt) REVERT: Bn 243 MET cc_start: 0.7597 (ttp) cc_final: 0.7316 (ttm) REVERT: Bn 263 LYS cc_start: 0.8212 (mttt) cc_final: 0.7736 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8224 (t0) cc_final: 0.7563 (t0) REVERT: Bp 118 ASN cc_start: 0.7687 (m-40) cc_final: 0.7356 (m-40) REVERT: Bp 160 LEU cc_start: 0.7955 (mt) cc_final: 0.7662 (mt) REVERT: Bp 214 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7411 (mmm) REVERT: Bp 242 ILE cc_start: 0.8685 (mt) cc_final: 0.8382 (mt) REVERT: Bq 12 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.5167 (t70) REVERT: Bs 13 LYS cc_start: 0.6414 (OUTLIER) cc_final: 0.6200 (mmtm) REVERT: Bu 253 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7610 (ptm-80) REVERT: Bu 263 LYS cc_start: 0.7909 (mttt) cc_final: 0.7564 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8413 (t0) cc_final: 0.7867 (t0) REVERT: Bw 110 LYS cc_start: 0.6972 (OUTLIER) cc_final: 0.6561 (tptm) REVERT: Bw 182 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7189 (mt) REVERT: Bw 184 SER cc_start: 0.7563 (m) cc_final: 0.7318 (m) REVERT: Bw 222 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8207 (m110) REVERT: Bw 241 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.7816 (mt) REVERT: Bx 6 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6068 (mm) REVERT: Bx 12 HIS cc_start: 0.6508 (OUTLIER) cc_final: 0.6026 (t70) REVERT: By 5 ILE cc_start: 0.5740 (OUTLIER) cc_final: 0.5176 (mp) REVERT: Bz 4 ILE cc_start: 0.0899 (OUTLIER) cc_final: 0.0651 (mp) REVERT: Bz 13 LYS cc_start: 0.5970 (OUTLIER) cc_final: 0.5722 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7804 (mmtt) cc_final: 0.7309 (mmtt) REVERT: Cb 253 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7434 (mtm110) REVERT: Cb 263 LYS cc_start: 0.7975 (mttt) cc_final: 0.7394 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8242 (t0) cc_final: 0.7744 (t0) REVERT: Cd 116 THR cc_start: 0.8129 (t) cc_final: 0.7831 (p) REVERT: Cd 210 SER cc_start: 0.8526 (p) cc_final: 0.8187 (p) REVERT: Cd 214 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: Cd 238 MET cc_start: 0.8500 (mmm) cc_final: 0.7950 (mmt) REVERT: Cd 241 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7791 (mt) REVERT: Cf 4 MET cc_start: 0.5992 (mmt) cc_final: 0.5297 (tpt) REVERT: Cg 4 ILE cc_start: 0.0231 (OUTLIER) cc_final: -0.0089 (mp) REVERT: Cg 13 LYS cc_start: 0.6084 (OUTLIER) cc_final: 0.5379 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8389 (mptt) cc_final: 0.7572 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8537 (t0) cc_final: 0.7975 (t0) REVERT: Cj 791 GLN cc_start: 0.5629 (tt0) cc_final: 0.5160 (mp10) REVERT: Cj 814 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.7780 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7133 (OUTLIER) cc_final: 0.6457 (ptpt) REVERT: Ck 115 MET cc_start: 0.8270 (tmm) cc_final: 0.7964 (tmm) REVERT: Ck 160 LEU cc_start: 0.7756 (mt) cc_final: 0.7386 (mp) REVERT: Ck 210 SER cc_start: 0.8684 (p) cc_final: 0.8301 (p) REVERT: Cp 237 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7737 (mmtt) REVERT: Cp 253 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7704 (mtm110) REVERT: Cp 263 LYS cc_start: 0.8194 (mttt) cc_final: 0.7509 (mtmm) REVERT: Cp 268 ASP cc_start: 0.7982 (t0) cc_final: 0.7339 (t0) REVERT: Cr 214 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8098 (mpt) REVERT: Cr 242 ILE cc_start: 0.8551 (mt) cc_final: 0.8248 (mt) REVERT: Cs 12 HIS cc_start: 0.6567 (OUTLIER) cc_final: 0.5977 (t-90) REVERT: Ct 5 ILE cc_start: 0.5912 (OUTLIER) cc_final: 0.5137 (mp) REVERT: Cu 4 ILE cc_start: 0.0284 (OUTLIER) cc_final: 0.0049 (mp) REVERT: Cu 13 LYS cc_start: 0.5951 (OUTLIER) cc_final: 0.5203 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8382 (m-80) cc_final: 0.7974 (m-80) REVERT: Cw 237 LYS cc_start: 0.7960 (mmtt) cc_final: 0.7595 (mmtp) REVERT: Cw 263 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7221 (mtmm) REVERT: Cw 268 ASP cc_start: 0.8509 (t0) cc_final: 0.7851 (t0) REVERT: Cy 115 MET cc_start: 0.8681 (tmm) cc_final: 0.7675 (tmm) REVERT: Cy 182 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7347 (mt) REVERT: Cy 214 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8190 (mtt) REVERT: Cz 12 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.5309 (t70) REVERT: Db 4 ILE cc_start: 0.1195 (OUTLIER) cc_final: 0.0939 (mp) REVERT: Db 13 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.5224 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8317 (mmtt) cc_final: 0.7972 (mmtm) REVERT: Dd 251 GLN cc_start: 0.8200 (mt0) cc_final: 0.7323 (mp10) REVERT: Dd 263 LYS cc_start: 0.8058 (mttt) cc_final: 0.7592 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8428 (t0) cc_final: 0.7871 (t0) REVERT: Df 110 LYS cc_start: 0.7214 (OUTLIER) cc_final: 0.6570 (tptm) REVERT: Df 115 MET cc_start: 0.8334 (tmm) cc_final: 0.8003 (tmm) REVERT: Df 214 MET cc_start: 0.8771 (mmt) cc_final: 0.8247 (mpp) REVERT: Di 13 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.5390 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9021 (mm) cc_final: 0.8764 (mm) REVERT: Dk 237 LYS cc_start: 0.8285 (mmtt) cc_final: 0.7894 (mmtp) REVERT: Dk 267 GLU cc_start: 0.8087 (mp0) cc_final: 0.7829 (mp0) REVERT: Dk 268 ASP cc_start: 0.8147 (t0) cc_final: 0.7544 (t0) REVERT: Dm 210 SER cc_start: 0.8725 (p) cc_final: 0.8311 (p) REVERT: Dm 214 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: Dp 13 LYS cc_start: 0.6238 (OUTLIER) cc_final: 0.5671 (mptt) REVERT: Dr 237 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7801 (mmtm) REVERT: Dr 253 ARG cc_start: 0.8039 (mtp85) cc_final: 0.7756 (mtp-110) REVERT: Dr 268 ASP cc_start: 0.8240 (t0) cc_final: 0.7748 (t0) REVERT: Ds 814 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8087 (tp-100) REVERT: Dt 110 LYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6301 (mttt) REVERT: Dt 170 ARG cc_start: 0.9000 (mpp80) cc_final: 0.8668 (mtm180) REVERT: Dt 240 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8268 (t) REVERT: Dy 237 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8031 (mmmt) REVERT: Dy 243 MET cc_start: 0.7600 (ttp) cc_final: 0.7332 (ttm) REVERT: Dy 253 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7705 (mtm110) REVERT: Dy 263 LYS cc_start: 0.8208 (mttt) cc_final: 0.7735 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8240 (t0) cc_final: 0.7600 (t0) REVERT: Dz 795 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: Ea 160 LEU cc_start: 0.7948 (mt) cc_final: 0.7648 (mt) REVERT: Ea 240 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8540 (t) REVERT: Ea 242 ILE cc_start: 0.8665 (mt) cc_final: 0.8360 (mt) REVERT: Eb 12 HIS cc_start: 0.6248 (OUTLIER) cc_final: 0.4834 (t70) REVERT: Ec 4 MET cc_start: 0.6039 (mmt) cc_final: 0.5127 (tpt) REVERT: Ef 263 LYS cc_start: 0.8012 (mttt) cc_final: 0.7513 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8483 (t0) cc_final: 0.8039 (t0) REVERT: Eh 222 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8208 (m110) REVERT: Eh 241 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.7864 (mt) REVERT: Ei 6 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.6061 (mm) REVERT: Ei 12 HIS cc_start: 0.6766 (OUTLIER) cc_final: 0.6028 (t70) REVERT: Ek 4 ILE cc_start: 0.1003 (OUTLIER) cc_final: 0.0710 (mp) REVERT: Ek 13 LYS cc_start: 0.5963 (OUTLIER) cc_final: 0.5562 (mmtm) REVERT: Em 237 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7325 (mmtt) REVERT: Em 253 ARG cc_start: 0.7937 (mtp85) cc_final: 0.7366 (mtm110) REVERT: Em 263 LYS cc_start: 0.7952 (mttt) cc_final: 0.7368 (mtmm) REVERT: Em 268 ASP cc_start: 0.8060 (t0) cc_final: 0.7523 (t0) REVERT: Eo 182 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7430 (mt) REVERT: Eo 210 SER cc_start: 0.8543 (p) cc_final: 0.8249 (p) REVERT: Eo 219 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8576 (mtpt) REVERT: Eo 238 MET cc_start: 0.8575 (mmm) cc_final: 0.7788 (mmp) REVERT: Eo 241 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7762 (mt) REVERT: Eq 4 MET cc_start: 0.6200 (mmt) cc_final: 0.5487 (tpt) REVERT: Er 4 ILE cc_start: 0.0740 (OUTLIER) cc_final: 0.0458 (mp) REVERT: Er 13 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5514 (mmtm) REVERT: Et 237 LYS cc_start: 0.8240 (mptt) cc_final: 0.7340 (mmtt) REVERT: Et 241 TYR cc_start: 0.8216 (m-80) cc_final: 0.8001 (m-80) REVERT: Et 268 ASP cc_start: 0.8529 (t0) cc_final: 0.7971 (t0) REVERT: Eu 814 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7796 (tm-30) REVERT: Ev 160 LEU cc_start: 0.7690 (mt) cc_final: 0.7315 (mp) REVERT: Ev 231 ARG cc_start: 0.7767 (mmt180) cc_final: 0.7539 (mmt180) outliers start: 216 outliers final: 128 residues processed: 918 average time/residue: 0.2465 time to fit residues: 368.0792 Evaluate side-chains 943 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 748 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 179 LEU Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 215 ILE Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ah residue 12 HIS Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Am residue 814 GLN Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain Au residue 218 THR Chi-restraints excluded: chain Au residue 219 LYS Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 241 LEU Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 182 LEU Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 5 ILE Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 231 THR Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 182 LEU Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 260 GLN Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 10 THR Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 214 MET Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Cs residue 12 HIS Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cx residue 814 GLN Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 182 LEU Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 10 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 214 MET Chi-restraints excluded: chain Dm residue 215 ILE Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dp residue 13 LYS Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 178 SER Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 3 SER Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dw residue 13 LYS Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 178 SER Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ej residue 4 MET Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 215 ILE Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 249 SER Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 276 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 332 optimal weight: 5.9990 chunk 410 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 347 optimal weight: 2.9990 chunk 418 optimal weight: 0.7980 chunk 378 optimal weight: 20.0000 chunk 167 optimal weight: 0.9990 chunk 420 optimal weight: 0.0770 chunk 155 optimal weight: 0.0970 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Bg 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 814 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.168343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132691 restraints weight = 44430.674| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.64 r_work: 0.3405 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42822 Z= 0.109 Angle : 0.462 10.394 58122 Z= 0.231 Chirality : 0.042 0.145 6660 Planarity : 0.004 0.038 7470 Dihedral : 4.985 80.638 5962 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.51 % Allowed : 21.07 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 5202 helix: 2.24 (0.13), residues: 1332 sheet: -0.44 (0.14), residues: 1206 loop : 0.06 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGEm 233 TYR 0.013 0.001 TYRDm 194 PHE 0.010 0.001 PHEBf 2 TRP 0.005 0.001 TRPAs 221 HIS 0.002 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00261 (42822) covalent geometry : angle 0.46166 (58122) hydrogen bonds : bond 0.03121 ( 1756) hydrogen bonds : angle 4.36165 ( 4860) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 751 time to evaluate : 1.715 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: Ab 5 ILE cc_start: 0.4741 (OUTLIER) cc_final: 0.3910 (mp) REVERT: Ae 237 LYS cc_start: 0.7963 (mmtt) cc_final: 0.7751 (mmtt) REVERT: Ae 250 LEU cc_start: 0.7143 (mt) cc_final: 0.6780 (mp) REVERT: Ae 263 LYS cc_start: 0.8161 (mttt) cc_final: 0.7467 (mtmm) REVERT: Ae 268 ASP cc_start: 0.7993 (t0) cc_final: 0.7341 (t0) REVERT: Ag 182 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7588 (mt) REVERT: Ah 12 HIS cc_start: 0.6645 (OUTLIER) cc_final: 0.6107 (t-90) REVERT: Aj 13 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5170 (mmtm) REVERT: Al 210 TYR cc_start: 0.8438 (m-80) cc_final: 0.8072 (m-80) REVERT: Al 237 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7576 (mmtp) REVERT: Al 268 ASP cc_start: 0.8513 (t0) cc_final: 0.7835 (t0) REVERT: An 110 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6648 (ptpt) REVERT: An 115 MET cc_start: 0.8654 (tmm) cc_final: 0.7764 (tmm) REVERT: An 170 ARG cc_start: 0.8870 (mpp80) cc_final: 0.8502 (mtm180) REVERT: An 214 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8120 (mtt) REVERT: Ao 12 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.5349 (t70) REVERT: Aq 4 ILE cc_start: 0.1100 (OUTLIER) cc_final: 0.0856 (mp) REVERT: Aq 13 LYS cc_start: 0.5968 (OUTLIER) cc_final: 0.5591 (mmtm) REVERT: As 237 LYS cc_start: 0.8414 (mmtt) cc_final: 0.8025 (mmtm) REVERT: As 263 LYS cc_start: 0.7999 (mttt) cc_final: 0.7567 (mtmm) REVERT: As 268 ASP cc_start: 0.8418 (t0) cc_final: 0.7880 (t0) REVERT: Av 12 HIS cc_start: 0.6321 (OUTLIER) cc_final: 0.6003 (t70) REVERT: Ax 13 LYS cc_start: 0.5950 (OUTLIER) cc_final: 0.5316 (mmtm) REVERT: Az 209 ILE cc_start: 0.9041 (mm) cc_final: 0.8794 (mm) REVERT: Az 237 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7904 (mmtp) REVERT: Az 253 ARG cc_start: 0.7818 (mtp-110) cc_final: 0.7599 (mtm110) REVERT: Az 268 ASP cc_start: 0.8247 (t0) cc_final: 0.7621 (t0) REVERT: Ba 820 TYR cc_start: 0.8844 (t80) cc_final: 0.8192 (t80) REVERT: Bb 182 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7749 (mt) REVERT: Bb 210 SER cc_start: 0.8694 (p) cc_final: 0.8285 (p) REVERT: Bb 214 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: Bb 219 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8526 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7876 (mmtm) REVERT: Bg 243 MET cc_start: 0.7605 (ttp) cc_final: 0.7190 (ttp) REVERT: Bg 268 ASP cc_start: 0.8249 (t0) cc_final: 0.7742 (t0) REVERT: Bh 814 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8034 (tp-100) REVERT: Bh 822 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8316 (mm-30) REVERT: Bi 110 LYS cc_start: 0.7207 (OUTLIER) cc_final: 0.6043 (ptpt) REVERT: Bi 170 ARG cc_start: 0.8910 (mpp80) cc_final: 0.8571 (mtm180) REVERT: Bi 240 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8200 (t) REVERT: Bj 12 HIS cc_start: 0.6479 (OUTLIER) cc_final: 0.6241 (t70) REVERT: Bl 13 LYS cc_start: 0.5852 (OUTLIER) cc_final: 0.5585 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7990 (mmmt) REVERT: Bn 243 MET cc_start: 0.7571 (ttp) cc_final: 0.7288 (ttm) REVERT: Bn 253 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7927 (mtm110) REVERT: Bn 263 LYS cc_start: 0.7811 (mttt) cc_final: 0.7332 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8211 (t0) cc_final: 0.7556 (t0) REVERT: Bp 160 LEU cc_start: 0.7929 (mt) cc_final: 0.7630 (mt) REVERT: Bp 214 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7440 (mmm) REVERT: Bp 242 ILE cc_start: 0.8643 (mt) cc_final: 0.8336 (mt) REVERT: Bq 12 HIS cc_start: 0.6262 (OUTLIER) cc_final: 0.4820 (t70) REVERT: Bs 13 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.6163 (mmtm) REVERT: Bu 237 LYS cc_start: 0.8231 (mmtm) cc_final: 0.7510 (mmmt) REVERT: Bu 253 ARG cc_start: 0.7867 (mtm110) cc_final: 0.7618 (ptm-80) REVERT: Bu 263 LYS cc_start: 0.7860 (mttt) cc_final: 0.7528 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8389 (t0) cc_final: 0.7829 (t0) REVERT: Bw 110 LYS cc_start: 0.6958 (OUTLIER) cc_final: 0.6560 (tptm) REVERT: Bw 182 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7195 (mt) REVERT: Bw 222 ASN cc_start: 0.8708 (OUTLIER) cc_final: 0.8205 (m110) REVERT: Bw 241 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.7844 (mt) REVERT: Bx 6 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6070 (mm) REVERT: Bx 12 HIS cc_start: 0.6471 (OUTLIER) cc_final: 0.6014 (t70) REVERT: By 5 ILE cc_start: 0.5565 (OUTLIER) cc_final: 0.4981 (mp) REVERT: Bz 4 ILE cc_start: 0.0907 (OUTLIER) cc_final: 0.0652 (mp) REVERT: Bz 13 LYS cc_start: 0.5841 (OUTLIER) cc_final: 0.5523 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7279 (mmtt) REVERT: Cb 253 ARG cc_start: 0.8020 (mtp85) cc_final: 0.7457 (mtm110) REVERT: Cb 263 LYS cc_start: 0.7967 (mttt) cc_final: 0.7389 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8201 (t0) cc_final: 0.7932 (t0) REVERT: Cd 210 SER cc_start: 0.8463 (p) cc_final: 0.8136 (p) REVERT: Cd 214 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: Cd 238 MET cc_start: 0.8496 (mmm) cc_final: 0.7975 (mmt) REVERT: Cd 241 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7794 (mt) REVERT: Cd 255 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7332 (mpt180) REVERT: Cf 4 MET cc_start: 0.6225 (mmt) cc_final: 0.5542 (tpt) REVERT: Cg 4 ILE cc_start: 0.0218 (OUTLIER) cc_final: -0.0094 (mp) REVERT: Cg 13 LYS cc_start: 0.6047 (OUTLIER) cc_final: 0.5357 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8205 (mptt) cc_final: 0.7323 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8504 (t0) cc_final: 0.7938 (t0) REVERT: Cj 791 GLN cc_start: 0.5638 (tt0) cc_final: 0.5169 (mp10) REVERT: Cj 814 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7714 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7125 (OUTLIER) cc_final: 0.6438 (ptpt) REVERT: Ck 115 MET cc_start: 0.8299 (tmm) cc_final: 0.7917 (tmm) REVERT: Ck 160 LEU cc_start: 0.7732 (mt) cc_final: 0.7364 (mp) REVERT: Ck 210 SER cc_start: 0.8653 (p) cc_final: 0.8250 (p) REVERT: Cp 237 LYS cc_start: 0.7972 (mmtt) cc_final: 0.7755 (mmtt) REVERT: Cp 253 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7700 (mtm110) REVERT: Cp 263 LYS cc_start: 0.8168 (mttt) cc_final: 0.7477 (mtmm) REVERT: Cp 268 ASP cc_start: 0.7961 (t0) cc_final: 0.7322 (t0) REVERT: Cq 814 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7172 (tm130) REVERT: Cr 214 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8050 (mpt) REVERT: Cr 242 ILE cc_start: 0.8548 (mt) cc_final: 0.8250 (mt) REVERT: Cs 12 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.5908 (t-90) REVERT: Ct 5 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5111 (mp) REVERT: Cu 4 ILE cc_start: 0.0179 (OUTLIER) cc_final: -0.0049 (mp) REVERT: Cu 13 LYS cc_start: 0.5899 (OUTLIER) cc_final: 0.5178 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8363 (m-80) cc_final: 0.7954 (m-80) REVERT: Cw 237 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7596 (mmtp) REVERT: Cw 263 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7172 (mtmm) REVERT: Cw 268 ASP cc_start: 0.8494 (t0) cc_final: 0.7892 (t0) REVERT: Cy 115 MET cc_start: 0.8714 (tmm) cc_final: 0.7657 (tmm) REVERT: Cy 170 ARG cc_start: 0.8871 (mpp80) cc_final: 0.8486 (mtm180) REVERT: Cy 182 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7275 (mt) REVERT: Cy 214 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8097 (mtt) REVERT: Cz 12 HIS cc_start: 0.6640 (OUTLIER) cc_final: 0.5289 (t70) REVERT: Db 4 ILE cc_start: 0.1083 (OUTLIER) cc_final: 0.0822 (mp) REVERT: Db 13 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.5259 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8007 (mmtm) REVERT: Dd 251 GLN cc_start: 0.8190 (mt0) cc_final: 0.7352 (mp10) REVERT: Dd 263 LYS cc_start: 0.8018 (mttt) cc_final: 0.7555 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8400 (t0) cc_final: 0.7851 (t0) REVERT: Df 110 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6562 (tptm) REVERT: Df 214 MET cc_start: 0.8760 (mmt) cc_final: 0.8267 (mpp) REVERT: Dg 12 HIS cc_start: 0.6547 (OUTLIER) cc_final: 0.6265 (t70) REVERT: Di 13 LYS cc_start: 0.6009 (OUTLIER) cc_final: 0.5366 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9019 (mm) cc_final: 0.8751 (mm) REVERT: Dk 237 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7865 (mmtp) REVERT: Dk 253 ARG cc_start: 0.7789 (mtp-110) cc_final: 0.7492 (mtm110) REVERT: Dk 268 ASP cc_start: 0.8123 (t0) cc_final: 0.7527 (t0) REVERT: Dm 182 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7735 (mt) REVERT: Dm 210 SER cc_start: 0.8694 (p) cc_final: 0.8276 (p) REVERT: Dm 214 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8152 (mtt) REVERT: Dm 219 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8553 (mtpt) REVERT: Dr 237 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7832 (mptt) REVERT: Dr 253 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7758 (mtp-110) REVERT: Dr 268 ASP cc_start: 0.8217 (t0) cc_final: 0.7743 (t0) REVERT: Ds 814 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8070 (tp-100) REVERT: Ds 822 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8342 (mm-30) REVERT: Dt 110 LYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6299 (mttt) REVERT: Dt 115 MET cc_start: 0.8010 (tmm) cc_final: 0.7785 (tmm) REVERT: Dt 170 ARG cc_start: 0.8976 (mpp80) cc_final: 0.8640 (mtm180) REVERT: Dt 240 THR cc_start: 0.8603 (OUTLIER) cc_final: 0.8252 (t) REVERT: Dy 237 LYS cc_start: 0.8319 (mmtt) cc_final: 0.8021 (mmmt) REVERT: Dy 243 MET cc_start: 0.7576 (ttp) cc_final: 0.7310 (ttm) REVERT: Dy 253 ARG cc_start: 0.7932 (mtm180) cc_final: 0.7663 (mtm110) REVERT: Dy 263 LYS cc_start: 0.8121 (mttt) cc_final: 0.7593 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8224 (t0) cc_final: 0.7593 (t0) REVERT: Dz 795 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7190 (mp10) REVERT: Ea 160 LEU cc_start: 0.7920 (mt) cc_final: 0.7607 (mt) REVERT: Ea 240 THR cc_start: 0.8853 (OUTLIER) cc_final: 0.8551 (t) REVERT: Eb 12 HIS cc_start: 0.6121 (OUTLIER) cc_final: 0.4835 (t70) REVERT: Ec 4 MET cc_start: 0.5985 (mmt) cc_final: 0.5048 (tpt) REVERT: Ed 13 LYS cc_start: 0.5361 (OUTLIER) cc_final: 0.4968 (mmtm) REVERT: Ef 263 LYS cc_start: 0.7985 (mttt) cc_final: 0.7495 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8436 (t0) cc_final: 0.7995 (t0) REVERT: Eh 222 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8191 (m110) REVERT: Eh 241 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.7866 (mt) REVERT: Ei 6 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6041 (mm) REVERT: Ei 12 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.6071 (t70) REVERT: Ek 4 ILE cc_start: 0.1248 (OUTLIER) cc_final: 0.0977 (mp) REVERT: Ek 13 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5555 (mmtm) REVERT: Em 237 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7296 (mmtt) REVERT: Em 253 ARG cc_start: 0.7939 (mtp85) cc_final: 0.7377 (mtm110) REVERT: Em 263 LYS cc_start: 0.7952 (mttt) cc_final: 0.7361 (mtmm) REVERT: Em 268 ASP cc_start: 0.8027 (t0) cc_final: 0.7534 (t0) REVERT: Eo 179 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8439 (mt) REVERT: Eo 182 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7369 (mt) REVERT: Eo 210 SER cc_start: 0.8497 (p) cc_final: 0.8199 (p) REVERT: Eo 238 MET cc_start: 0.8533 (mmm) cc_final: 0.7743 (mmt) REVERT: Eo 241 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7724 (mt) REVERT: Eq 4 MET cc_start: 0.6139 (mmt) cc_final: 0.5488 (tpt) REVERT: Er 4 ILE cc_start: 0.0899 (OUTLIER) cc_final: 0.0644 (mp) REVERT: Er 13 LYS cc_start: 0.6074 (OUTLIER) cc_final: 0.5395 (mmtm) REVERT: Et 237 LYS cc_start: 0.8221 (mptt) cc_final: 0.7318 (mmtt) REVERT: Et 241 TYR cc_start: 0.8243 (m-80) cc_final: 0.7966 (m-80) REVERT: Et 268 ASP cc_start: 0.8492 (t0) cc_final: 0.7902 (t0) REVERT: Eu 814 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7705 (tm-30) REVERT: Ev 141 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7924 (ttpp) REVERT: Ev 160 LEU cc_start: 0.7716 (mt) cc_final: 0.7359 (mp) REVERT: Ev 231 ARG cc_start: 0.7753 (mmt180) cc_final: 0.7519 (mmt180) outliers start: 207 outliers final: 117 residues processed: 906 average time/residue: 0.2627 time to fit residues: 385.2452 Evaluate side-chains 935 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 744 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 215 ILE Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ah residue 12 HIS Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 10 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Al residue 267 GLU Chi-restraints excluded: chain An residue 110 LYS Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain Au residue 209 THR Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 182 LEU Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bn residue 267 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 231 THR Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 182 LEU Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 179 LEU Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cd residue 255 ARG Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 214 MET Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Cs residue 12 HIS Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 3 SER Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 10 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 182 LEU Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dg residue 12 HIS Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 182 LEU Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 214 MET Chi-restraints excluded: chain Dm residue 219 LYS Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 178 SER Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 3 SER Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dw residue 13 LYS Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 178 SER Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 215 ILE Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 249 SER Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 295 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 463 optimal weight: 4.9990 chunk 436 optimal weight: 3.9990 chunk 84 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 402 optimal weight: 0.0770 chunk 477 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** As 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 814 GLN ** Cj 795 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.131105 restraints weight = 44666.219| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.65 r_work: 0.3368 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 42822 Z= 0.142 Angle : 0.493 9.872 58122 Z= 0.244 Chirality : 0.042 0.229 6660 Planarity : 0.004 0.046 7470 Dihedral : 5.066 80.403 5962 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.58 % Allowed : 21.09 % Favored : 74.34 % 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 are not related in a simple way. whole: 0.60 (0.12), residues: 5202 helix: 2.18 (0.13), residues: 1332 sheet: -0.45 (0.14), residues: 1206 loop : -0.01 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGCb 233 TYR 0.013 0.001 TYRDm 194 PHE 0.011 0.001 PHEEf 264 TRP 0.006 0.001 TRPAn 206 HIS 0.003 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00349 (42822) covalent geometry : angle 0.49275 (58122) hydrogen bonds : bond 0.03262 ( 1756) hydrogen bonds : angle 4.41066 ( 4860) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 747 time to evaluate : 1.661 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: Ab 5 ILE cc_start: 0.4858 (OUTLIER) cc_final: 0.3903 (mp) REVERT: Ae 237 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7766 (mmtt) REVERT: Ae 250 LEU cc_start: 0.7177 (mt) cc_final: 0.6806 (mp) REVERT: Ae 263 LYS cc_start: 0.8183 (mttt) cc_final: 0.7495 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8016 (t0) cc_final: 0.7356 (t0) REVERT: Af 814 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7236 (tm130) REVERT: Ag 182 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7584 (mt) REVERT: Ah 12 HIS cc_start: 0.6673 (OUTLIER) cc_final: 0.6185 (t-90) REVERT: Aj 13 LYS cc_start: 0.5764 (OUTLIER) cc_final: 0.5230 (mmtm) REVERT: Al 210 TYR cc_start: 0.8448 (m-80) cc_final: 0.8027 (m-80) REVERT: Al 237 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7590 (mmtp) REVERT: Al 268 ASP cc_start: 0.8528 (t0) cc_final: 0.7821 (t0) REVERT: An 110 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6595 (ptpt) REVERT: An 115 MET cc_start: 0.8624 (tmm) cc_final: 0.7783 (tmm) REVERT: An 214 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8163 (mtt) REVERT: Ao 12 HIS cc_start: 0.6757 (OUTLIER) cc_final: 0.5426 (t70) REVERT: Aq 4 ILE cc_start: 0.1531 (OUTLIER) cc_final: 0.1208 (mp) REVERT: Aq 13 LYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5679 (mmtm) REVERT: As 237 LYS cc_start: 0.8358 (mmtt) cc_final: 0.8040 (mmtm) REVERT: As 253 ARG cc_start: 0.8136 (mtm110) cc_final: 0.7897 (mtm110) REVERT: As 263 LYS cc_start: 0.8033 (mttt) cc_final: 0.7600 (mtmm) REVERT: As 268 ASP cc_start: 0.8438 (t0) cc_final: 0.7892 (t0) REVERT: Av 12 HIS cc_start: 0.6324 (OUTLIER) cc_final: 0.6005 (t70) REVERT: Ax 13 LYS cc_start: 0.5966 (OUTLIER) cc_final: 0.5345 (mmtm) REVERT: Az 209 ILE cc_start: 0.9042 (mm) cc_final: 0.8796 (mm) REVERT: Az 237 LYS cc_start: 0.8336 (mmtt) cc_final: 0.7932 (mmtp) REVERT: Az 268 ASP cc_start: 0.8165 (t0) cc_final: 0.7553 (t0) REVERT: Ba 820 TYR cc_start: 0.8857 (t80) cc_final: 0.8209 (t80) REVERT: Bb 182 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7759 (mt) REVERT: Bb 210 SER cc_start: 0.8718 (p) cc_final: 0.8318 (p) REVERT: Bb 214 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8216 (mtp) REVERT: Bb 219 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8523 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8272 (mmtt) cc_final: 0.7899 (mmtm) REVERT: Bg 243 MET cc_start: 0.7610 (ttp) cc_final: 0.7194 (ttp) REVERT: Bg 253 ARG cc_start: 0.8059 (mtm180) cc_final: 0.7811 (mtm110) REVERT: Bg 268 ASP cc_start: 0.8265 (t0) cc_final: 0.7770 (t0) REVERT: Bh 814 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8053 (tp-100) REVERT: Bh 822 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8320 (mm-30) REVERT: Bi 107 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6878 (mt) REVERT: Bi 110 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.5781 (ptpt) REVERT: Bi 115 MET cc_start: 0.8002 (tmm) cc_final: 0.7617 (tmm) REVERT: Bi 170 ARG cc_start: 0.8944 (mpp80) cc_final: 0.8607 (mtm180) REVERT: Bi 240 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8221 (t) REVERT: Bj 12 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.6248 (t70) REVERT: Bk 5 ILE cc_start: 0.5942 (OUTLIER) cc_final: 0.5403 (mp) REVERT: Bl 13 LYS cc_start: 0.5915 (OUTLIER) cc_final: 0.5681 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8314 (mmtt) cc_final: 0.8019 (mmmt) REVERT: Bn 243 MET cc_start: 0.7587 (ttp) cc_final: 0.7305 (ttm) REVERT: Bn 253 ARG cc_start: 0.8256 (mtm110) cc_final: 0.7916 (mtm110) REVERT: Bn 263 LYS cc_start: 0.7837 (mttt) cc_final: 0.7333 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8223 (t0) cc_final: 0.7556 (t0) REVERT: Bo 822 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8023 (tp30) REVERT: Bp 160 LEU cc_start: 0.7955 (mt) cc_final: 0.7647 (mt) REVERT: Bp 214 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7413 (mmm) REVERT: Bp 242 ILE cc_start: 0.8689 (mt) cc_final: 0.8383 (mt) REVERT: Bq 12 HIS cc_start: 0.6363 (OUTLIER) cc_final: 0.5018 (t70) REVERT: Bs 13 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.6191 (mmtm) REVERT: Bu 237 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7543 (mmmt) REVERT: Bu 253 ARG cc_start: 0.7999 (mtm110) cc_final: 0.7681 (ptm-80) REVERT: Bu 263 LYS cc_start: 0.7906 (mttt) cc_final: 0.7567 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8396 (t0) cc_final: 0.7829 (t0) REVERT: Bw 110 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6562 (tptm) REVERT: Bw 182 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7186 (mt) REVERT: Bw 222 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8237 (m110) REVERT: Bw 241 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7845 (mt) REVERT: Bx 6 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6054 (mm) REVERT: Bx 12 HIS cc_start: 0.6497 (OUTLIER) cc_final: 0.6036 (t70) REVERT: By 5 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.4969 (mp) REVERT: Bz 4 ILE cc_start: 0.0958 (OUTLIER) cc_final: 0.0727 (mp) REVERT: Bz 13 LYS cc_start: 0.5971 (OUTLIER) cc_final: 0.5721 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7799 (mmtt) cc_final: 0.7310 (mmtt) REVERT: Cb 253 ARG cc_start: 0.8078 (mtp85) cc_final: 0.7498 (mtm110) REVERT: Cb 263 LYS cc_start: 0.7980 (mttt) cc_final: 0.7398 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8259 (t0) cc_final: 0.7735 (t0) REVERT: Cd 116 THR cc_start: 0.8156 (t) cc_final: 0.7840 (p) REVERT: Cd 210 SER cc_start: 0.8537 (p) cc_final: 0.8196 (p) REVERT: Cd 214 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7737 (mtt) REVERT: Cd 238 MET cc_start: 0.8460 (mmm) cc_final: 0.7991 (mmt) REVERT: Cd 241 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7797 (mt) REVERT: Cd 255 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7400 (mpt180) REVERT: Cf 4 MET cc_start: 0.6020 (mmt) cc_final: 0.5339 (tpt) REVERT: Cg 4 ILE cc_start: 0.0286 (OUTLIER) cc_final: -0.0034 (mp) REVERT: Cg 13 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5383 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8386 (mptt) cc_final: 0.7572 (mmtt) REVERT: Ci 241 TYR cc_start: 0.8201 (m-80) cc_final: 0.7982 (m-80) REVERT: Ci 268 ASP cc_start: 0.8530 (t0) cc_final: 0.7985 (t0) REVERT: Cj 814 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.6417 (ptpt) REVERT: Ck 160 LEU cc_start: 0.7776 (mt) cc_final: 0.7416 (mp) REVERT: Ck 210 SER cc_start: 0.8683 (p) cc_final: 0.8299 (p) REVERT: Cp 237 LYS cc_start: 0.7990 (mmtt) cc_final: 0.7765 (mmtt) REVERT: Cp 253 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7786 (mtm110) REVERT: Cp 263 LYS cc_start: 0.8206 (mttt) cc_final: 0.7510 (mtmm) REVERT: Cp 268 ASP cc_start: 0.7978 (t0) cc_final: 0.7332 (t0) REVERT: Cq 814 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7220 (tm130) REVERT: Cr 242 ILE cc_start: 0.8558 (mt) cc_final: 0.8253 (mt) REVERT: Cs 12 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.6006 (t-90) REVERT: Ct 5 ILE cc_start: 0.6013 (OUTLIER) cc_final: 0.5255 (mp) REVERT: Cu 4 ILE cc_start: 0.0409 (OUTLIER) cc_final: 0.0149 (mp) REVERT: Cu 13 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5190 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8385 (m-80) cc_final: 0.7976 (m-80) REVERT: Cw 237 LYS cc_start: 0.7977 (mmtt) cc_final: 0.7609 (mmtp) REVERT: Cw 263 LYS cc_start: 0.8005 (mmmt) cc_final: 0.7195 (mtmm) REVERT: Cw 268 ASP cc_start: 0.8511 (t0) cc_final: 0.7829 (t0) REVERT: Cy 115 MET cc_start: 0.8705 (tmm) cc_final: 0.7731 (tmm) REVERT: Cy 182 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7349 (mt) REVERT: Cy 214 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: Cz 12 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.5292 (t70) REVERT: Db 4 ILE cc_start: 0.1172 (OUTLIER) cc_final: 0.0917 (mp) REVERT: Db 13 LYS cc_start: 0.5854 (OUTLIER) cc_final: 0.5265 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8206 (mmtm) REVERT: Dd 251 GLN cc_start: 0.8171 (mt0) cc_final: 0.7344 (mp10) REVERT: Dd 263 LYS cc_start: 0.8062 (mttt) cc_final: 0.7607 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8414 (t0) cc_final: 0.7855 (t0) REVERT: Df 110 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6588 (tptm) REVERT: Df 115 MET cc_start: 0.8332 (tmm) cc_final: 0.8024 (tmm) REVERT: Df 214 MET cc_start: 0.8777 (mmt) cc_final: 0.8253 (mpp) REVERT: Dg 12 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.6274 (t70) REVERT: Di 13 LYS cc_start: 0.6028 (OUTLIER) cc_final: 0.5379 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9019 (mm) cc_final: 0.8750 (mm) REVERT: Dk 237 LYS cc_start: 0.8314 (mmtt) cc_final: 0.7929 (mmtp) REVERT: Dk 253 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7567 (mtm110) REVERT: Dk 268 ASP cc_start: 0.8138 (t0) cc_final: 0.7534 (t0) REVERT: Dm 182 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7750 (mt) REVERT: Dm 210 SER cc_start: 0.8710 (p) cc_final: 0.8301 (p) REVERT: Dm 214 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8226 (mtt) REVERT: Dm 219 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8548 (mtpt) REVERT: Dr 237 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7884 (mptt) REVERT: Dr 253 ARG cc_start: 0.8110 (mtp85) cc_final: 0.7831 (mtp-110) REVERT: Dr 268 ASP cc_start: 0.8223 (t0) cc_final: 0.7737 (t0) REVERT: Ds 814 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8091 (tp-100) REVERT: Ds 822 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8294 (mm-30) REVERT: Dt 110 LYS cc_start: 0.6841 (OUTLIER) cc_final: 0.6275 (mttt) REVERT: Dt 170 ARG cc_start: 0.9010 (mpp80) cc_final: 0.8676 (mtm180) REVERT: Dt 240 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8275 (t) REVERT: Dy 237 LYS cc_start: 0.8333 (mmtt) cc_final: 0.8030 (mmmt) REVERT: Dy 243 MET cc_start: 0.7592 (ttp) cc_final: 0.7314 (ttm) REVERT: Dy 253 ARG cc_start: 0.8001 (mtm180) cc_final: 0.7697 (mtm110) REVERT: Dy 263 LYS cc_start: 0.8189 (mttt) cc_final: 0.7707 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8237 (t0) cc_final: 0.7589 (t0) REVERT: Dz 795 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: Ea 160 LEU cc_start: 0.7957 (mt) cc_final: 0.7650 (mt) REVERT: Ea 240 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8543 (t) REVERT: Ea 242 ILE cc_start: 0.8667 (mt) cc_final: 0.8360 (mt) REVERT: Eb 12 HIS cc_start: 0.6139 (OUTLIER) cc_final: 0.4902 (t70) REVERT: Ec 4 MET cc_start: 0.6017 (mmt) cc_final: 0.5118 (tpt) REVERT: Ed 13 LYS cc_start: 0.5471 (OUTLIER) cc_final: 0.5084 (mmtm) REVERT: Ef 263 LYS cc_start: 0.8081 (mttt) cc_final: 0.7479 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8486 (t0) cc_final: 0.8032 (t0) REVERT: Eh 222 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8223 (m110) REVERT: Eh 241 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.7878 (mt) REVERT: Ei 6 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6047 (mm) REVERT: Ei 12 HIS cc_start: 0.6779 (OUTLIER) cc_final: 0.6115 (t70) REVERT: Ek 4 ILE cc_start: 0.1037 (OUTLIER) cc_final: 0.0747 (mp) REVERT: Ek 13 LYS cc_start: 0.5888 (OUTLIER) cc_final: 0.5484 (mmtm) REVERT: Em 237 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7324 (mmtt) REVERT: Em 253 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7375 (mtm110) REVERT: Em 263 LYS cc_start: 0.7956 (mttt) cc_final: 0.7367 (mtmm) REVERT: Em 268 ASP cc_start: 0.8057 (t0) cc_final: 0.7517 (t0) REVERT: Eo 179 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (mt) REVERT: Eo 182 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7452 (mt) REVERT: Eo 210 SER cc_start: 0.8544 (p) cc_final: 0.8246 (p) REVERT: Eo 238 MET cc_start: 0.8560 (mmm) cc_final: 0.7807 (mmp) REVERT: Eo 241 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7741 (mt) REVERT: Eo 255 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7499 (mpt180) REVERT: Eq 4 MET cc_start: 0.6176 (mmt) cc_final: 0.5488 (tpt) REVERT: Er 4 ILE cc_start: 0.0779 (OUTLIER) cc_final: 0.0511 (mp) REVERT: Er 13 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5483 (mmtm) REVERT: Et 237 LYS cc_start: 0.8232 (mptt) cc_final: 0.7336 (mmtt) REVERT: Et 241 TYR cc_start: 0.8251 (m-80) cc_final: 0.7970 (m-80) REVERT: Et 268 ASP cc_start: 0.8522 (t0) cc_final: 0.7982 (t0) REVERT: Eu 814 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7728 (tm-30) REVERT: Ev 141 LYS cc_start: 0.8249 (ttpt) cc_final: 0.7933 (ttpp) REVERT: Ev 160 LEU cc_start: 0.7679 (mt) cc_final: 0.7309 (mp) REVERT: Ev 231 ARG cc_start: 0.7787 (mmt180) cc_final: 0.7556 (mmt180) outliers start: 210 outliers final: 125 residues processed: 911 average time/residue: 0.2561 time to fit residues: 379.9548 Evaluate side-chains 947 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 745 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 215 ILE Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ah residue 12 HIS Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 10 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Al residue 267 GLU Chi-restraints excluded: chain An residue 110 LYS Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain Au residue 209 THR Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 252 VAL Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 182 LEU Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 107 ILE Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 5 ILE Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bn residue 267 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 231 THR Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 182 LEU Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 214 MET Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cd residue 255 ARG Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 10 THR Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 249 SER Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Cs residue 12 HIS Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 10 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 182 LEU Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 252 VAL Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dg residue 12 HIS Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 10 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 168 VAL Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 182 LEU Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 214 MET Chi-restraints excluded: chain Dm residue 219 LYS Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Dr residue 267 GLU Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 178 SER Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 3 SER Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dw residue 13 LYS Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 178 SER Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ei residue 12 HIS Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 215 ILE Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Eo residue 255 ARG Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 249 SER Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 86 optimal weight: 0.5980 chunk 481 optimal weight: 0.6980 chunk 269 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 483 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 382 optimal weight: 0.9980 chunk 167 optimal weight: 0.0980 chunk 135 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 423 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ae 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** As 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 814 GLN En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.167922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.132159 restraints weight = 44581.647| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.65 r_work: 0.3380 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42822 Z= 0.120 Angle : 0.473 7.637 58122 Z= 0.236 Chirality : 0.042 0.202 6660 Planarity : 0.004 0.038 7470 Dihedral : 4.990 79.597 5962 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.38 % Allowed : 21.20 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.12), residues: 5202 helix: 2.24 (0.13), residues: 1332 sheet: -0.44 (0.14), residues: 1206 loop : 0.06 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGEm 233 TYR 0.012 0.001 TYRDm 194 PHE 0.018 0.001 PHEEl 2 TRP 0.005 0.001 TRPDd 221 HIS 0.003 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00292 (42822) covalent geometry : angle 0.47308 (58122) hydrogen bonds : bond 0.03157 ( 1756) hydrogen bonds : angle 4.38337 ( 4860) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10404 Ramachandran restraints generated. 5202 Oldfield, 0 Emsley, 5202 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 947 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 746 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Ab 5 ILE cc_start: 0.4661 (OUTLIER) cc_final: 0.3794 (mp) REVERT: Ae 237 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7613 (mptt) REVERT: Ae 250 LEU cc_start: 0.7190 (mt) cc_final: 0.6878 (mp) REVERT: Ae 263 LYS cc_start: 0.8171 (mttt) cc_final: 0.7484 (mtmm) REVERT: Ae 268 ASP cc_start: 0.8025 (t0) cc_final: 0.7360 (t0) REVERT: Af 814 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7264 (tm130) REVERT: Ag 182 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7574 (mt) REVERT: Ah 12 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.5889 (t-90) REVERT: Aj 13 LYS cc_start: 0.5723 (OUTLIER) cc_final: 0.5143 (mmtm) REVERT: Al 210 TYR cc_start: 0.8439 (m-80) cc_final: 0.8071 (m-80) REVERT: Al 237 LYS cc_start: 0.7951 (mmtt) cc_final: 0.7581 (mmtp) REVERT: Al 253 ARG cc_start: 0.8009 (mtm110) cc_final: 0.7440 (mtm110) REVERT: Al 268 ASP cc_start: 0.8520 (t0) cc_final: 0.7807 (t0) REVERT: An 110 LYS cc_start: 0.7254 (OUTLIER) cc_final: 0.6576 (ptpt) REVERT: An 115 MET cc_start: 0.8630 (tmm) cc_final: 0.7760 (tmm) REVERT: An 214 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8063 (mtt) REVERT: Ao 12 HIS cc_start: 0.6729 (OUTLIER) cc_final: 0.5418 (t70) REVERT: Aq 4 ILE cc_start: 0.1545 (OUTLIER) cc_final: 0.1229 (mp) REVERT: Aq 13 LYS cc_start: 0.6093 (OUTLIER) cc_final: 0.5636 (mmtm) REVERT: As 237 LYS cc_start: 0.8356 (mmtt) cc_final: 0.8039 (mmtm) REVERT: As 253 ARG cc_start: 0.8127 (mtm110) cc_final: 0.7917 (mtm110) REVERT: As 263 LYS cc_start: 0.8026 (mttt) cc_final: 0.7594 (mtmm) REVERT: As 268 ASP cc_start: 0.8417 (t0) cc_final: 0.7869 (t0) REVERT: Av 12 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.5998 (t70) REVERT: Ax 13 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5350 (mmtm) REVERT: Az 209 ILE cc_start: 0.9046 (mm) cc_final: 0.8791 (mm) REVERT: Az 237 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7960 (mmtp) REVERT: Az 253 ARG cc_start: 0.7824 (mtp-110) cc_final: 0.7582 (mtm110) REVERT: Az 268 ASP cc_start: 0.8167 (t0) cc_final: 0.7559 (t0) REVERT: Ba 820 TYR cc_start: 0.8848 (t80) cc_final: 0.8211 (t80) REVERT: Bb 182 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7762 (mt) REVERT: Bb 210 SER cc_start: 0.8690 (p) cc_final: 0.8286 (p) REVERT: Bb 214 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8164 (mtp) REVERT: Bb 219 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8530 (mtpt) REVERT: Bg 237 LYS cc_start: 0.8390 (mmtt) cc_final: 0.8043 (mmtm) REVERT: Bg 243 MET cc_start: 0.7589 (ttp) cc_final: 0.7184 (ttp) REVERT: Bg 253 ARG cc_start: 0.8073 (mtm180) cc_final: 0.7833 (mtm110) REVERT: Bg 268 ASP cc_start: 0.8246 (t0) cc_final: 0.7735 (t0) REVERT: Bh 814 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8034 (tp-100) REVERT: Bh 822 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8311 (mm-30) REVERT: Bi 107 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6862 (mp) REVERT: Bi 110 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.5848 (ptpt) REVERT: Bi 115 MET cc_start: 0.8148 (tmm) cc_final: 0.7632 (tmm) REVERT: Bi 170 ARG cc_start: 0.8921 (mpp80) cc_final: 0.8584 (mtm180) REVERT: Bi 240 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8066 (t) REVERT: Bj 12 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6226 (t70) REVERT: Bk 5 ILE cc_start: 0.5641 (OUTLIER) cc_final: 0.5153 (mp) REVERT: Bl 13 LYS cc_start: 0.5924 (OUTLIER) cc_final: 0.5707 (mmtm) REVERT: Bn 237 LYS cc_start: 0.8293 (mmtt) cc_final: 0.7993 (mmmt) REVERT: Bn 243 MET cc_start: 0.7565 (ttp) cc_final: 0.7294 (ttm) REVERT: Bn 253 ARG cc_start: 0.8251 (mtm110) cc_final: 0.7939 (mtm110) REVERT: Bn 263 LYS cc_start: 0.7818 (mttt) cc_final: 0.7316 (mtmm) REVERT: Bn 268 ASP cc_start: 0.8216 (t0) cc_final: 0.7555 (t0) REVERT: Bo 822 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8001 (tp30) REVERT: Bp 160 LEU cc_start: 0.7938 (mt) cc_final: 0.7642 (mt) REVERT: Bp 214 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7420 (mmm) REVERT: Bp 242 ILE cc_start: 0.8666 (mt) cc_final: 0.8359 (mt) REVERT: Bq 12 HIS cc_start: 0.6255 (OUTLIER) cc_final: 0.5894 (t70) REVERT: Bs 13 LYS cc_start: 0.6428 (OUTLIER) cc_final: 0.6225 (mmtm) REVERT: Bu 237 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7523 (mmmt) REVERT: Bu 253 ARG cc_start: 0.7962 (mtm110) cc_final: 0.7711 (ptm-80) REVERT: Bu 263 LYS cc_start: 0.7868 (mttt) cc_final: 0.7499 (mtmm) REVERT: Bu 268 ASP cc_start: 0.8389 (t0) cc_final: 0.7828 (t0) REVERT: Bw 110 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6545 (tptm) REVERT: Bw 182 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7154 (mt) REVERT: Bw 222 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8230 (m110) REVERT: Bw 241 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.7870 (mt) REVERT: Bx 6 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.6056 (mm) REVERT: Bx 12 HIS cc_start: 0.6467 (OUTLIER) cc_final: 0.6014 (t70) REVERT: By 5 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.4922 (mp) REVERT: Bz 4 ILE cc_start: 0.0984 (OUTLIER) cc_final: 0.0747 (mp) REVERT: Bz 13 LYS cc_start: 0.5960 (OUTLIER) cc_final: 0.5622 (mmtm) REVERT: Cb 237 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7289 (mmtt) REVERT: Cb 253 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7513 (mtm110) REVERT: Cb 263 LYS cc_start: 0.7974 (mttt) cc_final: 0.7388 (mtmm) REVERT: Cb 268 ASP cc_start: 0.8202 (t0) cc_final: 0.7712 (t0) REVERT: Cd 116 THR cc_start: 0.8169 (t) cc_final: 0.7823 (p) REVERT: Cd 210 SER cc_start: 0.8477 (p) cc_final: 0.8148 (p) REVERT: Cd 238 MET cc_start: 0.8457 (mmm) cc_final: 0.7990 (mmt) REVERT: Cd 241 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.7783 (mt) REVERT: Cf 4 MET cc_start: 0.6208 (mmt) cc_final: 0.5536 (tpt) REVERT: Cg 4 ILE cc_start: 0.0289 (OUTLIER) cc_final: -0.0034 (mp) REVERT: Cg 13 LYS cc_start: 0.6051 (OUTLIER) cc_final: 0.5359 (mmtm) REVERT: Ci 237 LYS cc_start: 0.8369 (mptt) cc_final: 0.7551 (mmtt) REVERT: Ci 268 ASP cc_start: 0.8507 (t0) cc_final: 0.7964 (t0) REVERT: Cj 814 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7732 (tm-30) REVERT: Ck 110 LYS cc_start: 0.7269 (OUTLIER) cc_final: 0.6431 (ptpt) REVERT: Ck 160 LEU cc_start: 0.7751 (mt) cc_final: 0.7392 (mp) REVERT: Ck 210 SER cc_start: 0.8662 (p) cc_final: 0.8262 (p) REVERT: Cp 237 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7760 (mmtt) REVERT: Cp 253 ARG cc_start: 0.8177 (mtp85) cc_final: 0.7735 (mtm110) REVERT: Cp 263 LYS cc_start: 0.8180 (mttt) cc_final: 0.7484 (mtmm) REVERT: Cp 268 ASP cc_start: 0.7974 (t0) cc_final: 0.7324 (t0) REVERT: Cq 814 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7237 (tm130) REVERT: Cr 242 ILE cc_start: 0.8560 (mt) cc_final: 0.8259 (mt) REVERT: Cs 12 HIS cc_start: 0.6449 (OUTLIER) cc_final: 0.5849 (t-90) REVERT: Ct 5 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5257 (mp) REVERT: Cu 4 ILE cc_start: 0.0402 (OUTLIER) cc_final: 0.0150 (mp) REVERT: Cu 13 LYS cc_start: 0.5904 (OUTLIER) cc_final: 0.5174 (mmtm) REVERT: Cw 210 TYR cc_start: 0.8381 (m-80) cc_final: 0.7972 (m-80) REVERT: Cw 237 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7599 (mmtp) REVERT: Cw 263 LYS cc_start: 0.7997 (mmmt) cc_final: 0.7185 (mtmm) REVERT: Cw 268 ASP cc_start: 0.8502 (t0) cc_final: 0.7769 (t0) REVERT: Cy 115 MET cc_start: 0.8723 (tmm) cc_final: 0.7733 (tmm) REVERT: Cy 182 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7295 (mt) REVERT: Cy 214 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8104 (mtt) REVERT: Cz 12 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.5285 (t70) REVERT: Db 4 ILE cc_start: 0.1470 (OUTLIER) cc_final: 0.1210 (mp) REVERT: Db 13 LYS cc_start: 0.5826 (OUTLIER) cc_final: 0.5201 (mmtm) REVERT: Dd 237 LYS cc_start: 0.8482 (mmtt) cc_final: 0.8190 (mmtm) REVERT: Dd 251 GLN cc_start: 0.8186 (mt0) cc_final: 0.7683 (mt0) REVERT: Dd 263 LYS cc_start: 0.8059 (mttt) cc_final: 0.7597 (mtmm) REVERT: Dd 268 ASP cc_start: 0.8392 (t0) cc_final: 0.7829 (t0) REVERT: Df 110 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6588 (tptm) REVERT: Df 214 MET cc_start: 0.8764 (mmt) cc_final: 0.8262 (mpp) REVERT: Dg 12 HIS cc_start: 0.6529 (OUTLIER) cc_final: 0.6232 (t70) REVERT: Di 13 LYS cc_start: 0.6005 (OUTLIER) cc_final: 0.5370 (mmtm) REVERT: Dk 209 ILE cc_start: 0.9019 (mm) cc_final: 0.8744 (mm) REVERT: Dk 237 LYS cc_start: 0.8302 (mmtt) cc_final: 0.7914 (mmtp) REVERT: Dk 253 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7434 (mtm110) REVERT: Dk 268 ASP cc_start: 0.8140 (t0) cc_final: 0.7536 (t0) REVERT: Dm 182 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7755 (mt) REVERT: Dm 210 SER cc_start: 0.8682 (p) cc_final: 0.8272 (p) REVERT: Dm 214 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8171 (mtt) REVERT: Dm 219 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8554 (mtpt) REVERT: Dr 237 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7872 (mptt) REVERT: Dr 253 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7853 (mtm110) REVERT: Dr 268 ASP cc_start: 0.8205 (t0) cc_final: 0.7732 (t0) REVERT: Ds 813 LYS cc_start: 0.8681 (mmtp) cc_final: 0.8335 (mttt) REVERT: Ds 814 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8087 (tp-100) REVERT: Ds 822 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8277 (mm-30) REVERT: Dt 110 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.6274 (mttt) REVERT: Dt 170 ARG cc_start: 0.8984 (mpp80) cc_final: 0.8648 (mtm180) REVERT: Dt 240 THR cc_start: 0.8619 (OUTLIER) cc_final: 0.8263 (t) REVERT: Dy 237 LYS cc_start: 0.8317 (mmtt) cc_final: 0.8011 (mmmt) REVERT: Dy 243 MET cc_start: 0.7576 (ttp) cc_final: 0.7309 (ttm) REVERT: Dy 253 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7708 (mtm110) REVERT: Dy 263 LYS cc_start: 0.8129 (mttt) cc_final: 0.7600 (mtmm) REVERT: Dy 268 ASP cc_start: 0.8226 (t0) cc_final: 0.7581 (t0) REVERT: Dz 795 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: Ea 160 LEU cc_start: 0.7928 (mt) cc_final: 0.7617 (mt) REVERT: Ea 240 THR cc_start: 0.8862 (OUTLIER) cc_final: 0.8541 (t) REVERT: Ea 242 ILE cc_start: 0.8644 (mt) cc_final: 0.8334 (mt) REVERT: Eb 12 HIS cc_start: 0.6107 (OUTLIER) cc_final: 0.4885 (t70) REVERT: Ec 4 MET cc_start: 0.5860 (mmt) cc_final: 0.4903 (tpt) REVERT: Ed 13 LYS cc_start: 0.5488 (OUTLIER) cc_final: 0.5114 (mmtm) REVERT: Ef 263 LYS cc_start: 0.8039 (mttt) cc_final: 0.7374 (mtmm) REVERT: Ef 268 ASP cc_start: 0.8445 (t0) cc_final: 0.7993 (t0) REVERT: Eh 182 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7140 (mt) REVERT: Eh 222 ASN cc_start: 0.8701 (OUTLIER) cc_final: 0.8212 (m110) REVERT: Eh 241 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.7887 (mt) REVERT: Ei 6 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6129 (mm) REVERT: Ek 4 ILE cc_start: 0.1079 (OUTLIER) cc_final: 0.0740 (mp) REVERT: Ek 13 LYS cc_start: 0.5929 (OUTLIER) cc_final: 0.5543 (mmtm) REVERT: Em 237 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7303 (mmtt) REVERT: Em 253 ARG cc_start: 0.7950 (mtp85) cc_final: 0.7312 (mtm110) REVERT: Em 263 LYS cc_start: 0.7949 (mttt) cc_final: 0.7354 (mtmm) REVERT: Em 268 ASP cc_start: 0.8036 (t0) cc_final: 0.7530 (t0) REVERT: Eo 179 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8422 (mt) REVERT: Eo 182 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7458 (mt) REVERT: Eo 210 SER cc_start: 0.8559 (p) cc_final: 0.8201 (p) REVERT: Eo 238 MET cc_start: 0.8533 (mmm) cc_final: 0.7773 (mmt) REVERT: Eo 241 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.7754 (mt) REVERT: Eo 255 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7483 (mpt180) REVERT: Eq 4 MET cc_start: 0.6117 (mmt) cc_final: 0.5434 (tpt) REVERT: Er 4 ILE cc_start: 0.0943 (OUTLIER) cc_final: 0.0685 (mp) REVERT: Er 13 LYS cc_start: 0.6060 (OUTLIER) cc_final: 0.5381 (mmtm) REVERT: Et 237 LYS cc_start: 0.8224 (mptt) cc_final: 0.7328 (mmtt) REVERT: Et 241 TYR cc_start: 0.8263 (m-80) cc_final: 0.7994 (m-80) REVERT: Et 268 ASP cc_start: 0.8501 (t0) cc_final: 0.7930 (t0) REVERT: Eu 814 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: Ev 141 LYS cc_start: 0.8242 (ttpt) cc_final: 0.7865 (tttp) REVERT: Ev 160 LEU cc_start: 0.7723 (mt) cc_final: 0.7368 (mp) REVERT: Ev 231 ARG cc_start: 0.7760 (mmt180) cc_final: 0.7527 (mmt180) outliers start: 201 outliers final: 121 residues processed: 903 average time/residue: 0.2652 time to fit residues: 388.9024 Evaluate side-chains 938 residues out of total 4590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 742 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 5 ILE Chi-restraints excluded: chain Ac residue 7 THR Chi-restraints excluded: chain Ac residue 10 THR Chi-restraints excluded: chain Ae residue 267 GLU Chi-restraints excluded: chain Af residue 814 GLN Chi-restraints excluded: chain Ag residue 128 VAL Chi-restraints excluded: chain Ag residue 182 LEU Chi-restraints excluded: chain Ag residue 215 ILE Chi-restraints excluded: chain Ag residue 241 LEU Chi-restraints excluded: chain Ag residue 252 VAL Chi-restraints excluded: chain Ah residue 12 HIS Chi-restraints excluded: chain Ai residue 5 ILE Chi-restraints excluded: chain Aj residue 7 THR Chi-restraints excluded: chain Aj residue 10 THR Chi-restraints excluded: chain Aj residue 13 LYS Chi-restraints excluded: chain Al residue 226 ASN Chi-restraints excluded: chain Al residue 267 GLU Chi-restraints excluded: chain An residue 110 LYS Chi-restraints excluded: chain An residue 128 VAL Chi-restraints excluded: chain An residue 214 MET Chi-restraints excluded: chain An residue 240 THR Chi-restraints excluded: chain An residue 246 LYS Chi-restraints excluded: chain Ao residue 12 HIS Chi-restraints excluded: chain Aq residue 4 ILE Chi-restraints excluded: chain Aq residue 7 THR Chi-restraints excluded: chain Aq residue 10 THR Chi-restraints excluded: chain Aq residue 13 LYS Chi-restraints excluded: chain Au residue 209 THR Chi-restraints excluded: chain Au residue 240 THR Chi-restraints excluded: chain Au residue 253 ASP Chi-restraints excluded: chain Av residue 12 HIS Chi-restraints excluded: chain Aw residue 4 MET Chi-restraints excluded: chain Ax residue 7 THR Chi-restraints excluded: chain Ax residue 10 THR Chi-restraints excluded: chain Ax residue 13 LYS Chi-restraints excluded: chain Bb residue 178 SER Chi-restraints excluded: chain Bb residue 182 LEU Chi-restraints excluded: chain Bb residue 214 MET Chi-restraints excluded: chain Bb residue 215 ILE Chi-restraints excluded: chain Bb residue 219 LYS Chi-restraints excluded: chain Bb residue 239 LEU Chi-restraints excluded: chain Bb residue 241 LEU Chi-restraints excluded: chain Be residue 7 THR Chi-restraints excluded: chain Be residue 13 LYS Chi-restraints excluded: chain Bg residue 267 GLU Chi-restraints excluded: chain Bh residue 822 GLU Chi-restraints excluded: chain Bi residue 107 ILE Chi-restraints excluded: chain Bi residue 110 LYS Chi-restraints excluded: chain Bi residue 128 VAL Chi-restraints excluded: chain Bi residue 214 MET Chi-restraints excluded: chain Bi residue 240 THR Chi-restraints excluded: chain Bj residue 12 HIS Chi-restraints excluded: chain Bk residue 5 ILE Chi-restraints excluded: chain Bl residue 3 SER Chi-restraints excluded: chain Bl residue 7 THR Chi-restraints excluded: chain Bl residue 10 THR Chi-restraints excluded: chain Bl residue 13 LYS Chi-restraints excluded: chain Bn residue 267 GLU Chi-restraints excluded: chain Bp residue 168 VAL Chi-restraints excluded: chain Bp residue 214 MET Chi-restraints excluded: chain Bp residue 240 THR Chi-restraints excluded: chain Bp residue 241 LEU Chi-restraints excluded: chain Bp residue 246 LYS Chi-restraints excluded: chain Bq residue 12 HIS Chi-restraints excluded: chain Bs residue 10 THR Chi-restraints excluded: chain Bs residue 13 LYS Chi-restraints excluded: chain Bu residue 231 THR Chi-restraints excluded: chain Bu residue 267 GLU Chi-restraints excluded: chain Bw residue 110 LYS Chi-restraints excluded: chain Bw residue 128 VAL Chi-restraints excluded: chain Bw residue 168 VAL Chi-restraints excluded: chain Bw residue 178 SER Chi-restraints excluded: chain Bw residue 182 LEU Chi-restraints excluded: chain Bw residue 209 THR Chi-restraints excluded: chain Bw residue 222 ASN Chi-restraints excluded: chain Bw residue 240 THR Chi-restraints excluded: chain Bw residue 241 LEU Chi-restraints excluded: chain Bx residue 6 LEU Chi-restraints excluded: chain Bx residue 12 HIS Chi-restraints excluded: chain By residue 4 MET Chi-restraints excluded: chain By residue 5 ILE Chi-restraints excluded: chain Bz residue 4 ILE Chi-restraints excluded: chain Bz residue 10 THR Chi-restraints excluded: chain Bz residue 13 LYS Chi-restraints excluded: chain Cb residue 267 GLU Chi-restraints excluded: chain Cc residue 802 LEU Chi-restraints excluded: chain Cd residue 128 VAL Chi-restraints excluded: chain Cd residue 215 ILE Chi-restraints excluded: chain Cd residue 241 LEU Chi-restraints excluded: chain Cg residue 4 ILE Chi-restraints excluded: chain Cg residue 10 THR Chi-restraints excluded: chain Cg residue 13 LYS Chi-restraints excluded: chain Ci residue 267 GLU Chi-restraints excluded: chain Cj residue 814 GLN Chi-restraints excluded: chain Ck residue 110 LYS Chi-restraints excluded: chain Ck residue 128 VAL Chi-restraints excluded: chain Ck residue 240 THR Chi-restraints excluded: chain Ck residue 241 LEU Chi-restraints excluded: chain Cm residue 4 MET Chi-restraints excluded: chain Cm residue 5 ILE Chi-restraints excluded: chain Cn residue 10 THR Chi-restraints excluded: chain Cp residue 267 GLU Chi-restraints excluded: chain Cq residue 814 GLN Chi-restraints excluded: chain Cr residue 128 VAL Chi-restraints excluded: chain Cr residue 240 THR Chi-restraints excluded: chain Cr residue 241 LEU Chi-restraints excluded: chain Cr residue 252 VAL Chi-restraints excluded: chain Cs residue 12 HIS Chi-restraints excluded: chain Ct residue 5 ILE Chi-restraints excluded: chain Cu residue 4 ILE Chi-restraints excluded: chain Cu residue 7 THR Chi-restraints excluded: chain Cu residue 10 THR Chi-restraints excluded: chain Cu residue 13 LYS Chi-restraints excluded: chain Cw residue 267 GLU Chi-restraints excluded: chain Cy residue 128 VAL Chi-restraints excluded: chain Cy residue 182 LEU Chi-restraints excluded: chain Cy residue 214 MET Chi-restraints excluded: chain Cy residue 218 THR Chi-restraints excluded: chain Cy residue 240 THR Chi-restraints excluded: chain Cz residue 12 HIS Chi-restraints excluded: chain Db residue 4 ILE Chi-restraints excluded: chain Db residue 7 THR Chi-restraints excluded: chain Db residue 13 LYS Chi-restraints excluded: chain Dd residue 249 SER Chi-restraints excluded: chain Df residue 110 LYS Chi-restraints excluded: chain Df residue 128 VAL Chi-restraints excluded: chain Df residue 219 LYS Chi-restraints excluded: chain Df residue 240 THR Chi-restraints excluded: chain Df residue 253 ASP Chi-restraints excluded: chain Dg residue 12 HIS Chi-restraints excluded: chain Dh residue 4 MET Chi-restraints excluded: chain Dh residue 5 ILE Chi-restraints excluded: chain Di residue 7 THR Chi-restraints excluded: chain Di residue 10 THR Chi-restraints excluded: chain Di residue 13 LYS Chi-restraints excluded: chain Dm residue 178 SER Chi-restraints excluded: chain Dm residue 182 LEU Chi-restraints excluded: chain Dm residue 209 THR Chi-restraints excluded: chain Dm residue 214 MET Chi-restraints excluded: chain Dm residue 219 LYS Chi-restraints excluded: chain Dm residue 239 LEU Chi-restraints excluded: chain Dm residue 241 LEU Chi-restraints excluded: chain Dp residue 10 THR Chi-restraints excluded: chain Ds residue 822 GLU Chi-restraints excluded: chain Dt residue 110 LYS Chi-restraints excluded: chain Dt residue 128 VAL Chi-restraints excluded: chain Dt residue 178 SER Chi-restraints excluded: chain Dt residue 209 THR Chi-restraints excluded: chain Dt residue 214 MET Chi-restraints excluded: chain Dt residue 240 THR Chi-restraints excluded: chain Dv residue 5 ILE Chi-restraints excluded: chain Dw residue 3 SER Chi-restraints excluded: chain Dw residue 7 THR Chi-restraints excluded: chain Dw residue 10 THR Chi-restraints excluded: chain Dw residue 13 LYS Chi-restraints excluded: chain Dy residue 267 GLU Chi-restraints excluded: chain Dz residue 795 GLN Chi-restraints excluded: chain Ea residue 168 VAL Chi-restraints excluded: chain Ea residue 178 SER Chi-restraints excluded: chain Ea residue 214 MET Chi-restraints excluded: chain Ea residue 240 THR Chi-restraints excluded: chain Ea residue 241 LEU Chi-restraints excluded: chain Ea residue 246 LYS Chi-restraints excluded: chain Eb residue 12 HIS Chi-restraints excluded: chain Ed residue 10 THR Chi-restraints excluded: chain Ed residue 13 LYS Chi-restraints excluded: chain Ef residue 267 GLU Chi-restraints excluded: chain Eh residue 168 VAL Chi-restraints excluded: chain Eh residue 178 SER Chi-restraints excluded: chain Eh residue 182 LEU Chi-restraints excluded: chain Eh residue 185 THR Chi-restraints excluded: chain Eh residue 209 THR Chi-restraints excluded: chain Eh residue 222 ASN Chi-restraints excluded: chain Eh residue 240 THR Chi-restraints excluded: chain Eh residue 241 LEU Chi-restraints excluded: chain Ei residue 6 LEU Chi-restraints excluded: chain Ek residue 4 ILE Chi-restraints excluded: chain Ek residue 10 THR Chi-restraints excluded: chain Ek residue 13 LYS Chi-restraints excluded: chain En residue 802 LEU Chi-restraints excluded: chain Eo residue 128 VAL Chi-restraints excluded: chain Eo residue 179 LEU Chi-restraints excluded: chain Eo residue 182 LEU Chi-restraints excluded: chain Eo residue 215 ILE Chi-restraints excluded: chain Eo residue 241 LEU Chi-restraints excluded: chain Eo residue 255 ARG Chi-restraints excluded: chain Ep residue 3 ASP Chi-restraints excluded: chain Er residue 4 ILE Chi-restraints excluded: chain Er residue 10 THR Chi-restraints excluded: chain Er residue 13 LYS Chi-restraints excluded: chain Et residue 249 SER Chi-restraints excluded: chain Et residue 267 GLU Chi-restraints excluded: chain Eu residue 814 GLN Chi-restraints excluded: chain Ev residue 128 VAL Chi-restraints excluded: chain Ev residue 240 THR Chi-restraints excluded: chain Ev residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 101 optimal weight: 0.1980 chunk 207 optimal weight: 0.5980 chunk 421 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 361 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 461 optimal weight: 1.9990 chunk 405 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** As 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Az 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Bv 814 GLN Cc 814 GLN En 814 GLN ** Ev 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.167867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.132103 restraints weight = 44733.807| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.65 r_work: 0.3398 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 42822 Z= 0.121 Angle : 0.475 10.666 58122 Z= 0.236 Chirality : 0.042 0.198 6660 Planarity : 0.004 0.040 7470 Dihedral : 4.969 79.034 5962 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.42 % Allowed : 21.24 % Favored : 74.34 % 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 are not related in a simple way. whole: 0.74 (0.11), residues: 5202 helix: 2.27 (0.13), residues: 1332 sheet: -0.35 (0.15), residues: 1170 loop : 0.06 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGEm 233 TYR 0.013 0.001 TYRDm 194 PHE 0.013 0.001 PHEEl 2 TRP 0.005 0.001 TRPDd 221 HIS 0.003 0.001 HISCs 12 Details of bonding type rmsd covalent geometry : bond 0.00296 (42822) covalent geometry : angle 0.47520 (58122) hydrogen bonds : bond 0.03161 ( 1756) hydrogen bonds : angle 4.36727 ( 4860) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12182.03 seconds wall clock time: 209 minutes 30.05 seconds (12570.05 seconds total)