Starting phenix.real_space_refine on Mon Mar 11 10:46:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e81_31007/03_2024/7e81_31007.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.040 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 125 5.16 5 C 35016 2.51 5 N 10563 2.21 5 O 11474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 57178 Number of models: 1 Model: "" Number of chains: 68 Chain: "Da" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Db" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dc" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dd" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "De" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 696 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "Df" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 687 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "Dg" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dh" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Di" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dj" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dk" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dl" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dm" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Dn" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 637 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Chain: "Do" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 687 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 89} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "Dp" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dq" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dr" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Ds" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dt" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Du" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dv" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "Dw" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 746 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 7, 'TRANS': 101} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "GA" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "GF" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "GG" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "GH" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "GI" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 75 Classifications: {'peptide': 15} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 14} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'UNK:plan-1': 15} Unresolved non-hydrogen planarities: 15 Chain: "GJ" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "GK" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 90 Classifications: {'peptide': 18} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'TRANS': 17} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "GC" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 55 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UNK:plan-1': 11} Unresolved non-hydrogen planarities: 11 Chain: "GE" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "GD" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 50 Classifications: {'peptide': 10} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'UNK:plan-1': 10} Unresolved non-hydrogen planarities: 10 Chain: "GB" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "Ca" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cb" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cc" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cd" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ce" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cf" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "cg" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ch" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ci" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cj" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ck" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cl" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cm" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cn" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Co" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cp" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cq" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cr" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cs" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ct" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cu" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cv" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cw" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cx" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cy" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Cz" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ea" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Eb" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ec" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ed" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ee" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Ef" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Eg" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Chain: "Fh" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1185 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 2 Time building chain proxies: 22.40, per 1000 atoms: 0.39 Number of scatterers: 57178 At special positions: 0 Unit cell: (254.865, 253.558, 134.621, 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 125 16.00 O 11474 8.00 N 10563 7.00 C 35016 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.36 Conformation dependent library (CDL) restraints added in 8.2 seconds 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14346 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 110 sheets defined 32.6% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'Da' and resid 113 through 118 Processing helix chain 'Da' and resid 127 through 132 Processing helix chain 'Da' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDa 146 " --> pdb=" O ARGDa 142 " (cutoff:3.500A) Processing helix chain 'Da' and resid 188 through 200 removed outlier: 4.399A pdb=" N SERDa 192 " --> pdb=" O GLUDa 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADa 193 " --> pdb=" O GLYDa 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDa 194 " --> pdb=" O GLNDa 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDa 198 " --> pdb=" O VALDa 194 " (cutoff:3.500A) Processing helix chain 'Db' and resid 114 through 118 Processing helix chain 'Db' and resid 124 through 132 removed outlier: 3.776A pdb=" N GLNDb 129 " --> pdb=" O GLNDb 125 " (cutoff:3.500A) Processing helix chain 'Db' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDb 146 " --> pdb=" O ARGDb 142 " (cutoff:3.500A) Processing helix chain 'Db' and resid 188 through 200 removed outlier: 4.400A pdb=" N SERDb 192 " --> pdb=" O GLUDb 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADb 193 " --> pdb=" O GLYDb 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDb 194 " --> pdb=" O GLNDb 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDb 198 " --> pdb=" O VALDb 194 " (cutoff:3.500A) Processing helix chain 'Dc' and resid 114 through 118 Processing helix chain 'Dc' and resid 127 through 132 Processing helix chain 'Dc' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDc 146 " --> pdb=" O ARGDc 142 " (cutoff:3.500A) Processing helix chain 'Dc' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDc 192 " --> pdb=" O GLUDc 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADc 193 " --> pdb=" O GLYDc 189 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VALDc 194 " --> pdb=" O GLNDc 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDc 198 " --> pdb=" O VALDc 194 " (cutoff:3.500A) Processing helix chain 'Dd' and resid 114 through 118 Processing helix chain 'Dd' and resid 127 through 132 Processing helix chain 'Dd' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDd 146 " --> pdb=" O ARGDd 142 " (cutoff:3.500A) Processing helix chain 'Dd' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDd 192 " --> pdb=" O GLUDd 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADd 193 " --> pdb=" O GLYDd 189 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALDd 194 " --> pdb=" O GLNDd 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDd 198 " --> pdb=" O VALDd 194 " (cutoff:3.500A) Processing helix chain 'De' and resid 114 through 118 Processing helix chain 'De' and resid 127 through 132 Processing helix chain 'De' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDe 146 " --> pdb=" O ARGDe 142 " (cutoff:3.500A) Processing helix chain 'De' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDe 192 " --> pdb=" O GLUDe 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADe 193 " --> pdb=" O GLYDe 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDe 194 " --> pdb=" O GLNDe 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDe 198 " --> pdb=" O VALDe 194 " (cutoff:3.500A) Processing helix chain 'Df' and resid 127 through 132 Processing helix chain 'Df' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDf 146 " --> pdb=" O ARGDf 142 " (cutoff:3.500A) Processing helix chain 'Df' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDf 192 " --> pdb=" O GLUDf 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADf 193 " --> pdb=" O GLYDf 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDf 194 " --> pdb=" O GLNDf 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDf 198 " --> pdb=" O VALDf 194 " (cutoff:3.500A) Processing helix chain 'Dg' and resid 127 through 132 Processing helix chain 'Dg' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDg 146 " --> pdb=" O ARGDg 142 " (cutoff:3.500A) Processing helix chain 'Dg' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDg 192 " --> pdb=" O GLUDg 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADg 193 " --> pdb=" O GLYDg 189 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALDg 194 " --> pdb=" O GLNDg 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDg 198 " --> pdb=" O VALDg 194 " (cutoff:3.500A) Processing helix chain 'Dh' and resid 127 through 132 Processing helix chain 'Dh' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDh 146 " --> pdb=" O ARGDh 142 " (cutoff:3.500A) Processing helix chain 'Dh' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDh 192 " --> pdb=" O GLUDh 188 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALADh 193 " --> pdb=" O GLYDh 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDh 194 " --> pdb=" O GLNDh 190 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALDh 198 " --> pdb=" O VALDh 194 " (cutoff:3.500A) Processing helix chain 'Di' and resid 127 through 132 Processing helix chain 'Di' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDi 146 " --> pdb=" O ARGDi 142 " (cutoff:3.500A) Processing helix chain 'Di' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDi 192 " --> pdb=" O GLUDi 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADi 193 " --> pdb=" O GLYDi 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDi 194 " --> pdb=" O GLNDi 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDi 198 " --> pdb=" O VALDi 194 " (cutoff:3.500A) Processing helix chain 'Dj' and resid 127 through 132 Processing helix chain 'Dj' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDj 146 " --> pdb=" O ARGDj 142 " (cutoff:3.500A) Processing helix chain 'Dj' and resid 188 through 200 removed outlier: 4.400A pdb=" N SERDj 192 " --> pdb=" O GLUDj 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADj 193 " --> pdb=" O GLYDj 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDj 194 " --> pdb=" O GLNDj 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VALDj 198 " --> pdb=" O VALDj 194 " (cutoff:3.500A) Processing helix chain 'Dk' and resid 127 through 132 Processing helix chain 'Dk' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDk 146 " --> pdb=" O ARGDk 142 " (cutoff:3.500A) Processing helix chain 'Dk' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDk 192 " --> pdb=" O GLUDk 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADk 193 " --> pdb=" O GLYDk 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDk 194 " --> pdb=" O GLNDk 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDk 198 " --> pdb=" O VALDk 194 " (cutoff:3.500A) Processing helix chain 'Dl' and resid 127 through 132 Processing helix chain 'Dl' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDl 146 " --> pdb=" O ARGDl 142 " (cutoff:3.500A) Processing helix chain 'Dl' and resid 188 through 200 removed outlier: 4.403A pdb=" N SERDl 192 " --> pdb=" O GLUDl 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADl 193 " --> pdb=" O GLYDl 189 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALDl 194 " --> pdb=" O GLNDl 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDl 198 " --> pdb=" O VALDl 194 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 127 through 132 Processing helix chain 'Dm' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDm 146 " --> pdb=" O ARGDm 142 " (cutoff:3.500A) Processing helix chain 'Dm' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDm 192 " --> pdb=" O GLUDm 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADm 193 " --> pdb=" O GLYDm 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDm 194 " --> pdb=" O GLNDm 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDm 198 " --> pdb=" O VALDm 194 " (cutoff:3.500A) Processing helix chain 'Dn' and resid 127 through 132 Processing helix chain 'Dn' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDn 146 " --> pdb=" O ARGDn 142 " (cutoff:3.500A) Processing helix chain 'Dn' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDn 192 " --> pdb=" O GLUDn 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADn 193 " --> pdb=" O GLYDn 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDn 194 " --> pdb=" O GLNDn 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDn 198 " --> pdb=" O VALDn 194 " (cutoff:3.500A) Processing helix chain 'Do' and resid 127 through 132 Processing helix chain 'Do' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDo 146 " --> pdb=" O ARGDo 142 " (cutoff:3.500A) Processing helix chain 'Do' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDo 192 " --> pdb=" O GLUDo 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADo 193 " --> pdb=" O GLYDo 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDo 194 " --> pdb=" O GLNDo 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDo 198 " --> pdb=" O VALDo 194 " (cutoff:3.500A) Processing helix chain 'Dp' and resid 114 through 118 Processing helix chain 'Dp' and resid 127 through 132 Processing helix chain 'Dp' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDp 146 " --> pdb=" O ARGDp 142 " (cutoff:3.500A) Processing helix chain 'Dp' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDp 192 " --> pdb=" O GLUDp 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADp 193 " --> pdb=" O GLYDp 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDp 194 " --> pdb=" O GLNDp 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDp 198 " --> pdb=" O VALDp 194 " (cutoff:3.500A) Processing helix chain 'Dq' and resid 114 through 118 Processing helix chain 'Dq' and resid 127 through 132 Processing helix chain 'Dq' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDq 146 " --> pdb=" O ARGDq 142 " (cutoff:3.500A) Processing helix chain 'Dq' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDq 192 " --> pdb=" O GLUDq 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADq 193 " --> pdb=" O GLYDq 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDq 194 " --> pdb=" O GLNDq 190 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALDq 198 " --> pdb=" O VALDq 194 " (cutoff:3.500A) Processing helix chain 'Dr' and resid 114 through 118 Processing helix chain 'Dr' and resid 127 through 132 Processing helix chain 'Dr' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDr 146 " --> pdb=" O ARGDr 142 " (cutoff:3.500A) Processing helix chain 'Dr' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDr 192 " --> pdb=" O GLUDr 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADr 193 " --> pdb=" O GLYDr 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDr 194 " --> pdb=" O GLNDr 190 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VALDr 198 " --> pdb=" O VALDr 194 " (cutoff:3.500A) Processing helix chain 'Ds' and resid 114 through 118 Processing helix chain 'Ds' and resid 127 through 132 Processing helix chain 'Ds' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDs 146 " --> pdb=" O ARGDs 142 " (cutoff:3.500A) Processing helix chain 'Ds' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDs 192 " --> pdb=" O GLUDs 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADs 193 " --> pdb=" O GLYDs 189 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VALDs 194 " --> pdb=" O GLNDs 190 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VALDs 198 " --> pdb=" O VALDs 194 " (cutoff:3.500A) Processing helix chain 'Dt' and resid 114 through 118 Processing helix chain 'Dt' and resid 127 through 132 Processing helix chain 'Dt' and resid 132 through 146 removed outlier: 3.633A pdb=" N THRDt 146 " --> pdb=" O ARGDt 142 " (cutoff:3.500A) Processing helix chain 'Dt' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDt 192 " --> pdb=" O GLUDt 188 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALADt 193 " --> pdb=" O GLYDt 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDt 194 " --> pdb=" O GLNDt 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDt 198 " --> pdb=" O VALDt 194 " (cutoff:3.500A) Processing helix chain 'Du' and resid 114 through 118 Processing helix chain 'Du' and resid 127 through 132 Processing helix chain 'Du' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDu 146 " --> pdb=" O ARGDu 142 " (cutoff:3.500A) Processing helix chain 'Du' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDu 192 " --> pdb=" O GLUDu 188 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALADu 193 " --> pdb=" O GLYDu 189 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALDu 194 " --> pdb=" O GLNDu 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDu 198 " --> pdb=" O VALDu 194 " (cutoff:3.500A) Processing helix chain 'Dv' and resid 114 through 118 Processing helix chain 'Dv' and resid 127 through 132 Processing helix chain 'Dv' and resid 132 through 146 removed outlier: 3.632A pdb=" N THRDv 146 " --> pdb=" O ARGDv 142 " (cutoff:3.500A) Processing helix chain 'Dv' and resid 188 through 200 removed outlier: 4.401A pdb=" N SERDv 192 " --> pdb=" O GLUDv 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADv 193 " --> pdb=" O GLYDv 189 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALDv 194 " --> pdb=" O GLNDv 190 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VALDv 198 " --> pdb=" O VALDv 194 " (cutoff:3.500A) Processing helix chain 'Dw' and resid 114 through 118 Processing helix chain 'Dw' and resid 127 through 132 Processing helix chain 'Dw' and resid 132 through 146 removed outlier: 3.634A pdb=" N THRDw 146 " --> pdb=" O ARGDw 142 " (cutoff:3.500A) Processing helix chain 'Dw' and resid 188 through 200 removed outlier: 4.402A pdb=" N SERDw 192 " --> pdb=" O GLUDw 188 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALADw 193 " --> pdb=" O GLYDw 189 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VALDw 194 " --> pdb=" O GLNDw 190 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALDw 198 " --> pdb=" O VALDw 194 " (cutoff:3.500A) Processing helix chain 'GF' and resid 2 through 18 Processing helix chain 'GG' and resid 2 through 18 Processing helix chain 'GH' and resid 2 through 18 Processing helix chain 'GI' and resid 2 through 15 Processing helix chain 'GJ' and resid 2 through 18 Processing helix chain 'GK' and resid 2 through 18 Processing helix chain 'Ca' and resid 233 through 258 Proline residue: Ca 255 - end of helix Processing helix chain 'Ca' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCa 421 " --> pdb=" O ARGCa 417 " (cutoff:3.500A) Processing helix chain 'Cb' and resid 233 through 258 Proline residue: Cb 255 - end of helix Processing helix chain 'Cb' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCb 421 " --> pdb=" O ARGCb 417 " (cutoff:3.500A) Processing helix chain 'Cc' and resid 233 through 258 Proline residue: Cc 255 - end of helix Processing helix chain 'Cc' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCc 421 " --> pdb=" O ARGCc 417 " (cutoff:3.500A) Processing helix chain 'Cd' and resid 233 through 258 Proline residue: Cd 255 - end of helix Processing helix chain 'Cd' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCd 421 " --> pdb=" O ARGCd 417 " (cutoff:3.500A) Processing helix chain 'Ce' and resid 233 through 258 Proline residue: Ce 255 - end of helix Processing helix chain 'Ce' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCe 421 " --> pdb=" O ARGCe 417 " (cutoff:3.500A) Processing helix chain 'Cf' and resid 233 through 258 Proline residue: Cf 255 - end of helix Processing helix chain 'Cf' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCf 421 " --> pdb=" O ARGCf 417 " (cutoff:3.500A) Processing helix chain 'cg' and resid 233 through 258 Proline residue: cg 255 - end of helix Processing helix chain 'cg' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYcg 421 " --> pdb=" O ARGcg 417 " (cutoff:3.500A) Processing helix chain 'Ch' and resid 233 through 258 Proline residue: Ch 255 - end of helix Processing helix chain 'Ch' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCh 421 " --> pdb=" O ARGCh 417 " (cutoff:3.500A) Processing helix chain 'Ci' and resid 233 through 258 Proline residue: Ci 255 - end of helix Processing helix chain 'Ci' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCi 421 " --> pdb=" O ARGCi 417 " (cutoff:3.500A) Processing helix chain 'Cj' and resid 233 through 258 Proline residue: Cj 255 - end of helix Processing helix chain 'Cj' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCj 421 " --> pdb=" O ARGCj 417 " (cutoff:3.500A) Processing helix chain 'Ck' and resid 233 through 258 Proline residue: Ck 255 - end of helix Processing helix chain 'Ck' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCk 421 " --> pdb=" O ARGCk 417 " (cutoff:3.500A) Processing helix chain 'Cl' and resid 233 through 258 Proline residue: Cl 255 - end of helix Processing helix chain 'Cl' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCl 421 " --> pdb=" O ARGCl 417 " (cutoff:3.500A) Processing helix chain 'Cm' and resid 233 through 258 Proline residue: Cm 255 - end of helix Processing helix chain 'Cm' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCm 421 " --> pdb=" O ARGCm 417 " (cutoff:3.500A) Processing helix chain 'Cn' and resid 233 through 258 Proline residue: Cn 255 - end of helix Processing helix chain 'Cn' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCn 421 " --> pdb=" O ARGCn 417 " (cutoff:3.500A) Processing helix chain 'Co' and resid 233 through 258 Proline residue: Co 255 - end of helix Processing helix chain 'Co' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCo 421 " --> pdb=" O ARGCo 417 " (cutoff:3.500A) Processing helix chain 'Cp' and resid 233 through 258 Proline residue: Cp 255 - end of helix Processing helix chain 'Cp' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCp 421 " --> pdb=" O ARGCp 417 " (cutoff:3.500A) Processing helix chain 'Cq' and resid 233 through 258 Proline residue: Cq 255 - end of helix Processing helix chain 'Cq' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCq 421 " --> pdb=" O ARGCq 417 " (cutoff:3.500A) Processing helix chain 'Cr' and resid 233 through 258 Proline residue: Cr 255 - end of helix Processing helix chain 'Cr' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCr 421 " --> pdb=" O ARGCr 417 " (cutoff:3.500A) Processing helix chain 'Cs' and resid 233 through 258 Proline residue: Cs 255 - end of helix Processing helix chain 'Cs' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCs 421 " --> pdb=" O ARGCs 417 " (cutoff:3.500A) Processing helix chain 'Ct' and resid 233 through 258 Proline residue: Ct 255 - end of helix Processing helix chain 'Ct' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCt 421 " --> pdb=" O ARGCt 417 " (cutoff:3.500A) Processing helix chain 'Cu' and resid 233 through 258 Proline residue: Cu 255 - end of helix Processing helix chain 'Cu' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCu 421 " --> pdb=" O ARGCu 417 " (cutoff:3.500A) Processing helix chain 'Cv' and resid 233 through 258 Proline residue: Cv 255 - end of helix Processing helix chain 'Cv' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYCv 421 " --> pdb=" O ARGCv 417 " (cutoff:3.500A) Processing helix chain 'Cw' and resid 233 through 258 Proline residue: Cw 255 - end of helix Processing helix chain 'Cw' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCw 421 " --> pdb=" O ARGCw 417 " (cutoff:3.500A) Processing helix chain 'Cx' and resid 233 through 258 Proline residue: Cx 255 - end of helix Processing helix chain 'Cx' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCx 421 " --> pdb=" O ARGCx 417 " (cutoff:3.500A) Processing helix chain 'Cy' and resid 233 through 258 Proline residue: Cy 255 - end of helix Processing helix chain 'Cy' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCy 421 " --> pdb=" O ARGCy 417 " (cutoff:3.500A) Processing helix chain 'Cz' and resid 233 through 258 Proline residue: Cz 255 - end of helix Processing helix chain 'Cz' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYCz 421 " --> pdb=" O ARGCz 417 " (cutoff:3.500A) Processing helix chain 'Ea' and resid 233 through 258 Proline residue: Ea 255 - end of helix Processing helix chain 'Ea' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYEa 421 " --> pdb=" O ARGEa 417 " (cutoff:3.500A) Processing helix chain 'Eb' and resid 233 through 258 Proline residue: Eb 255 - end of helix Processing helix chain 'Eb' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYEb 421 " --> pdb=" O ARGEb 417 " (cutoff:3.500A) Processing helix chain 'Ec' and resid 233 through 258 Proline residue: Ec 255 - end of helix Processing helix chain 'Ec' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYEc 421 " --> pdb=" O ARGEc 417 " (cutoff:3.500A) Processing helix chain 'Ed' and resid 233 through 258 Proline residue: Ed 255 - end of helix Processing helix chain 'Ed' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYEd 421 " --> pdb=" O ARGEd 417 " (cutoff:3.500A) Processing helix chain 'Ee' and resid 233 through 258 Proline residue: Ee 255 - end of helix Processing helix chain 'Ee' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYEe 421 " --> pdb=" O ARGEe 417 " (cutoff:3.500A) Processing helix chain 'Ef' and resid 233 through 258 Proline residue: Ef 255 - end of helix Processing helix chain 'Ef' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYEf 421 " --> pdb=" O ARGEf 417 " (cutoff:3.500A) Processing helix chain 'Eg' and resid 233 through 258 Proline residue: Eg 255 - end of helix Processing helix chain 'Eg' and resid 405 through 421 removed outlier: 3.778A pdb=" N GLYEg 421 " --> pdb=" O ARGEg 417 " (cutoff:3.500A) Processing helix chain 'Fh' and resid 233 through 258 Proline residue: Fh 255 - end of helix Processing helix chain 'Fh' and resid 405 through 421 removed outlier: 3.777A pdb=" N GLYFh 421 " --> pdb=" O ARGFh 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Da' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDa 179 " --> pdb=" O LYSDa 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Da' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDa 156 " --> pdb=" O SERDa 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Db' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDb 179 " --> pdb=" O LYSDb 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Db' and resid 156 through 157 removed outlier: 3.546A pdb=" N HISDb 156 " --> pdb=" O SERDb 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Dc' and resid 150 through 152 removed outlier: 6.696A pdb=" N THRDc 179 " --> pdb=" O LYSDc 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Dc' and resid 156 through 157 removed outlier: 3.546A pdb=" N HISDc 156 " --> pdb=" O SERDc 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Dd' and resid 150 through 152 removed outlier: 6.695A pdb=" N THRDd 179 " --> pdb=" O LYSDd 151 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Dd' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDd 156 " --> pdb=" O SERDd 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'De' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDe 179 " --> pdb=" O LYSDe 151 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'De' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDe 156 " --> pdb=" O SERDe 175 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Df' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDf 179 " --> pdb=" O LYSDf 151 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Df' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDf 156 " --> pdb=" O SERDf 175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Dg' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDg 179 " --> pdb=" O LYSDg 151 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Dg' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDg 156 " --> pdb=" O SERDg 175 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Dh' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDh 179 " --> pdb=" O LYSDh 151 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Dh' and resid 156 through 157 removed outlier: 3.546A pdb=" N HISDh 156 " --> pdb=" O SERDh 175 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Di' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDi 179 " --> pdb=" O LYSDi 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Di' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDi 156 " --> pdb=" O SERDi 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Dj' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDj 179 " --> pdb=" O LYSDj 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Dj' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDj 156 " --> pdb=" O SERDj 175 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Dk' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDk 179 " --> pdb=" O LYSDk 151 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Dk' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDk 156 " --> pdb=" O SERDk 175 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Dl' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDl 179 " --> pdb=" O LYSDl 151 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Dl' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDl 156 " --> pdb=" O SERDl 175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Dm' and resid 150 through 152 removed outlier: 6.695A pdb=" N THRDm 179 " --> pdb=" O LYSDm 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Dm' and resid 156 through 157 removed outlier: 3.543A pdb=" N HISDm 156 " --> pdb=" O SERDm 175 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Dn' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDn 179 " --> pdb=" O LYSDn 151 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Dn' and resid 156 through 157 removed outlier: 3.544A pdb=" N HISDn 156 " --> pdb=" O SERDn 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Do' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDo 179 " --> pdb=" O LYSDo 151 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Do' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDo 156 " --> pdb=" O SERDo 175 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Dp' and resid 150 through 152 removed outlier: 6.695A pdb=" N THRDp 179 " --> pdb=" O LYSDp 151 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Dp' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDp 156 " --> pdb=" O SERDp 175 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Dq' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDq 179 " --> pdb=" O LYSDq 151 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Dq' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDq 156 " --> pdb=" O SERDq 175 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'Dr' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDr 179 " --> pdb=" O LYSDr 151 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'Dr' and resid 156 through 157 removed outlier: 3.543A pdb=" N HISDr 156 " --> pdb=" O SERDr 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Ds' and resid 150 through 152 removed outlier: 6.695A pdb=" N THRDs 179 " --> pdb=" O LYSDs 151 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Ds' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDs 156 " --> pdb=" O SERDs 175 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Dt' and resid 150 through 152 removed outlier: 6.693A pdb=" N THRDt 179 " --> pdb=" O LYSDt 151 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Dt' and resid 156 through 157 removed outlier: 3.546A pdb=" N HISDt 156 " --> pdb=" O SERDt 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Du' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDu 179 " --> pdb=" O LYSDu 151 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Du' and resid 156 through 157 removed outlier: 3.543A pdb=" N HISDu 156 " --> pdb=" O SERDu 175 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Dv' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDv 179 " --> pdb=" O LYSDv 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Dv' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDv 156 " --> pdb=" O SERDv 175 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Dw' and resid 150 through 152 removed outlier: 6.694A pdb=" N THRDw 179 " --> pdb=" O LYSDw 151 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Dw' and resid 156 through 157 removed outlier: 3.545A pdb=" N HISDw 156 " --> pdb=" O SERDw 175 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'Ca' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCa 271 " --> pdb=" O ILECa 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECa 382 " --> pdb=" O ASPCa 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THRCa 429 " --> pdb=" O GLUCa 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCa 385 " --> pdb=" O THRCa 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCa 431 " --> pdb=" O LEUCa 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VALCa 387 " --> pdb=" O ASNCa 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCa 433 " --> pdb=" O VALCa 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCa 389 " --> pdb=" O VALCa 433 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Ca' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCa 373 " --> pdb=" O GLUCa 279 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Ca' and resid 293 through 302 removed outlier: 6.754A pdb=" N ASNCa 365 " --> pdb=" O ARGCa 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCa 296 " --> pdb=" O THRCa 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCa 363 " --> pdb=" O ARGCa 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCa 298 " --> pdb=" O ASNCa 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCa 361 " --> pdb=" O LEUCa 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECa 300 " --> pdb=" O GLNCa 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCa 359 " --> pdb=" O ILECa 300 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLUCb 302 " --> pdb=" O THRCa 358 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARGCb 294 " --> pdb=" O TYRCa 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCb 365 " --> pdb=" O ARGCb 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCb 296 " --> pdb=" O THRCb 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCb 363 " --> pdb=" O ARGCb 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCb 298 " --> pdb=" O ASNCb 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCb 361 " --> pdb=" O LEUCb 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECb 300 " --> pdb=" O GLNCb 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCb 359 " --> pdb=" O ILECb 300 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLUCc 302 " --> pdb=" O THRCb 358 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ARGCc 294 " --> pdb=" O TYRCb 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCc 365 " --> pdb=" O ARGCc 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCc 296 " --> pdb=" O THRCc 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCc 363 " --> pdb=" O ARGCc 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCc 298 " --> pdb=" O ASNCc 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCc 361 " --> pdb=" O LEUCc 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECc 300 " --> pdb=" O GLNCc 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCc 359 " --> pdb=" O ILECc 300 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLUCd 302 " --> pdb=" O THRCc 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARGCd 294 " --> pdb=" O TYRCc 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCd 365 " --> pdb=" O ARGCd 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCd 296 " --> pdb=" O THRCd 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCd 363 " --> pdb=" O ARGCd 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCd 298 " --> pdb=" O ASNCd 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCd 361 " --> pdb=" O LEUCd 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECd 300 " --> pdb=" O GLNCd 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNCd 359 " --> pdb=" O ILECd 300 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLUCe 302 " --> pdb=" O THRCd 358 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARGCe 294 " --> pdb=" O TYRCd 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCe 365 " --> pdb=" O ARGCe 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCe 296 " --> pdb=" O THRCe 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCe 363 " --> pdb=" O ARGCe 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCe 298 " --> pdb=" O ASNCe 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCe 361 " --> pdb=" O LEUCe 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECe 300 " --> pdb=" O GLNCe 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCe 359 " --> pdb=" O ILECe 300 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLUCf 302 " --> pdb=" O THRCe 358 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ARGCf 294 " --> pdb=" O TYRCe 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASNCf 365 " --> pdb=" O ARGCf 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCf 296 " --> pdb=" O THRCf 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THRCf 363 " --> pdb=" O ARGCf 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCf 298 " --> pdb=" O ASNCf 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCf 361 " --> pdb=" O LEUCf 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILECf 300 " --> pdb=" O GLNCf 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNCf 359 " --> pdb=" O ILECf 300 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLUcg 302 " --> pdb=" O THRCf 358 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLUCf 362 " --> pdb=" O LEUcg 298 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARGcg 294 " --> pdb=" O TYRCf 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNcg 365 " --> pdb=" O ARGcg 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGcg 296 " --> pdb=" O THRcg 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THRcg 363 " --> pdb=" O ARGcg 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUcg 298 " --> pdb=" O ASNcg 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNcg 361 " --> pdb=" O LEUcg 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEcg 300 " --> pdb=" O GLNcg 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNcg 359 " --> pdb=" O ILEcg 300 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLUCh 302 " --> pdb=" O THRcg 358 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARGCh 294 " --> pdb=" O TYRcg 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASNCh 365 " --> pdb=" O ARGCh 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCh 296 " --> pdb=" O THRCh 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCh 363 " --> pdb=" O ARGCh 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCh 298 " --> pdb=" O ASNCh 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCh 361 " --> pdb=" O LEUCh 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECh 300 " --> pdb=" O GLNCh 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCh 359 " --> pdb=" O ILECh 300 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLUCi 302 " --> pdb=" O THRCh 358 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ARGCi 294 " --> pdb=" O TYRCh 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASNCi 365 " --> pdb=" O ARGCi 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCi 296 " --> pdb=" O THRCi 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCi 363 " --> pdb=" O ARGCi 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCi 298 " --> pdb=" O ASNCi 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCi 361 " --> pdb=" O LEUCi 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECi 300 " --> pdb=" O GLNCi 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCi 359 " --> pdb=" O ILECi 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUCj 302 " --> pdb=" O THRCi 358 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARGCj 294 " --> pdb=" O TYRCi 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCj 365 " --> pdb=" O ARGCj 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCj 296 " --> pdb=" O THRCj 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCj 363 " --> pdb=" O ARGCj 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCj 298 " --> pdb=" O ASNCj 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCj 361 " --> pdb=" O LEUCj 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECj 300 " --> pdb=" O GLNCj 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCj 359 " --> pdb=" O ILECj 300 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLUCk 302 " --> pdb=" O THRCj 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARGCk 294 " --> pdb=" O TYRCj 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCk 365 " --> pdb=" O ARGCk 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCk 296 " --> pdb=" O THRCk 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCk 363 " --> pdb=" O ARGCk 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCk 298 " --> pdb=" O ASNCk 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCk 361 " --> pdb=" O LEUCk 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECk 300 " --> pdb=" O GLNCk 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCk 359 " --> pdb=" O ILECk 300 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLUCl 302 " --> pdb=" O THRCk 358 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ARGCl 294 " --> pdb=" O TYRCk 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCl 365 " --> pdb=" O ARGCl 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCl 296 " --> pdb=" O THRCl 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCl 363 " --> pdb=" O ARGCl 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCl 298 " --> pdb=" O ASNCl 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCl 361 " --> pdb=" O LEUCl 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECl 300 " --> pdb=" O GLNCl 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCl 359 " --> pdb=" O ILECl 300 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLUCm 302 " --> pdb=" O THRCl 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARGCm 294 " --> pdb=" O TYRCl 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCm 365 " --> pdb=" O ARGCm 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCm 296 " --> pdb=" O THRCm 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCm 363 " --> pdb=" O ARGCm 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCm 298 " --> pdb=" O ASNCm 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCm 361 " --> pdb=" O LEUCm 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECm 300 " --> pdb=" O GLNCm 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCm 359 " --> pdb=" O ILECm 300 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLUCn 302 " --> pdb=" O THRCm 358 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLUCm 362 " --> pdb=" O LEUCn 298 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARGCn 294 " --> pdb=" O TYRCm 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASNCn 365 " --> pdb=" O ARGCn 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCn 296 " --> pdb=" O THRCn 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCn 363 " --> pdb=" O ARGCn 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCn 298 " --> pdb=" O ASNCn 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCn 361 " --> pdb=" O LEUCn 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECn 300 " --> pdb=" O GLNCn 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCn 359 " --> pdb=" O ILECn 300 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLUCo 302 " --> pdb=" O THRCn 358 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARGCo 294 " --> pdb=" O TYRCn 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCo 365 " --> pdb=" O ARGCo 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCo 296 " --> pdb=" O THRCo 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCo 363 " --> pdb=" O ARGCo 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCo 298 " --> pdb=" O ASNCo 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCo 361 " --> pdb=" O LEUCo 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECo 300 " --> pdb=" O GLNCo 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCo 359 " --> pdb=" O ILECo 300 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLUCp 302 " --> pdb=" O THRCo 358 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUCo 362 " --> pdb=" O LEUCp 298 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARGCp 294 " --> pdb=" O TYRCo 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASNCp 365 " --> pdb=" O ARGCp 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCp 296 " --> pdb=" O THRCp 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCp 363 " --> pdb=" O ARGCp 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCp 298 " --> pdb=" O ASNCp 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCp 361 " --> pdb=" O LEUCp 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECp 300 " --> pdb=" O GLNCp 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCp 359 " --> pdb=" O ILECp 300 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLUCq 302 " --> pdb=" O THRCp 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARGCq 294 " --> pdb=" O TYRCp 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASNCq 365 " --> pdb=" O ARGCq 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCq 296 " --> pdb=" O THRCq 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCq 363 " --> pdb=" O ARGCq 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCq 298 " --> pdb=" O ASNCq 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCq 361 " --> pdb=" O LEUCq 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECq 300 " --> pdb=" O GLNCq 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCq 359 " --> pdb=" O ILECq 300 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLUCr 302 " --> pdb=" O THRCq 358 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLUCq 362 " --> pdb=" O LEUCr 298 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARGCr 294 " --> pdb=" O TYRCq 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCr 365 " --> pdb=" O ARGCr 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCr 296 " --> pdb=" O THRCr 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCr 363 " --> pdb=" O ARGCr 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCr 298 " --> pdb=" O ASNCr 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCr 361 " --> pdb=" O LEUCr 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILECr 300 " --> pdb=" O GLNCr 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCr 359 " --> pdb=" O ILECr 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLUCs 302 " --> pdb=" O THRCr 358 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARGCs 294 " --> pdb=" O TYRCr 366 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASNCs 365 " --> pdb=" O ARGCs 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCs 296 " --> pdb=" O THRCs 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCs 363 " --> pdb=" O ARGCs 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCs 298 " --> pdb=" O ASNCs 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCs 361 " --> pdb=" O LEUCs 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECs 300 " --> pdb=" O GLNCs 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCs 359 " --> pdb=" O ILECs 300 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLUCt 302 " --> pdb=" O THRCs 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLUCs 362 " --> pdb=" O LEUCt 298 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARGCt 294 " --> pdb=" O TYRCs 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCt 365 " --> pdb=" O ARGCt 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCt 296 " --> pdb=" O THRCt 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCt 363 " --> pdb=" O ARGCt 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCt 298 " --> pdb=" O ASNCt 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCt 361 " --> pdb=" O LEUCt 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECt 300 " --> pdb=" O GLNCt 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCt 359 " --> pdb=" O ILECt 300 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLUCu 302 " --> pdb=" O THRCt 358 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARGCu 294 " --> pdb=" O TYRCt 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCu 365 " --> pdb=" O ARGCu 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGCu 296 " --> pdb=" O THRCu 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCu 363 " --> pdb=" O ARGCu 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCu 298 " --> pdb=" O ASNCu 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCu 361 " --> pdb=" O LEUCu 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECu 300 " --> pdb=" O GLNCu 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCu 359 " --> pdb=" O ILECu 300 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLUCv 302 " --> pdb=" O THRCu 358 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLUCu 362 " --> pdb=" O LEUCv 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARGCv 294 " --> pdb=" O TYRCu 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCv 365 " --> pdb=" O ARGCv 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCv 296 " --> pdb=" O THRCv 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCv 363 " --> pdb=" O ARGCv 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCv 298 " --> pdb=" O ASNCv 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCv 361 " --> pdb=" O LEUCv 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECv 300 " --> pdb=" O GLNCv 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCv 359 " --> pdb=" O ILECv 300 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLUCw 302 " --> pdb=" O THRCv 358 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARGCw 294 " --> pdb=" O TYRCv 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCw 365 " --> pdb=" O ARGCw 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCw 296 " --> pdb=" O THRCw 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THRCw 363 " --> pdb=" O ARGCw 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUCw 298 " --> pdb=" O ASNCw 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCw 361 " --> pdb=" O LEUCw 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILECw 300 " --> pdb=" O GLNCw 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCw 359 " --> pdb=" O ILECw 300 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLUCx 302 " --> pdb=" O THRCw 358 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARGCx 294 " --> pdb=" O TYRCw 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCx 365 " --> pdb=" O ARGCx 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCx 296 " --> pdb=" O THRCx 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCx 363 " --> pdb=" O ARGCx 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCx 298 " --> pdb=" O ASNCx 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNCx 361 " --> pdb=" O LEUCx 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILECx 300 " --> pdb=" O GLNCx 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNCx 359 " --> pdb=" O ILECx 300 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLUCy 302 " --> pdb=" O THRCx 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARGCy 294 " --> pdb=" O TYRCx 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCy 365 " --> pdb=" O ARGCy 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCy 296 " --> pdb=" O THRCy 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRCy 363 " --> pdb=" O ARGCy 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCy 298 " --> pdb=" O ASNCy 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCy 361 " --> pdb=" O LEUCy 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILECy 300 " --> pdb=" O GLNCy 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCy 359 " --> pdb=" O ILECy 300 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLUCz 302 " --> pdb=" O THRCy 358 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARGCz 294 " --> pdb=" O TYRCy 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNCz 365 " --> pdb=" O ARGCz 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGCz 296 " --> pdb=" O THRCz 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THRCz 363 " --> pdb=" O ARGCz 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUCz 298 " --> pdb=" O ASNCz 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNCz 361 " --> pdb=" O LEUCz 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILECz 300 " --> pdb=" O GLNCz 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNCz 359 " --> pdb=" O ILECz 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLUEa 302 " --> pdb=" O THRCz 358 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLUCz 362 " --> pdb=" O LEUEa 298 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N ARGEa 294 " --> pdb=" O TYRCz 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEa 365 " --> pdb=" O ARGEa 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGEa 296 " --> pdb=" O THREa 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THREa 363 " --> pdb=" O ARGEa 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUEa 298 " --> pdb=" O ASNEa 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEa 361 " --> pdb=" O LEUEa 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEEa 300 " --> pdb=" O GLNEa 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNEa 359 " --> pdb=" O ILEEa 300 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLUEc 302 " --> pdb=" O THREa 358 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARGEc 294 " --> pdb=" O TYREa 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEc 365 " --> pdb=" O ARGEc 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGEc 296 " --> pdb=" O THREc 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THREc 363 " --> pdb=" O ARGEc 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUEc 298 " --> pdb=" O ASNEc 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEc 361 " --> pdb=" O LEUEc 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILEEc 300 " --> pdb=" O GLNEc 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNEc 359 " --> pdb=" O ILEEc 300 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLUEb 302 " --> pdb=" O THREc 358 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARGEb 294 " --> pdb=" O TYREc 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEb 365 " --> pdb=" O ARGEb 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGEb 296 " --> pdb=" O THREb 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THREb 363 " --> pdb=" O ARGEb 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUEb 298 " --> pdb=" O ASNEb 361 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASNEb 361 " --> pdb=" O LEUEb 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEEb 300 " --> pdb=" O GLNEb 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNEb 359 " --> pdb=" O ILEEb 300 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLUEd 302 " --> pdb=" O THREb 358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLUEb 362 " --> pdb=" O LEUEd 298 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARGEd 294 " --> pdb=" O TYREb 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEd 365 " --> pdb=" O ARGEd 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGEd 296 " --> pdb=" O THREd 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THREd 363 " --> pdb=" O ARGEd 296 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEUEd 298 " --> pdb=" O ASNEd 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEd 361 " --> pdb=" O LEUEd 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEEd 300 " --> pdb=" O GLNEd 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNEd 359 " --> pdb=" O ILEEd 300 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLUEe 302 " --> pdb=" O THREd 358 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ARGEe 294 " --> pdb=" O TYREd 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEe 365 " --> pdb=" O ARGEe 294 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARGEe 296 " --> pdb=" O THREe 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THREe 363 " --> pdb=" O ARGEe 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUEe 298 " --> pdb=" O ASNEe 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEe 361 " --> pdb=" O LEUEe 298 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ILEEe 300 " --> pdb=" O GLNEe 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNEe 359 " --> pdb=" O ILEEe 300 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLUEf 302 " --> pdb=" O THREe 358 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARGEf 294 " --> pdb=" O TYREe 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASNEf 365 " --> pdb=" O ARGEf 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGEf 296 " --> pdb=" O THREf 363 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THREf 363 " --> pdb=" O ARGEf 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUEf 298 " --> pdb=" O ASNEf 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEf 361 " --> pdb=" O LEUEf 298 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILEEf 300 " --> pdb=" O GLNEf 359 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLNEf 359 " --> pdb=" O ILEEf 300 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUEg 302 " --> pdb=" O THREf 358 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLUEf 362 " --> pdb=" O LEUEg 298 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ARGEg 294 " --> pdb=" O TYREf 366 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASNEg 365 " --> pdb=" O ARGEg 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGEg 296 " --> pdb=" O THREg 363 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THREg 363 " --> pdb=" O ARGEg 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUEg 298 " --> pdb=" O ASNEg 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNEg 361 " --> pdb=" O LEUEg 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEEg 300 " --> pdb=" O GLNEg 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNEg 359 " --> pdb=" O ILEEg 300 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLUFh 302 " --> pdb=" O THREg 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLUEg 362 " --> pdb=" O LEUFh 298 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ARGFh 294 " --> pdb=" O TYREg 366 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASNFh 365 " --> pdb=" O ARGFh 294 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ARGFh 296 " --> pdb=" O THRFh 363 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N THRFh 363 " --> pdb=" O ARGFh 296 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LEUFh 298 " --> pdb=" O ASNFh 361 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASNFh 361 " --> pdb=" O LEUFh 298 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N ILEFh 300 " --> pdb=" O GLNFh 359 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLNFh 359 " --> pdb=" O ILEFh 300 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLUCa 302 " --> pdb=" O THRFh 358 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLUFh 362 " --> pdb=" O LEUCa 298 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SERFh 364 " --> pdb=" O ARGCa 296 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARGCa 294 " --> pdb=" O TYRFh 366 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Cb' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCb 271 " --> pdb=" O ILECb 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECb 382 " --> pdb=" O ASPCb 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCb 429 " --> pdb=" O GLUCb 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCb 385 " --> pdb=" O THRCb 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCb 431 " --> pdb=" O LEUCb 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALCb 387 " --> pdb=" O ASNCb 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCb 433 " --> pdb=" O VALCb 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCb 389 " --> pdb=" O VALCb 433 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Cb' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCb 373 " --> pdb=" O GLUCb 279 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Cc' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCc 271 " --> pdb=" O ILECc 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECc 382 " --> pdb=" O ASPCc 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCc 429 " --> pdb=" O GLUCc 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCc 385 " --> pdb=" O THRCc 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCc 431 " --> pdb=" O LEUCc 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCc 387 " --> pdb=" O ASNCc 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCc 433 " --> pdb=" O VALCc 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCc 389 " --> pdb=" O VALCc 433 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Cc' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCc 373 " --> pdb=" O GLUCc 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Cd' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCd 271 " --> pdb=" O ILECd 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECd 382 " --> pdb=" O ASPCd 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCd 429 " --> pdb=" O GLUCd 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCd 385 " --> pdb=" O THRCd 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCd 431 " --> pdb=" O LEUCd 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCd 387 " --> pdb=" O ASNCd 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCd 433 " --> pdb=" O VALCd 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCd 389 " --> pdb=" O VALCd 433 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Cd' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCd 373 " --> pdb=" O GLUCd 279 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Ce' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCe 271 " --> pdb=" O ILECe 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECe 382 " --> pdb=" O ASPCe 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCe 429 " --> pdb=" O GLUCe 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCe 385 " --> pdb=" O THRCe 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCe 431 " --> pdb=" O LEUCe 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCe 387 " --> pdb=" O ASNCe 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCe 433 " --> pdb=" O VALCe 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VALCe 389 " --> pdb=" O VALCe 433 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Ce' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCe 373 " --> pdb=" O GLUCe 279 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Cf' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCf 271 " --> pdb=" O ILECf 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECf 382 " --> pdb=" O ASPCf 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THRCf 429 " --> pdb=" O GLUCf 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCf 385 " --> pdb=" O THRCf 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCf 431 " --> pdb=" O LEUCf 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCf 387 " --> pdb=" O ASNCf 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCf 433 " --> pdb=" O VALCf 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCf 389 " --> pdb=" O VALCf 433 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Cf' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCf 373 " --> pdb=" O GLUCf 279 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'cg' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPcg 271 " --> pdb=" O ILEcg 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEcg 382 " --> pdb=" O ASPcg 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRcg 429 " --> pdb=" O GLUcg 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUcg 385 " --> pdb=" O THRcg 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNcg 431 " --> pdb=" O LEUcg 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALcg 387 " --> pdb=" O ASNcg 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALcg 433 " --> pdb=" O VALcg 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALcg 389 " --> pdb=" O VALcg 433 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'cg' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGcg 373 " --> pdb=" O GLUcg 279 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Ch' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCh 271 " --> pdb=" O ILECh 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECh 382 " --> pdb=" O ASPCh 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THRCh 429 " --> pdb=" O GLUCh 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCh 385 " --> pdb=" O THRCh 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCh 431 " --> pdb=" O LEUCh 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCh 387 " --> pdb=" O ASNCh 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCh 433 " --> pdb=" O VALCh 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCh 389 " --> pdb=" O VALCh 433 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Ch' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCh 373 " --> pdb=" O GLUCh 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Ci' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCi 271 " --> pdb=" O ILECi 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECi 382 " --> pdb=" O ASPCi 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCi 429 " --> pdb=" O GLUCi 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCi 385 " --> pdb=" O THRCi 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCi 431 " --> pdb=" O LEUCi 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCi 387 " --> pdb=" O ASNCi 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCi 433 " --> pdb=" O VALCi 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCi 389 " --> pdb=" O VALCi 433 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Ci' and resid 371 through 373 removed outlier: 3.731A pdb=" N ARGCi 373 " --> pdb=" O GLUCi 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILECj 372 " --> pdb=" O THRCi 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGCj 373 " --> pdb=" O GLUCj 279 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Cj' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCj 271 " --> pdb=" O ILECj 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECj 382 " --> pdb=" O ASPCj 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCj 429 " --> pdb=" O GLUCj 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCj 385 " --> pdb=" O THRCj 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCj 431 " --> pdb=" O LEUCj 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALCj 387 " --> pdb=" O ASNCj 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCj 433 " --> pdb=" O VALCj 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCj 389 " --> pdb=" O VALCj 433 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Ck' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCk 271 " --> pdb=" O ILECk 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECk 382 " --> pdb=" O ASPCk 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCk 429 " --> pdb=" O GLUCk 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCk 385 " --> pdb=" O THRCk 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCk 431 " --> pdb=" O LEUCk 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCk 387 " --> pdb=" O ASNCk 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCk 433 " --> pdb=" O VALCk 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCk 389 " --> pdb=" O VALCk 433 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Ck' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCk 373 " --> pdb=" O GLUCk 279 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Cl' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCl 271 " --> pdb=" O ILECl 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECl 382 " --> pdb=" O ASPCl 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCl 429 " --> pdb=" O GLUCl 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCl 385 " --> pdb=" O THRCl 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCl 431 " --> pdb=" O LEUCl 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCl 387 " --> pdb=" O ASNCl 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCl 433 " --> pdb=" O VALCl 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCl 389 " --> pdb=" O VALCl 433 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Cl' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCl 373 " --> pdb=" O GLUCl 279 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Cm' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCm 271 " --> pdb=" O ILECm 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECm 382 " --> pdb=" O ASPCm 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THRCm 429 " --> pdb=" O GLUCm 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCm 385 " --> pdb=" O THRCm 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCm 431 " --> pdb=" O LEUCm 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCm 387 " --> pdb=" O ASNCm 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCm 433 " --> pdb=" O VALCm 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCm 389 " --> pdb=" O VALCm 433 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Cm' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCm 373 " --> pdb=" O GLUCm 279 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Cn' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCn 271 " --> pdb=" O ILECn 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECn 382 " --> pdb=" O ASPCn 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCn 429 " --> pdb=" O GLUCn 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCn 385 " --> pdb=" O THRCn 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCn 431 " --> pdb=" O LEUCn 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCn 387 " --> pdb=" O ASNCn 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCn 433 " --> pdb=" O VALCn 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCn 389 " --> pdb=" O VALCn 433 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'Cn' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCn 373 " --> pdb=" O GLUCn 279 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Co' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCo 271 " --> pdb=" O ILECo 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECo 382 " --> pdb=" O ASPCo 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCo 429 " --> pdb=" O GLUCo 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCo 385 " --> pdb=" O THRCo 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCo 431 " --> pdb=" O LEUCo 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCo 387 " --> pdb=" O ASNCo 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCo 433 " --> pdb=" O VALCo 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCo 389 " --> pdb=" O VALCo 433 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Co' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARGCo 373 " --> pdb=" O GLUCo 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGCp 373 " --> pdb=" O GLUCp 279 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILECq 372 " --> pdb=" O THRCp 278 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARGCq 373 " --> pdb=" O GLUCq 279 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Cp' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCp 271 " --> pdb=" O ILECp 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECp 382 " --> pdb=" O ASPCp 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THRCp 429 " --> pdb=" O GLUCp 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCp 385 " --> pdb=" O THRCp 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCp 431 " --> pdb=" O LEUCp 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCp 387 " --> pdb=" O ASNCp 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCp 433 " --> pdb=" O VALCp 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCp 389 " --> pdb=" O VALCp 433 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Cq' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCq 271 " --> pdb=" O ILECq 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECq 382 " --> pdb=" O ASPCq 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCq 429 " --> pdb=" O GLUCq 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCq 385 " --> pdb=" O THRCq 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCq 431 " --> pdb=" O LEUCq 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALCq 387 " --> pdb=" O ASNCq 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCq 433 " --> pdb=" O VALCq 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCq 389 " --> pdb=" O VALCq 433 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Cr' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCr 271 " --> pdb=" O ILECr 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECr 382 " --> pdb=" O ASPCr 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCr 429 " --> pdb=" O GLUCr 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCr 385 " --> pdb=" O THRCr 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCr 431 " --> pdb=" O LEUCr 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCr 387 " --> pdb=" O ASNCr 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCr 433 " --> pdb=" O VALCr 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCr 389 " --> pdb=" O VALCr 433 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Cr' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCr 373 " --> pdb=" O GLUCr 279 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Cs' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCs 271 " --> pdb=" O ILECs 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECs 382 " --> pdb=" O ASPCs 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCs 429 " --> pdb=" O GLUCs 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCs 385 " --> pdb=" O THRCs 429 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASNCs 431 " --> pdb=" O LEUCs 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCs 387 " --> pdb=" O ASNCs 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCs 433 " --> pdb=" O VALCs 387 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VALCs 389 " --> pdb=" O VALCs 433 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Cs' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARGCs 373 " --> pdb=" O GLUCs 279 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILECt 372 " --> pdb=" O THRCs 278 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGCt 373 " --> pdb=" O GLUCt 279 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Ct' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCt 271 " --> pdb=" O ILECt 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECt 382 " --> pdb=" O ASPCt 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCt 429 " --> pdb=" O GLUCt 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCt 385 " --> pdb=" O THRCt 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCt 431 " --> pdb=" O LEUCt 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALCt 387 " --> pdb=" O ASNCt 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCt 433 " --> pdb=" O VALCt 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCt 389 " --> pdb=" O VALCt 433 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'Cu' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCu 271 " --> pdb=" O ILECu 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECu 382 " --> pdb=" O ASPCu 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCu 429 " --> pdb=" O GLUCu 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCu 385 " --> pdb=" O THRCu 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCu 431 " --> pdb=" O LEUCu 385 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VALCu 387 " --> pdb=" O ASNCu 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCu 433 " --> pdb=" O VALCu 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALCu 389 " --> pdb=" O VALCu 433 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'Cu' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCu 373 " --> pdb=" O GLUCu 279 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'Cv' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCv 271 " --> pdb=" O ILECv 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECv 382 " --> pdb=" O ASPCv 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCv 429 " --> pdb=" O GLUCv 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCv 385 " --> pdb=" O THRCv 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCv 431 " --> pdb=" O LEUCv 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCv 387 " --> pdb=" O ASNCv 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCv 433 " --> pdb=" O VALCv 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCv 389 " --> pdb=" O VALCv 433 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'Cv' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCv 373 " --> pdb=" O GLUCv 279 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'Cw' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCw 271 " --> pdb=" O ILECw 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECw 382 " --> pdb=" O ASPCw 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCw 429 " --> pdb=" O GLUCw 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCw 385 " --> pdb=" O THRCw 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCw 431 " --> pdb=" O LEUCw 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALCw 387 " --> pdb=" O ASNCw 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALCw 433 " --> pdb=" O VALCw 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCw 389 " --> pdb=" O VALCw 433 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'Cw' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCw 373 " --> pdb=" O GLUCw 279 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'Cx' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCx 271 " --> pdb=" O ILECx 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILECx 382 " --> pdb=" O ASPCx 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THRCx 429 " --> pdb=" O GLUCx 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCx 385 " --> pdb=" O THRCx 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCx 431 " --> pdb=" O LEUCx 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCx 387 " --> pdb=" O ASNCx 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCx 433 " --> pdb=" O VALCx 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCx 389 " --> pdb=" O VALCx 433 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'Cx' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGCx 373 " --> pdb=" O GLUCx 279 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'Cy' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPCy 271 " --> pdb=" O ILECy 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECy 382 " --> pdb=" O ASPCy 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCy 429 " --> pdb=" O GLUCy 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUCy 385 " --> pdb=" O THRCy 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNCy 431 " --> pdb=" O LEUCy 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCy 387 " --> pdb=" O ASNCy 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCy 433 " --> pdb=" O VALCy 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCy 389 " --> pdb=" O VALCy 433 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'Cy' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCy 373 " --> pdb=" O GLUCy 279 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'Cz' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPCz 271 " --> pdb=" O ILECz 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILECz 382 " --> pdb=" O ASPCz 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRCz 429 " --> pdb=" O GLUCz 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUCz 385 " --> pdb=" O THRCz 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNCz 431 " --> pdb=" O LEUCz 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALCz 387 " --> pdb=" O ASNCz 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALCz 433 " --> pdb=" O VALCz 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALCz 389 " --> pdb=" O VALCz 433 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Cz' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGCz 373 " --> pdb=" O GLUCz 279 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'Ea' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPEa 271 " --> pdb=" O ILEEa 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEa 382 " --> pdb=" O ASPEa 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THREa 429 " --> pdb=" O GLUEa 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUEa 385 " --> pdb=" O THREa 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNEa 431 " --> pdb=" O LEUEa 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALEa 387 " --> pdb=" O ASNEa 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALEa 433 " --> pdb=" O VALEa 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALEa 389 " --> pdb=" O VALEa 433 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'Ea' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGEa 373 " --> pdb=" O GLUEa 279 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'Eb' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPEb 271 " --> pdb=" O ILEEb 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEb 382 " --> pdb=" O ASPEb 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THREb 429 " --> pdb=" O GLUEb 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUEb 385 " --> pdb=" O THREb 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNEb 431 " --> pdb=" O LEUEb 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALEb 387 " --> pdb=" O ASNEb 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALEb 433 " --> pdb=" O VALEb 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALEb 389 " --> pdb=" O VALEb 433 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'Eb' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGEb 373 " --> pdb=" O GLUEb 279 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'Ec' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPEc 271 " --> pdb=" O ILEEc 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEc 382 " --> pdb=" O ASPEc 271 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N THREc 429 " --> pdb=" O GLUEc 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUEc 385 " --> pdb=" O THREc 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNEc 431 " --> pdb=" O LEUEc 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALEc 387 " --> pdb=" O ASNEc 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALEc 433 " --> pdb=" O VALEc 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALEc 389 " --> pdb=" O VALEc 433 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'Ec' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGEc 373 " --> pdb=" O GLUEc 279 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'Ed' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPEd 271 " --> pdb=" O ILEEd 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEd 382 " --> pdb=" O ASPEd 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THREd 429 " --> pdb=" O GLUEd 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUEd 385 " --> pdb=" O THREd 429 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N ASNEd 431 " --> pdb=" O LEUEd 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALEd 387 " --> pdb=" O ASNEd 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALEd 433 " --> pdb=" O VALEd 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALEd 389 " --> pdb=" O VALEd 433 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'Ed' and resid 279 through 281 removed outlier: 3.732A pdb=" N ARGEd 373 " --> pdb=" O GLUEd 279 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Ee' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPEe 271 " --> pdb=" O ILEEe 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEe 382 " --> pdb=" O ASPEe 271 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THREe 429 " --> pdb=" O GLUEe 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUEe 385 " --> pdb=" O THREe 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNEe 431 " --> pdb=" O LEUEe 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALEe 387 " --> pdb=" O ASNEe 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALEe 433 " --> pdb=" O VALEe 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALEe 389 " --> pdb=" O VALEe 433 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'Ee' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGEe 373 " --> pdb=" O GLUEe 279 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'Ef' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPEf 271 " --> pdb=" O ILEEf 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEEf 382 " --> pdb=" O ASPEf 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THREf 429 " --> pdb=" O GLUEf 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUEf 385 " --> pdb=" O THREf 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNEf 431 " --> pdb=" O LEUEf 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALEf 387 " --> pdb=" O ASNEf 431 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VALEf 433 " --> pdb=" O VALEf 387 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VALEf 389 " --> pdb=" O VALEf 433 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Ef' and resid 279 through 281 removed outlier: 3.731A pdb=" N ARGEf 373 " --> pdb=" O GLUEf 279 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'Eg' and resid 262 through 271 removed outlier: 6.708A pdb=" N ASPEg 271 " --> pdb=" O ILEEg 382 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILEEg 382 " --> pdb=" O ASPEg 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THREg 429 " --> pdb=" O GLUEg 383 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEUEg 385 " --> pdb=" O THREg 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNEg 431 " --> pdb=" O LEUEg 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VALEg 387 " --> pdb=" O ASNEg 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALEg 433 " --> pdb=" O VALEg 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALEg 389 " --> pdb=" O VALEg 433 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Eg' and resid 371 through 373 removed outlier: 3.732A pdb=" N ARGEg 373 " --> pdb=" O GLUEg 279 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARGFh 373 " --> pdb=" O GLUFh 279 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'Fh' and resid 262 through 271 removed outlier: 6.707A pdb=" N ASPFh 271 " --> pdb=" O ILEFh 382 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILEFh 382 " --> pdb=" O ASPFh 271 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N THRFh 429 " --> pdb=" O GLUFh 383 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEUFh 385 " --> pdb=" O THRFh 429 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ASNFh 431 " --> pdb=" O LEUFh 385 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VALFh 387 " --> pdb=" O ASNFh 431 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VALFh 433 " --> pdb=" O VALFh 387 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VALFh 389 " --> pdb=" O VALFh 433 " (cutoff:3.500A) 2313 hydrogen bonds defined for protein. 6633 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: 18.13 Time building geometry restraints manager: 19.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15911 1.33 - 1.45: 8433 1.45 - 1.57: 33200 1.57 - 1.69: 2 1.69 - 1.82: 250 Bond restraints: 57796 Sorted by residual: bond pdb=" N PRODb 160 " pdb=" CA PRODb 160 " ideal model delta sigma weight residual 1.469 1.692 -0.224 1.28e-02 6.10e+03 3.06e+02 bond pdb=" N PRODf 160 " pdb=" CA PRODf 160 " ideal model delta sigma weight residual 1.469 1.692 -0.224 1.28e-02 6.10e+03 3.05e+02 bond pdb=" C SERDr 171 " pdb=" N PRODr 172 " ideal model delta sigma weight residual 1.328 1.503 -0.175 1.25e-02 6.40e+03 1.96e+02 bond pdb=" C SERDs 171 " pdb=" N PRODs 172 " ideal model delta sigma weight residual 1.328 1.500 -0.171 1.26e-02 6.30e+03 1.85e+02 bond pdb=" C SERDf 171 " pdb=" N PRODf 172 " ideal model delta sigma weight residual 1.334 1.507 -0.173 2.34e-02 1.83e+03 5.46e+01 ... (remaining 57791 not shown) Histogram of bond angle deviations from ideal: 90.67 - 100.86: 122 100.86 - 111.06: 24512 111.06 - 121.25: 38383 121.25 - 131.44: 15215 131.44 - 141.63: 6 Bond angle restraints: 78238 Sorted by residual: angle pdb=" C SERDs 171 " pdb=" N PRODs 172 " pdb=" CA PRODs 172 " ideal model delta sigma weight residual 120.52 138.28 -17.76 9.90e-01 1.02e+00 3.22e+02 angle pdb=" C METDb 159 " pdb=" N PRODb 160 " pdb=" CA PRODb 160 " ideal model delta sigma weight residual 119.84 141.63 -21.79 1.25e+00 6.40e-01 3.04e+02 angle pdb=" C METDf 159 " pdb=" N PRODf 160 " pdb=" CA PRODf 160 " ideal model delta sigma weight residual 119.84 141.21 -21.37 1.25e+00 6.40e-01 2.92e+02 angle pdb=" C SERDr 171 " pdb=" N PRODr 172 " pdb=" CA PRODr 172 " ideal model delta sigma weight residual 120.85 137.41 -16.56 1.08e+00 8.57e-01 2.35e+02 angle pdb=" C SERDb 171 " pdb=" N PRODb 172 " pdb=" CA PRODb 172 " ideal model delta sigma weight residual 119.84 137.84 -18.00 1.25e+00 6.40e-01 2.07e+02 ... (remaining 78233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.44: 32360 16.44 - 32.88: 2814 32.88 - 49.32: 509 49.32 - 65.75: 114 65.75 - 82.19: 24 Dihedral angle restraints: 35821 sinusoidal: 13944 harmonic: 21877 Sorted by residual: dihedral pdb=" C PRODq 160 " pdb=" N PRODq 160 " pdb=" CA PRODq 160 " pdb=" CB PRODq 160 " ideal model delta harmonic sigma weight residual -120.70 -99.90 -20.80 0 2.50e+00 1.60e-01 6.92e+01 dihedral pdb=" N PRODq 160 " pdb=" C PRODq 160 " pdb=" CA PRODq 160 " pdb=" CB PRODq 160 " ideal model delta harmonic sigma weight residual 115.10 96.35 18.75 0 2.50e+00 1.60e-01 5.62e+01 dihedral pdb=" N PRODd 160 " pdb=" C PRODd 160 " pdb=" CA PRODd 160 " pdb=" CB PRODd 160 " ideal model delta harmonic sigma weight residual 115.10 98.96 16.14 0 2.50e+00 1.60e-01 4.17e+01 ... (remaining 35818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 7941 0.066 - 0.131: 1148 0.131 - 0.197: 120 0.197 - 0.262: 34 0.262 - 0.328: 14 Chirality restraints: 9257 Sorted by residual: chirality pdb=" CA PRODf 160 " pdb=" N PRODf 160 " pdb=" C PRODf 160 " pdb=" CB PRODf 160 " both_signs ideal model delta sigma weight residual False 2.72 3.05 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA PRODb 160 " pdb=" N PRODb 160 " pdb=" C PRODb 160 " pdb=" CB PRODb 160 " both_signs ideal model delta sigma weight residual False 2.72 3.05 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA UNKGE 4 " pdb=" N UNKGE 4 " pdb=" C UNKGE 4 " pdb=" CB UNKGE 4 " both_signs ideal model delta sigma weight residual False 2.52 2.21 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 9254 not shown) Planarity restraints: 10442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SERDs 171 " -0.016 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C SERDs 171 " 0.053 2.00e-02 2.50e+03 pdb=" O SERDs 171 " -0.020 2.00e-02 2.50e+03 pdb=" N PRODs 172 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALDp 166 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.54e+00 pdb=" C VALDp 166 " 0.051 2.00e-02 2.50e+03 pdb=" O VALDp 166 " -0.019 2.00e-02 2.50e+03 pdb=" N ARGDp 167 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SERDh 171 " -0.044 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRODh 172 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRODh 172 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRODh 172 " -0.037 5.00e-02 4.00e+02 ... (remaining 10439 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 829 2.60 - 3.18: 49363 3.18 - 3.75: 78365 3.75 - 4.33: 111569 4.33 - 4.90: 193145 Nonbonded interactions: 433271 Sorted by model distance: nonbonded pdb=" OD2 ASPCa 414 " pdb=" ND2 ASNFh 431 " model vdw 2.027 2.520 nonbonded pdb=" ND2 ASNEg 431 " pdb=" OD2 ASPFh 414 " model vdw 2.043 2.520 nonbonded pdb=" ND2 ASNCn 431 " pdb=" OD2 ASPCo 414 " model vdw 2.047 2.520 nonbonded pdb=" O UNKGE 5 " pdb=" OG SERFh 295 " model vdw 2.052 2.440 nonbonded pdb=" ND2 ASNEb 431 " pdb=" OD2 ASPEd 414 " model vdw 2.061 2.520 ... (remaining 433266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'Ca' selection = chain 'Cb' selection = chain 'Cc' selection = chain 'Cd' selection = chain 'Ce' selection = chain 'Cf' selection = chain 'Ch' selection = chain 'Ci' selection = chain 'Cj' selection = chain 'Ck' selection = chain 'Cl' selection = chain 'Cm' selection = chain 'Cn' selection = chain 'Co' selection = chain 'Cp' selection = chain 'Cq' selection = chain 'Cr' selection = chain 'Cs' selection = chain 'Ct' selection = chain 'Cu' selection = chain 'Cv' selection = chain 'Cw' selection = chain 'Cx' selection = chain 'Cy' selection = chain 'Cz' selection = chain 'Ea' selection = chain 'Eb' selection = chain 'Ec' selection = chain 'Ed' selection = chain 'Ee' selection = chain 'Ef' selection = chain 'Eg' selection = chain 'Fh' selection = chain 'cg' } ncs_group { reference = (chain 'Da' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Db' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dc' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dd' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'De' and resid 125 through 221) selection = (chain 'Df' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Do' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dp' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dq' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dr' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Ds' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dt' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Du' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dv' and (resid 125 through 160 or resid 171 through 221)) selection = (chain 'Dw' and (resid 125 through 160 or resid 171 through 221)) } ncs_group { reference = chain 'Dg' selection = chain 'Dh' selection = chain 'Di' selection = chain 'Dj' selection = chain 'Dk' selection = chain 'Dl' selection = chain 'Dm' selection = chain 'Dn' } ncs_group { reference = (chain 'GA' and resid 2 through 11) selection = (chain 'GC' and resid 2 through 11) selection = chain 'GD' selection = (chain 'GE' and resid 3 through 12) } ncs_group { reference = chain 'GF' selection = chain 'GG' selection = chain 'GH' selection = chain 'GJ' selection = chain 'GK' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 27.360 Check model and map are aligned: 0.630 Set scattering table: 0.400 Process input model: 117.900 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.710 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: 0.020 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.224 57796 Z= 0.467 Angle : 0.826 21.795 78238 Z= 0.536 Chirality : 0.049 0.328 9257 Planarity : 0.004 0.068 10442 Dihedral : 13.137 82.192 21475 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.73 % Favored : 92.68 % Rotamer: Outliers : 2.21 % Allowed : 7.73 % Favored : 90.06 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.09), residues: 7129 helix: -0.91 (0.11), residues: 2079 sheet: -2.96 (0.09), residues: 2858 loop : -2.65 (0.10), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HISDa 156 PHE 0.007 0.001 PHEDr 126 TYR 0.011 0.001 TYRCb 393 ARG 0.003 0.000 ARGDl 134 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2959 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 2823 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Da 147 LEU cc_start: 0.8962 (tp) cc_final: 0.8682 (mt) REVERT: Db 130 VAL cc_start: 0.9696 (t) cc_final: 0.9492 (p) REVERT: Db 132 TYR cc_start: 0.9459 (t80) cc_final: 0.9213 (t80) REVERT: Db 144 ILE cc_start: 0.9660 (mt) cc_final: 0.9332 (mm) REVERT: Db 150 VAL cc_start: 0.7417 (t) cc_final: 0.6978 (t) REVERT: Db 181 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8223 (tm-30) REVERT: Db 196 HIS cc_start: 0.8583 (m90) cc_final: 0.8305 (m-70) REVERT: Dc 173 SER cc_start: 0.8559 (m) cc_final: 0.8339 (t) REVERT: Dc 181 GLU cc_start: 0.9274 (mm-30) cc_final: 0.8889 (tm-30) REVERT: Dc 197 LEU cc_start: 0.8937 (tp) cc_final: 0.8737 (tp) REVERT: Dc 213 VAL cc_start: 0.9166 (t) cc_final: 0.8965 (p) REVERT: De 128 GLU cc_start: 0.8583 (tt0) cc_final: 0.8374 (tt0) REVERT: De 131 ASN cc_start: 0.9453 (m-40) cc_final: 0.8897 (t0) REVERT: De 187 ASP cc_start: 0.9044 (m-30) cc_final: 0.8773 (m-30) REVERT: Df 157 LEU cc_start: 0.8951 (mt) cc_final: 0.8350 (pp) REVERT: Df 205 LEU cc_start: 0.7462 (tp) cc_final: 0.6549 (tp) REVERT: Dg 126 PHE cc_start: 0.9292 (t80) cc_final: 0.8612 (t80) REVERT: Dg 144 ILE cc_start: 0.9334 (mt) cc_final: 0.9001 (mm) REVERT: Dg 147 LEU cc_start: 0.9075 (tp) cc_final: 0.8764 (mt) REVERT: Dh 132 TYR cc_start: 0.9102 (t80) cc_final: 0.8896 (t80) REVERT: Dh 214 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7406 (m-30) REVERT: Dh 220 LEU cc_start: 0.8692 (mt) cc_final: 0.8393 (mp) REVERT: Di 172 PRO cc_start: 0.8137 (Cg_endo) cc_final: 0.7260 (Cg_exo) REVERT: Dk 214 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7989 (m-30) REVERT: Dl 132 TYR cc_start: 0.9049 (t80) cc_final: 0.8745 (t80) REVERT: Dl 151 LYS cc_start: 0.9383 (ttmt) cc_final: 0.8540 (ttpp) REVERT: Dl 180 LEU cc_start: 0.8882 (mt) cc_final: 0.8424 (mt) REVERT: Dm 150 VAL cc_start: 0.8325 (t) cc_final: 0.7961 (t) REVERT: Dm 205 LEU cc_start: 0.6730 (tp) cc_final: 0.6152 (mp) REVERT: Dm 214 ASP cc_start: 0.9003 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: Dn 130 VAL cc_start: 0.9272 (t) cc_final: 0.9068 (m) REVERT: Dn 180 LEU cc_start: 0.8649 (mt) cc_final: 0.8435 (mt) REVERT: Dn 212 LEU cc_start: 0.9341 (tp) cc_final: 0.9140 (mt) REVERT: Do 147 LEU cc_start: 0.9006 (tp) cc_final: 0.8690 (mt) REVERT: Do 178 VAL cc_start: 0.9424 (m) cc_final: 0.9198 (p) REVERT: Do 196 HIS cc_start: 0.8880 (m90) cc_final: 0.8662 (m-70) REVERT: Do 221 THR cc_start: 0.6272 (t) cc_final: 0.5909 (t) REVERT: Dq 147 LEU cc_start: 0.9184 (tp) cc_final: 0.8889 (mt) REVERT: Dq 159 MET cc_start: 0.8349 (mtm) cc_final: 0.7769 (mmm) REVERT: Dq 160 PRO cc_start: 0.8358 (OUTLIER) cc_final: 0.8102 (Cg_endo) REVERT: Dq 195 VAL cc_start: 0.9664 (t) cc_final: 0.9320 (t) REVERT: Dq 205 LEU cc_start: 0.8630 (tp) cc_final: 0.8279 (tp) REVERT: Dq 213 VAL cc_start: 0.9262 (t) cc_final: 0.9041 (p) REVERT: Dr 196 HIS cc_start: 0.9312 (m90) cc_final: 0.8853 (m90) REVERT: Dr 197 LEU cc_start: 0.9480 (tp) cc_final: 0.9233 (tp) REVERT: Dr 205 LEU cc_start: 0.7967 (tp) cc_final: 0.7687 (tp) REVERT: Dr 210 VAL cc_start: 0.8665 (t) cc_final: 0.8352 (p) REVERT: Dr 218 HIS cc_start: 0.8749 (m-70) cc_final: 0.8516 (m170) REVERT: Ds 181 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9337 (tm-30) REVERT: Ds 220 LEU cc_start: 0.8474 (mt) cc_final: 0.8060 (mp) REVERT: Dt 126 PHE cc_start: 0.9059 (t80) cc_final: 0.8815 (t80) REVERT: Dt 127 SER cc_start: 0.9686 (t) cc_final: 0.9467 (p) REVERT: Dt 147 LEU cc_start: 0.9021 (tp) cc_final: 0.8812 (mt) REVERT: Dt 205 LEU cc_start: 0.8988 (tp) cc_final: 0.8678 (tp) REVERT: Dt 218 HIS cc_start: 0.8682 (m-70) cc_final: 0.8405 (m170) REVERT: Du 132 TYR cc_start: 0.9252 (t80) cc_final: 0.8951 (t80) REVERT: Du 147 LEU cc_start: 0.8599 (tp) cc_final: 0.8380 (mt) REVERT: Du 150 VAL cc_start: 0.8338 (t) cc_final: 0.8045 (t) REVERT: Dv 147 LEU cc_start: 0.9131 (tp) cc_final: 0.8844 (mt) REVERT: Dv 178 VAL cc_start: 0.9693 (m) cc_final: 0.9452 (p) REVERT: Dv 196 HIS cc_start: 0.9340 (m90) cc_final: 0.9041 (m90) REVERT: Dv 221 THR cc_start: 0.3419 (t) cc_final: 0.3120 (t) REVERT: Dw 127 SER cc_start: 0.9744 (t) cc_final: 0.9477 (p) REVERT: Dw 145 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8740 (mt-10) REVERT: Dw 157 LEU cc_start: 0.9195 (mt) cc_final: 0.8317 (mt) REVERT: Dw 160 PRO cc_start: 0.6655 (OUTLIER) cc_final: 0.6280 (Cg_exo) REVERT: Dw 205 LEU cc_start: 0.8275 (tp) cc_final: 0.7848 (tp) REVERT: Dw 210 VAL cc_start: 0.8965 (t) cc_final: 0.8722 (t) REVERT: Dw 218 HIS cc_start: 0.7956 (m-70) cc_final: 0.7683 (m170) REVERT: Ca 270 LEU cc_start: 0.8329 (mt) cc_final: 0.7992 (mm) REVERT: Cc 375 THR cc_start: 0.7854 (m) cc_final: 0.7411 (p) REVERT: Cc 404 LEU cc_start: 0.6805 (mp) cc_final: 0.5271 (tt) REVERT: Cc 430 LEU cc_start: 0.7090 (tp) cc_final: 0.6399 (tp) REVERT: Cd 416 THR cc_start: 0.8939 (m) cc_final: 0.8571 (p) REVERT: Ce 368 VAL cc_start: 0.6563 (m) cc_final: 0.6346 (m) REVERT: Ce 404 LEU cc_start: 0.6702 (mp) cc_final: 0.5278 (tp) REVERT: Cf 249 ILE cc_start: 0.8779 (mt) cc_final: 0.8524 (tp) REVERT: Ch 249 ILE cc_start: 0.8882 (mt) cc_final: 0.8580 (tp) REVERT: Ch 363 THR cc_start: 0.6783 (m) cc_final: 0.6475 (t) REVERT: Ci 301 SER cc_start: 0.6063 (t) cc_final: 0.4246 (p) REVERT: Ci 418 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7822 (mm-30) REVERT: Cj 242 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7694 (pt0) REVERT: Cj 243 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.7638 (p) REVERT: Cj 250 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6846 (pt0) REVERT: Cj 416 THR cc_start: 0.8814 (m) cc_final: 0.8537 (p) REVERT: Ck 243 SER cc_start: 0.8475 (OUTLIER) cc_final: 0.7437 (p) REVERT: Cn 404 LEU cc_start: 0.7334 (mp) cc_final: 0.6534 (tp) REVERT: Co 235 LEU cc_start: 0.8653 (mt) cc_final: 0.8315 (mp) REVERT: Co 239 ASN cc_start: 0.8520 (t0) cc_final: 0.8137 (t0) REVERT: Co 409 MET cc_start: 0.7345 (tmm) cc_final: 0.7015 (tmm) REVERT: Co 414 ASP cc_start: 0.7618 (t0) cc_final: 0.7126 (t0) REVERT: Cq 242 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7860 (pt0) REVERT: Cq 372 ILE cc_start: 0.7034 (mt) cc_final: 0.6464 (mt) REVERT: Cq 404 LEU cc_start: 0.6631 (mp) cc_final: 0.5892 (tp) REVERT: Cr 243 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8986 (p) REVERT: Cr 301 SER cc_start: 0.6907 (t) cc_final: 0.5666 (p) REVERT: Cr 361 ASN cc_start: 0.7459 (m-40) cc_final: 0.5839 (m-40) REVERT: Cs 301 SER cc_start: 0.6560 (t) cc_final: 0.6241 (p) REVERT: Cs 361 ASN cc_start: 0.6631 (m110) cc_final: 0.5401 (m-40) REVERT: Ct 243 SER cc_start: 0.8374 (OUTLIER) cc_final: 0.8060 (p) REVERT: Ct 416 THR cc_start: 0.8531 (m) cc_final: 0.8281 (p) REVERT: Cu 249 ILE cc_start: 0.9047 (mt) cc_final: 0.8724 (tp) REVERT: Cu 363 THR cc_start: 0.7179 (m) cc_final: 0.6349 (p) REVERT: Cv 271 ASP cc_start: 0.6269 (t0) cc_final: 0.5770 (t70) REVERT: Cv 414 ASP cc_start: 0.7179 (t0) cc_final: 0.6845 (t0) REVERT: Cv 430 LEU cc_start: 0.7989 (tp) cc_final: 0.6595 (tp) REVERT: Cw 370 ARG cc_start: 0.6547 (ttp-170) cc_final: 0.6251 (ttp-170) REVERT: Cw 416 THR cc_start: 0.9071 (m) cc_final: 0.8732 (p) REVERT: Cx 375 THR cc_start: 0.7708 (m) cc_final: 0.6815 (m) REVERT: Cx 430 LEU cc_start: 0.7232 (tp) cc_final: 0.6611 (tp) REVERT: Cy 301 SER cc_start: 0.6852 (t) cc_final: 0.5191 (p) REVERT: Cy 361 ASN cc_start: 0.7293 (m-40) cc_final: 0.6583 (m-40) REVERT: Cy 363 THR cc_start: 0.6121 (m) cc_final: 0.5559 (p) REVERT: Cy 365 ASN cc_start: 0.7121 (m-40) cc_final: 0.6551 (m-40) REVERT: Cy 404 LEU cc_start: 0.5576 (mp) cc_final: 0.4082 (tp) REVERT: Cz 416 THR cc_start: 0.8630 (m) cc_final: 0.8391 (p) REVERT: Ea 242 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8169 (pt0) REVERT: Ea 243 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.6855 (p) REVERT: Ea 412 ILE cc_start: 0.9207 (mt) cc_final: 0.9005 (mt) REVERT: Eb 404 LEU cc_start: 0.7499 (mp) cc_final: 0.6484 (tp) REVERT: Ec 372 ILE cc_start: 0.6957 (mt) cc_final: 0.6180 (mt) REVERT: Eg 271 ASP cc_start: 0.6753 (t0) cc_final: 0.6182 (t70) REVERT: Eg 358 THR cc_start: 0.6793 (m) cc_final: 0.5849 (p) REVERT: Fh 404 LEU cc_start: 0.7837 (mp) cc_final: 0.7546 (tp) outliers start: 136 outliers final: 14 residues processed: 2907 average time/residue: 0.5299 time to fit residues: 2558.4902 Evaluate side-chains 1363 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1339 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 617 optimal weight: 7.9990 chunk 554 optimal weight: 10.0000 chunk 307 optimal weight: 1.9990 chunk 189 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 296 optimal weight: 4.9990 chunk 572 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 426 optimal weight: 9.9990 chunk 663 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Da 125 GLN ** Db 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Db 156 HIS Db 218 HIS Dc 131 ASN ** Dc 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dd 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dd 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** De 131 ASN De 218 HIS Dg 131 ASN ** Dg 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dg 218 HIS Dh 156 HIS Di 131 ASN ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Di 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dk 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 131 ASN Dl 156 HIS Dl 196 HIS Dl 218 HIS ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dm 218 HIS Dn 196 HIS Do 156 HIS ** Dp 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dq 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dq 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dr 125 GLN ** Dr 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dr 218 HIS ** Ds 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dt 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dv 125 GLN Dv 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 361 ASN Cb 365 ASN ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cc 261 ASN ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 265 GLN ** Cd 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 365 ASN ** Cd 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 274 ASN ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 274 ASN ** Ch 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 303 GLN ** Ck 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 246 GLN ** Cl 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 274 ASN ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 374 HIS Cm 408 GLN ** Cm 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 246 GLN ** Cp 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 281 HIS ** Cs 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 274 ASN ** Cu 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cv 265 GLN Cv 365 ASN ** Cv 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 297 GLN ** Cy 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN ** Cz 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 297 GLN ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 281 HIS ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN Ed 374 HIS ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ee 303 GLN ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ef 246 GLN Ef 263 HIS Ef 274 ASN ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 274 ASN ** Eg 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 411 GLN ** Fh 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Fh 274 ASN ** Fh 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.128 57796 Z= 0.498 Angle : 0.912 13.472 78238 Z= 0.482 Chirality : 0.046 0.443 9257 Planarity : 0.007 0.132 10442 Dihedral : 5.531 43.192 8031 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 29.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.41 % Favored : 96.51 % Rotamer: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.09), residues: 7129 helix: -0.13 (0.11), residues: 2108 sheet: -1.83 (0.09), residues: 2915 loop : -1.94 (0.12), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.021 0.004 HISEb 281 PHE 0.028 0.003 PHEEc 272 TYR 0.024 0.003 TYREg 282 ARG 0.032 0.001 ARGCk 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1545 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1530 time to evaluate : 5.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Da 147 LEU cc_start: 0.9268 (tp) cc_final: 0.9062 (mt) REVERT: Da 212 LEU cc_start: 0.9083 (mp) cc_final: 0.8864 (mt) REVERT: Db 132 TYR cc_start: 0.9620 (t80) cc_final: 0.9369 (t80) REVERT: Db 137 GLU cc_start: 0.9120 (tt0) cc_final: 0.8911 (tt0) REVERT: Db 196 HIS cc_start: 0.8896 (m90) cc_final: 0.8484 (m90) REVERT: Dc 173 SER cc_start: 0.9087 (m) cc_final: 0.8613 (t) REVERT: Dc 197 LEU cc_start: 0.8967 (tp) cc_final: 0.8617 (tp) REVERT: Dc 205 LEU cc_start: 0.8614 (tp) cc_final: 0.8345 (tp) REVERT: Df 126 PHE cc_start: 0.9177 (t80) cc_final: 0.8924 (t80) REVERT: Df 132 TYR cc_start: 0.9214 (t80) cc_final: 0.8874 (t80) REVERT: Df 157 LEU cc_start: 0.9112 (mt) cc_final: 0.8054 (pp) REVERT: Df 205 LEU cc_start: 0.6199 (tp) cc_final: 0.5671 (tp) REVERT: Dg 144 ILE cc_start: 0.9480 (mt) cc_final: 0.9247 (mm) REVERT: Dg 147 LEU cc_start: 0.9114 (tp) cc_final: 0.8882 (mt) REVERT: Dg 151 LYS cc_start: 0.9651 (ttmt) cc_final: 0.9342 (ptmt) REVERT: Di 157 LEU cc_start: 0.8045 (pp) cc_final: 0.7386 (pp) REVERT: Di 159 MET cc_start: 0.8010 (mmm) cc_final: 0.6830 (ptt) REVERT: Di 160 PRO cc_start: 0.4941 (Cg_endo) cc_final: 0.4476 (Cg_exo) REVERT: Di 172 PRO cc_start: 0.8277 (Cg_endo) cc_final: 0.7965 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9135 (m-30) cc_final: 0.8653 (p0) REVERT: Dk 131 ASN cc_start: 0.9475 (p0) cc_final: 0.9218 (p0) REVERT: Dk 212 LEU cc_start: 0.9555 (tp) cc_final: 0.9306 (tp) REVERT: Dk 220 LEU cc_start: 0.8850 (mp) cc_final: 0.8013 (mp) REVERT: Dl 151 LYS cc_start: 0.9059 (ttmt) cc_final: 0.8737 (ttpp) REVERT: Dl 187 ASP cc_start: 0.8751 (m-30) cc_final: 0.8191 (p0) REVERT: Dm 159 MET cc_start: 0.8153 (tpt) cc_final: 0.7737 (tmm) REVERT: Dn 196 HIS cc_start: 0.9454 (m90) cc_final: 0.9232 (m-70) REVERT: Dn 218 HIS cc_start: 0.8797 (t-90) cc_final: 0.8451 (t70) REVERT: Do 147 LEU cc_start: 0.9348 (tp) cc_final: 0.9074 (mt) REVERT: Dp 205 LEU cc_start: 0.8645 (tp) cc_final: 0.8377 (tp) REVERT: Dr 142 ARG cc_start: 0.9639 (ptp-110) cc_final: 0.9417 (ptp-110) REVERT: Dr 150 VAL cc_start: 0.9422 (t) cc_final: 0.9120 (m) REVERT: Dr 196 HIS cc_start: 0.9373 (m90) cc_final: 0.9010 (m90) REVERT: Dr 197 LEU cc_start: 0.9609 (tp) cc_final: 0.9242 (tp) REVERT: Dr 213 VAL cc_start: 0.8941 (t) cc_final: 0.8698 (p) REVERT: Ds 126 PHE cc_start: 0.9526 (t80) cc_final: 0.9142 (t80) REVERT: Ds 150 VAL cc_start: 0.9502 (t) cc_final: 0.8839 (t) REVERT: Ds 212 LEU cc_start: 0.9642 (tp) cc_final: 0.9419 (tp) REVERT: Dt 126 PHE cc_start: 0.9203 (t80) cc_final: 0.8915 (t80) REVERT: Dt 136 LEU cc_start: 0.9641 (mt) cc_final: 0.9183 (mt) REVERT: Dt 147 LEU cc_start: 0.9369 (tp) cc_final: 0.9158 (mt) REVERT: Dt 159 MET cc_start: 0.9040 (pmm) cc_final: 0.8381 (tpp) REVERT: Dt 197 LEU cc_start: 0.9347 (tp) cc_final: 0.8999 (tp) REVERT: Du 126 PHE cc_start: 0.9376 (t80) cc_final: 0.9166 (t80) REVERT: Du 137 GLU cc_start: 0.9213 (tt0) cc_final: 0.8690 (tp30) REVERT: Du 147 LEU cc_start: 0.9222 (tp) cc_final: 0.8735 (mt) REVERT: Dv 136 LEU cc_start: 0.9698 (mt) cc_final: 0.9288 (mt) REVERT: Dv 147 LEU cc_start: 0.9341 (tp) cc_final: 0.8916 (mt) REVERT: Dv 178 VAL cc_start: 0.9612 (m) cc_final: 0.9384 (p) REVERT: Dv 196 HIS cc_start: 0.9423 (m90) cc_final: 0.9188 (m90) REVERT: Dv 205 LEU cc_start: 0.8467 (tp) cc_final: 0.8229 (tp) REVERT: Dw 127 SER cc_start: 0.9724 (t) cc_final: 0.9432 (p) REVERT: Dw 128 GLU cc_start: 0.9421 (tm-30) cc_final: 0.9215 (tm-30) REVERT: Dw 157 LEU cc_start: 0.8917 (mt) cc_final: 0.8125 (mt) REVERT: Dw 176 VAL cc_start: 0.8926 (t) cc_final: 0.8715 (t) REVERT: Dw 218 HIS cc_start: 0.8264 (m-70) cc_final: 0.7898 (m170) REVERT: Ca 413 GLU cc_start: 0.8945 (pt0) cc_final: 0.8559 (pt0) REVERT: Cb 385 LEU cc_start: 0.7594 (tp) cc_final: 0.7202 (tp) REVERT: Cc 385 LEU cc_start: 0.8441 (tp) cc_final: 0.8048 (mp) REVERT: Cc 404 LEU cc_start: 0.7342 (mp) cc_final: 0.6816 (mm) REVERT: Cc 416 THR cc_start: 0.8673 (m) cc_final: 0.8313 (p) REVERT: Cc 430 LEU cc_start: 0.7900 (tp) cc_final: 0.7172 (tt) REVERT: Cd 416 THR cc_start: 0.8772 (m) cc_final: 0.8561 (p) REVERT: Cd 420 MET cc_start: 0.8439 (ttm) cc_final: 0.8189 (ttm) REVERT: Ce 420 MET cc_start: 0.8439 (ptm) cc_final: 0.8198 (ppp) REVERT: Cf 385 LEU cc_start: 0.8747 (tp) cc_final: 0.8273 (mt) REVERT: Cf 413 GLU cc_start: 0.8570 (pt0) cc_final: 0.8307 (pt0) REVERT: cg 245 ILE cc_start: 0.8304 (tp) cc_final: 0.8025 (pt) REVERT: Ch 249 ILE cc_start: 0.9223 (mt) cc_final: 0.8858 (tp) REVERT: Ci 249 ILE cc_start: 0.9244 (pt) cc_final: 0.9026 (tp) REVERT: Cj 385 LEU cc_start: 0.8332 (tp) cc_final: 0.7884 (mp) REVERT: Cj 413 GLU cc_start: 0.8785 (pt0) cc_final: 0.8540 (pt0) REVERT: Cj 416 THR cc_start: 0.9009 (m) cc_final: 0.8802 (p) REVERT: Cl 416 THR cc_start: 0.9233 (p) cc_final: 0.8896 (p) REVERT: Cn 270 LEU cc_start: 0.8424 (mm) cc_final: 0.8182 (mm) REVERT: Cn 363 THR cc_start: 0.7147 (p) cc_final: 0.6890 (p) REVERT: Cn 420 MET cc_start: 0.8728 (pmm) cc_final: 0.8413 (pmm) REVERT: Co 409 MET cc_start: 0.7782 (tmm) cc_final: 0.7006 (tmm) REVERT: Co 413 GLU cc_start: 0.8749 (pt0) cc_final: 0.8465 (pt0) REVERT: Co 416 THR cc_start: 0.9012 (p) cc_final: 0.8653 (p) REVERT: Cp 416 THR cc_start: 0.8563 (p) cc_final: 0.8363 (p) REVERT: Cq 359 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7618 (tm-30) REVERT: Cr 385 LEU cc_start: 0.8379 (tt) cc_final: 0.8067 (mt) REVERT: Cr 420 MET cc_start: 0.8775 (ptp) cc_final: 0.8422 (ptp) REVERT: Ct 253 LEU cc_start: 0.7942 (mt) cc_final: 0.7663 (mt) REVERT: Ct 416 THR cc_start: 0.8816 (m) cc_final: 0.8120 (p) REVERT: Cu 249 ILE cc_start: 0.9301 (mt) cc_final: 0.9095 (tp) REVERT: Cv 414 ASP cc_start: 0.8217 (t0) cc_final: 0.7904 (t70) REVERT: Cv 416 THR cc_start: 0.8714 (p) cc_final: 0.8476 (p) REVERT: Cy 249 ILE cc_start: 0.9254 (mt) cc_final: 0.8773 (tp) REVERT: Cy 385 LEU cc_start: 0.8114 (tp) cc_final: 0.7826 (tp) REVERT: Cy 416 THR cc_start: 0.8907 (m) cc_final: 0.8632 (p) REVERT: Cy 428 ASP cc_start: 0.7392 (t0) cc_final: 0.6263 (t0) REVERT: Cy 430 LEU cc_start: 0.8106 (tp) cc_final: 0.7856 (tp) REVERT: Cz 413 GLU cc_start: 0.8774 (pt0) cc_final: 0.8380 (pt0) REVERT: Cz 416 THR cc_start: 0.8926 (m) cc_final: 0.8342 (p) REVERT: Ea 385 LEU cc_start: 0.8465 (tp) cc_final: 0.8126 (pp) REVERT: Ea 413 GLU cc_start: 0.9102 (pt0) cc_final: 0.8746 (pt0) REVERT: Ea 424 ASP cc_start: 0.8089 (p0) cc_final: 0.7745 (p0) REVERT: Eb 407 ASP cc_start: 0.8138 (p0) cc_final: 0.7840 (p0) REVERT: Ec 259 ASN cc_start: 0.7761 (p0) cc_final: 0.7553 (p0) REVERT: Ed 385 LEU cc_start: 0.8831 (mt) cc_final: 0.8607 (mp) REVERT: Ef 420 MET cc_start: 0.8297 (ptp) cc_final: 0.8064 (ptp) REVERT: Eg 259 ASN cc_start: 0.7672 (p0) cc_final: 0.7471 (p0) REVERT: Fh 404 LEU cc_start: 0.8344 (mp) cc_final: 0.7613 (tt) REVERT: Fh 413 GLU cc_start: 0.8578 (pt0) cc_final: 0.8000 (pt0) outliers start: 15 outliers final: 7 residues processed: 1542 average time/residue: 0.5251 time to fit residues: 1353.7814 Evaluate side-chains 990 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 983 time to evaluate : 5.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 368 optimal weight: 0.8980 chunk 206 optimal weight: 0.0270 chunk 552 optimal weight: 0.8980 chunk 452 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 665 optimal weight: 0.9990 chunk 718 optimal weight: 0.7980 chunk 592 optimal weight: 3.9990 chunk 659 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 533 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Da 209 ASN Da 218 HIS Db 131 ASN ** Dd 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** De 209 ASN Df 125 GLN Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dj 125 GLN ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dq 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ds 218 HIS Dt 156 HIS Dt 218 HIS Ca 274 ASN ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 365 ASN ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 374 HIS ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 411 GLN ** Ci 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 274 ASN Cj 297 GLN ** Cj 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ck 411 GLN ** Cl 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 281 HIS ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 303 GLN Cm 408 GLN ** Cm 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 261 ASN Cn 297 GLN ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 246 GLN ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 265 GLN ** Cq 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cq 411 GLN Cr 246 GLN ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 411 GLN Ct 359 GLN ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 411 GLN Cw 261 ASN ** Cw 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cw 365 ASN Cx 274 ASN Cx 297 GLN ** Cx 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cy 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN Cz 246 GLN Cz 411 GLN ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ee 359 GLN ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ef 411 GLN Eg 246 GLN Eg 297 GLN Fh 274 ASN ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.6182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 57796 Z= 0.198 Angle : 0.643 9.286 78238 Z= 0.329 Chirality : 0.043 0.171 9257 Planarity : 0.004 0.099 10442 Dihedral : 4.887 39.494 8031 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.61 % Favored : 97.35 % Rotamer: Outliers : 0.31 % Allowed : 3.22 % Favored : 96.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.10), residues: 7129 helix: 0.72 (0.12), residues: 2113 sheet: -1.45 (0.09), residues: 3033 loop : -1.53 (0.12), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HISCl 281 PHE 0.023 0.002 PHECi 422 TYR 0.017 0.002 TYRDm 132 ARG 0.013 0.001 ARGcg 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 1532 time to evaluate : 5.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Da 126 PHE cc_start: 0.9222 (p90) cc_final: 0.8967 (p90) REVERT: Db 132 TYR cc_start: 0.9621 (t80) cc_final: 0.9272 (t80) REVERT: Db 196 HIS cc_start: 0.8872 (m90) cc_final: 0.8500 (m-70) REVERT: Dc 126 PHE cc_start: 0.9338 (t80) cc_final: 0.9115 (t80) REVERT: Dc 151 LYS cc_start: 0.9628 (ttmt) cc_final: 0.9407 (ptmm) REVERT: Dc 159 MET cc_start: 0.8857 (mmp) cc_final: 0.8650 (mmm) REVERT: Dc 173 SER cc_start: 0.8706 (m) cc_final: 0.8284 (t) REVERT: Dc 197 LEU cc_start: 0.8971 (tp) cc_final: 0.8696 (tp) REVERT: Dc 205 LEU cc_start: 0.8387 (tp) cc_final: 0.8099 (tp) REVERT: Df 128 GLU cc_start: 0.9225 (mp0) cc_final: 0.9001 (mp0) REVERT: Df 132 TYR cc_start: 0.8957 (t80) cc_final: 0.8538 (t80) REVERT: Df 157 LEU cc_start: 0.9127 (mt) cc_final: 0.8086 (pp) REVERT: Df 205 LEU cc_start: 0.5708 (tp) cc_final: 0.5103 (tp) REVERT: Dg 151 LYS cc_start: 0.9621 (ttmt) cc_final: 0.9335 (ptpp) REVERT: Dh 128 GLU cc_start: 0.9437 (pt0) cc_final: 0.9219 (pt0) REVERT: Di 157 LEU cc_start: 0.7835 (pp) cc_final: 0.6110 (pp) REVERT: Di 159 MET cc_start: 0.8176 (mmm) cc_final: 0.6915 (ptt) REVERT: Di 172 PRO cc_start: 0.8512 (Cg_endo) cc_final: 0.8155 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9094 (m-30) cc_final: 0.8620 (p0) REVERT: Dl 151 LYS cc_start: 0.8956 (ttmt) cc_final: 0.8559 (ptmm) REVERT: Dn 196 HIS cc_start: 0.9298 (m90) cc_final: 0.8844 (m170) REVERT: Do 196 HIS cc_start: 0.9333 (m-70) cc_final: 0.8978 (m-70) REVERT: Do 214 ASP cc_start: 0.8923 (m-30) cc_final: 0.8716 (m-30) REVERT: Do 218 HIS cc_start: 0.9120 (t-170) cc_final: 0.8842 (t-170) REVERT: Dp 205 LEU cc_start: 0.8578 (tp) cc_final: 0.8363 (tp) REVERT: Dq 159 MET cc_start: 0.8819 (mmp) cc_final: 0.8555 (mmm) REVERT: Dr 142 ARG cc_start: 0.9551 (ptp-110) cc_final: 0.9298 (ptt-90) REVERT: Dr 196 HIS cc_start: 0.9224 (m90) cc_final: 0.8833 (m-70) REVERT: Dr 205 LEU cc_start: 0.8168 (tp) cc_final: 0.7964 (tp) REVERT: Ds 126 PHE cc_start: 0.9384 (t80) cc_final: 0.9155 (t80) REVERT: Ds 136 LEU cc_start: 0.9723 (mt) cc_final: 0.9498 (mt) REVERT: Ds 151 LYS cc_start: 0.9502 (ptpt) cc_final: 0.9275 (ptpt) REVERT: Ds 157 LEU cc_start: 0.9468 (tt) cc_final: 0.8875 (mm) REVERT: Ds 212 LEU cc_start: 0.9520 (tp) cc_final: 0.9231 (tp) REVERT: Ds 220 LEU cc_start: 0.9099 (mp) cc_final: 0.8609 (mp) REVERT: Dt 126 PHE cc_start: 0.9056 (t80) cc_final: 0.8815 (t80) REVERT: Dt 136 LEU cc_start: 0.9693 (mt) cc_final: 0.9116 (mt) REVERT: Du 126 PHE cc_start: 0.9338 (t80) cc_final: 0.9106 (t80) REVERT: Du 137 GLU cc_start: 0.9171 (tt0) cc_final: 0.8664 (tp30) REVERT: Du 147 LEU cc_start: 0.9277 (tp) cc_final: 0.8874 (mt) REVERT: Du 213 VAL cc_start: 0.9113 (m) cc_final: 0.8896 (p) REVERT: Dv 128 GLU cc_start: 0.9691 (tt0) cc_final: 0.9477 (mm-30) REVERT: Dv 136 LEU cc_start: 0.9750 (mt) cc_final: 0.9364 (mt) REVERT: Dv 139 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9171 (pm20) REVERT: Dv 196 HIS cc_start: 0.9393 (m90) cc_final: 0.9099 (m90) REVERT: Dv 205 LEU cc_start: 0.8428 (tp) cc_final: 0.8141 (tp) REVERT: Dw 218 HIS cc_start: 0.8375 (m-70) cc_final: 0.7953 (m170) REVERT: Ca 271 ASP cc_start: 0.5859 (t0) cc_final: 0.5134 (t0) REVERT: Ca 414 ASP cc_start: 0.8132 (m-30) cc_final: 0.7011 (m-30) REVERT: Cb 300 ILE cc_start: 0.8362 (mt) cc_final: 0.7822 (mt) REVERT: Ce 241 VAL cc_start: 0.8862 (m) cc_final: 0.8532 (p) REVERT: Ce 420 MET cc_start: 0.8184 (ptm) cc_final: 0.7880 (ppp) REVERT: Cf 249 ILE cc_start: 0.9014 (mm) cc_final: 0.8720 (pt) REVERT: cg 242 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7504 (pt0) REVERT: cg 293 LEU cc_start: 0.8645 (tp) cc_final: 0.8403 (tp) REVERT: Ch 249 ILE cc_start: 0.9162 (mt) cc_final: 0.8800 (tp) REVERT: Ch 267 THR cc_start: 0.5390 (m) cc_final: 0.5049 (m) REVERT: Ch 385 LEU cc_start: 0.8267 (mt) cc_final: 0.8047 (mp) REVERT: Ch 430 LEU cc_start: 0.8112 (tp) cc_final: 0.7832 (tt) REVERT: Ci 249 ILE cc_start: 0.9082 (pt) cc_final: 0.8857 (tp) REVERT: Ci 409 MET cc_start: 0.6868 (mmm) cc_final: 0.6248 (mmt) REVERT: Ci 414 ASP cc_start: 0.8034 (m-30) cc_final: 0.7566 (m-30) REVERT: Cj 299 ASN cc_start: 0.7182 (m-40) cc_final: 0.6867 (m-40) REVERT: Cj 385 LEU cc_start: 0.8038 (tp) cc_final: 0.7436 (mp) REVERT: Cj 414 ASP cc_start: 0.7871 (m-30) cc_final: 0.6403 (m-30) REVERT: Cj 416 THR cc_start: 0.8875 (m) cc_final: 0.8577 (p) REVERT: Cl 293 LEU cc_start: 0.8182 (tp) cc_final: 0.7228 (tt) REVERT: Cn 363 THR cc_start: 0.7220 (p) cc_final: 0.6918 (p) REVERT: Co 409 MET cc_start: 0.7716 (tmm) cc_final: 0.6906 (tmm) REVERT: Cp 236 LYS cc_start: 0.9399 (pptt) cc_final: 0.9041 (pptt) REVERT: Cp 410 LYS cc_start: 0.9279 (ptpp) cc_final: 0.9019 (ptpp) REVERT: Cp 430 LEU cc_start: 0.7435 (tt) cc_final: 0.6824 (tp) REVERT: Cq 430 LEU cc_start: 0.7488 (tp) cc_final: 0.7196 (tp) REVERT: Cr 414 ASP cc_start: 0.7559 (t0) cc_final: 0.7134 (t70) REVERT: Cs 385 LEU cc_start: 0.8222 (tp) cc_final: 0.8019 (mm) REVERT: Cv 391 VAL cc_start: 0.8070 (m) cc_final: 0.7848 (p) REVERT: Cv 414 ASP cc_start: 0.7934 (t0) cc_final: 0.7444 (t70) REVERT: Cx 301 SER cc_start: 0.5323 (p) cc_final: 0.4608 (t) REVERT: Cx 430 LEU cc_start: 0.7112 (tp) cc_final: 0.6663 (mt) REVERT: Cy 236 LYS cc_start: 0.9012 (ptpp) cc_final: 0.8791 (ptpp) REVERT: Cy 249 ILE cc_start: 0.9187 (mt) cc_final: 0.8816 (tp) REVERT: Cz 242 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7488 (mt-10) REVERT: Cz 430 LEU cc_start: 0.8324 (tp) cc_final: 0.8018 (tp) REVERT: Ea 253 LEU cc_start: 0.8438 (mt) cc_final: 0.8233 (mt) REVERT: Ea 385 LEU cc_start: 0.8500 (tp) cc_final: 0.8208 (pp) REVERT: Eb 259 ASN cc_start: 0.8037 (p0) cc_final: 0.7608 (p0) REVERT: Ec 236 LYS cc_start: 0.8813 (pptt) cc_final: 0.8409 (pptt) REVERT: Ec 424 ASP cc_start: 0.7808 (p0) cc_final: 0.7545 (p0) REVERT: Ed 375 THR cc_start: 0.7401 (m) cc_final: 0.7060 (m) REVERT: Ed 414 ASP cc_start: 0.8129 (t0) cc_final: 0.7766 (t0) REVERT: Eg 259 ASN cc_start: 0.7703 (p0) cc_final: 0.7438 (p0) REVERT: Fh 404 LEU cc_start: 0.8166 (mp) cc_final: 0.7733 (mt) outliers start: 19 outliers final: 7 residues processed: 1536 average time/residue: 0.5352 time to fit residues: 1374.2551 Evaluate side-chains 1025 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1017 time to evaluate : 5.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 657 optimal weight: 2.9990 chunk 499 optimal weight: 6.9990 chunk 345 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 317 optimal weight: 10.0000 chunk 446 optimal weight: 9.9990 chunk 667 optimal weight: 3.9990 chunk 706 optimal weight: 10.0000 chunk 348 optimal weight: 10.0000 chunk 632 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Da 218 HIS Db 209 ASN ** Dd 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Df 209 ASN Dg 209 ASN Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 131 ASN Dl 196 HIS Dl 218 HIS ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dn 218 HIS ** Dp 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dr 209 ASN Dr 218 HIS Ds 209 ASN Dt 218 HIS Dv 209 ASN Dw 209 ASN ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 365 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 365 ASN Ch 411 GLN ** Ci 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 365 ASN ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cm 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 239 ASN ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 411 GLN Ct 265 GLN ** Ct 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 411 GLN Cw 365 ASN ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cy 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 365 ASN ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN Ee 365 ASN ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ef 374 HIS Ef 411 GLN ** Eg 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 411 GLN Fh 246 GLN Fh 261 ASN Fh 265 GLN ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.7230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 57796 Z= 0.395 Angle : 0.756 9.932 78238 Z= 0.402 Chirality : 0.043 0.187 9257 Planarity : 0.006 0.106 10442 Dihedral : 5.242 36.150 8031 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 0.06 % Allowed : 4.70 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.10), residues: 7129 helix: 0.32 (0.11), residues: 2160 sheet: -1.20 (0.09), residues: 2999 loop : -1.27 (0.13), residues: 1970 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HISCr 281 PHE 0.024 0.002 PHECt 272 TYR 0.023 0.003 TYRFh 393 ARG 0.013 0.001 ARGCi 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1218 time to evaluate : 5.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: Da 126 PHE cc_start: 0.9289 (p90) cc_final: 0.9033 (p90) REVERT: Db 132 TYR cc_start: 0.9674 (t80) cc_final: 0.9459 (t80) REVERT: Db 196 HIS cc_start: 0.9035 (m90) cc_final: 0.8720 (m-70) REVERT: Dc 147 LEU cc_start: 0.9176 (mt) cc_final: 0.8960 (mt) REVERT: Dc 173 SER cc_start: 0.8874 (m) cc_final: 0.8607 (t) REVERT: Dc 197 LEU cc_start: 0.8997 (tp) cc_final: 0.8660 (tp) REVERT: Dd 157 LEU cc_start: 0.8124 (pp) cc_final: 0.7716 (pp) REVERT: Dd 159 MET cc_start: 0.8969 (mmp) cc_final: 0.8397 (mmp) REVERT: Df 205 LEU cc_start: 0.6028 (tp) cc_final: 0.5279 (tp) REVERT: Dh 144 ILE cc_start: 0.9112 (mm) cc_final: 0.8894 (tp) REVERT: Di 159 MET cc_start: 0.8285 (mmm) cc_final: 0.7012 (ptt) REVERT: Di 172 PRO cc_start: 0.8804 (Cg_endo) cc_final: 0.8413 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9148 (m-30) cc_final: 0.8585 (p0) REVERT: Dm 218 HIS cc_start: 0.8576 (m90) cc_final: 0.8324 (m-70) REVERT: Dn 196 HIS cc_start: 0.9229 (m90) cc_final: 0.8732 (m-70) REVERT: Do 196 HIS cc_start: 0.9296 (m-70) cc_final: 0.8937 (m-70) REVERT: Dp 136 LEU cc_start: 0.9760 (tp) cc_final: 0.9556 (tp) REVERT: Dp 196 HIS cc_start: 0.8863 (m90) cc_final: 0.8384 (m90) REVERT: Dp 205 LEU cc_start: 0.8817 (tp) cc_final: 0.8611 (tp) REVERT: Dr 126 PHE cc_start: 0.9201 (t80) cc_final: 0.8999 (t80) REVERT: Dr 196 HIS cc_start: 0.9206 (m90) cc_final: 0.8854 (m-70) REVERT: Dr 205 LEU cc_start: 0.8285 (tp) cc_final: 0.7967 (tp) REVERT: Ds 151 LYS cc_start: 0.9532 (ptpt) cc_final: 0.9280 (ptpt) REVERT: Dt 159 MET cc_start: 0.9079 (pmm) cc_final: 0.8384 (tpp) REVERT: Du 126 PHE cc_start: 0.9409 (t80) cc_final: 0.9209 (t80) REVERT: Du 205 LEU cc_start: 0.8779 (tp) cc_final: 0.8565 (tp) REVERT: Du 213 VAL cc_start: 0.9359 (m) cc_final: 0.9097 (p) REVERT: Dv 126 PHE cc_start: 0.9437 (t80) cc_final: 0.9136 (t80) REVERT: Dv 136 LEU cc_start: 0.9692 (mt) cc_final: 0.9483 (mt) REVERT: Dv 196 HIS cc_start: 0.9345 (m90) cc_final: 0.9004 (m90) REVERT: Dv 205 LEU cc_start: 0.8776 (tp) cc_final: 0.8479 (tp) REVERT: Cc 430 LEU cc_start: 0.7916 (tp) cc_final: 0.6904 (tt) REVERT: Cd 420 MET cc_start: 0.8117 (ttt) cc_final: 0.7685 (ttm) REVERT: Cf 413 GLU cc_start: 0.8506 (pt0) cc_final: 0.8046 (pt0) REVERT: cg 242 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7782 (mt-10) REVERT: Ch 249 ILE cc_start: 0.9070 (mt) cc_final: 0.8833 (tp) REVERT: Ch 414 ASP cc_start: 0.7750 (t0) cc_final: 0.7540 (t0) REVERT: Ci 409 MET cc_start: 0.7044 (mmm) cc_final: 0.6704 (mmt) REVERT: Ci 413 GLU cc_start: 0.8609 (pt0) cc_final: 0.8386 (pt0) REVERT: Cj 385 LEU cc_start: 0.8295 (tp) cc_final: 0.7731 (mp) REVERT: Cj 416 THR cc_start: 0.9016 (m) cc_final: 0.8760 (p) REVERT: Ck 413 GLU cc_start: 0.9060 (pt0) cc_final: 0.8433 (pt0) REVERT: Cm 414 ASP cc_start: 0.8103 (t70) cc_final: 0.7859 (t70) REVERT: Cn 413 GLU cc_start: 0.8758 (pt0) cc_final: 0.8434 (pt0) REVERT: Cp 236 LYS cc_start: 0.9391 (pptt) cc_final: 0.9158 (pptt) REVERT: Cp 413 GLU cc_start: 0.7775 (tp30) cc_final: 0.7481 (tp30) REVERT: Cp 416 THR cc_start: 0.8881 (p) cc_final: 0.8591 (p) REVERT: Cr 420 MET cc_start: 0.7959 (ptt) cc_final: 0.6994 (ppp) REVERT: Ct 253 LEU cc_start: 0.8012 (mt) cc_final: 0.7808 (mt) REVERT: Cu 270 LEU cc_start: 0.8052 (tp) cc_final: 0.7729 (tp) REVERT: Cv 385 LEU cc_start: 0.8662 (tp) cc_final: 0.8243 (tp) REVERT: Cv 414 ASP cc_start: 0.8296 (t0) cc_final: 0.7666 (t70) REVERT: Cw 413 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7333 (tp30) REVERT: Cx 381 ASP cc_start: 0.7635 (m-30) cc_final: 0.7182 (m-30) REVERT: Cx 430 LEU cc_start: 0.7434 (tp) cc_final: 0.7177 (mt) REVERT: Cy 249 ILE cc_start: 0.9297 (mt) cc_final: 0.8839 (tp) REVERT: Cy 366 TYR cc_start: 0.7079 (m-80) cc_final: 0.6868 (m-10) REVERT: Cy 385 LEU cc_start: 0.8438 (tp) cc_final: 0.7469 (tp) REVERT: Cy 430 LEU cc_start: 0.8347 (tp) cc_final: 0.7998 (tp) REVERT: Cz 385 LEU cc_start: 0.8397 (mt) cc_final: 0.8122 (mp) REVERT: Ea 385 LEU cc_start: 0.8639 (tp) cc_final: 0.8305 (pp) REVERT: Ea 416 THR cc_start: 0.8617 (p) cc_final: 0.8379 (p) REVERT: Eb 259 ASN cc_start: 0.8141 (p0) cc_final: 0.7597 (p0) REVERT: Eb 407 ASP cc_start: 0.8199 (p0) cc_final: 0.7819 (p0) REVERT: Ec 236 LYS cc_start: 0.9084 (pptt) cc_final: 0.8607 (pptt) REVERT: Ec 249 ILE cc_start: 0.8914 (mm) cc_final: 0.8705 (pt) REVERT: Ec 259 ASN cc_start: 0.7773 (p0) cc_final: 0.7483 (p0) REVERT: Ec 424 ASP cc_start: 0.8207 (p0) cc_final: 0.7837 (p0) REVERT: Ed 409 MET cc_start: 0.8482 (mtm) cc_final: 0.8214 (mtt) REVERT: Ed 414 ASP cc_start: 0.8252 (t0) cc_final: 0.7978 (t0) REVERT: Ee 252 ILE cc_start: 0.7536 (tp) cc_final: 0.7294 (tp) REVERT: Ee 270 LEU cc_start: 0.8246 (mm) cc_final: 0.8003 (mm) REVERT: Eg 259 ASN cc_start: 0.7850 (p0) cc_final: 0.7541 (p0) outliers start: 4 outliers final: 0 residues processed: 1221 average time/residue: 0.5248 time to fit residues: 1074.1706 Evaluate side-chains 840 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 840 time to evaluate : 5.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 588 optimal weight: 9.9990 chunk 401 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 526 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 602 optimal weight: 5.9990 chunk 488 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 360 optimal weight: 2.9990 chunk 634 optimal weight: 3.9990 chunk 178 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Dd 209 ASN Dd 218 HIS De 131 ASN ** Dh 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dh 218 HIS Di 131 ASN ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 196 HIS Dl 209 ASN Dl 218 HIS Dn 218 HIS Do 209 ASN Dp 209 ASN ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dr 218 HIS ** Dt 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dt 218 HIS Du 209 ASN Du 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 365 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ce 297 GLN ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 365 ASN Ch 411 GLN Ch 431 ASN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 374 HIS ** Cq 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cr 281 HIS ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 411 GLN ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 411 GLN ** Cw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cy 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 246 GLN Eb 303 GLN ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ef 411 GLN ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 411 GLN ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 57796 Z= 0.266 Angle : 0.643 8.019 78238 Z= 0.338 Chirality : 0.042 0.168 9257 Planarity : 0.004 0.085 10442 Dihedral : 4.962 35.062 8031 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.96 % Favored : 97.03 % Rotamer: Outliers : 0.08 % Allowed : 2.92 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.10), residues: 7129 helix: 0.58 (0.11), residues: 2125 sheet: -1.07 (0.09), residues: 3033 loop : -1.23 (0.13), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HISCr 281 PHE 0.022 0.002 PHECt 272 TYR 0.036 0.002 TYRCb 282 ARG 0.011 0.001 ARGCr 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1180 time to evaluate : 5.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Da 126 PHE cc_start: 0.9282 (p90) cc_final: 0.9034 (p90) REVERT: Db 196 HIS cc_start: 0.8996 (m90) cc_final: 0.8622 (m-70) REVERT: Dc 173 SER cc_start: 0.8590 (m) cc_final: 0.8359 (t) REVERT: Dc 197 LEU cc_start: 0.8971 (tp) cc_final: 0.8767 (tp) REVERT: Dd 159 MET cc_start: 0.9084 (mmp) cc_final: 0.8557 (mmp) REVERT: De 131 ASN cc_start: 0.9509 (m-40) cc_final: 0.8979 (t0) REVERT: Df 205 LEU cc_start: 0.6032 (tp) cc_final: 0.5391 (tp) REVERT: Dh 144 ILE cc_start: 0.9070 (mm) cc_final: 0.8856 (tp) REVERT: Di 159 MET cc_start: 0.8351 (mmm) cc_final: 0.7135 (ptt) REVERT: Di 172 PRO cc_start: 0.8929 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9167 (m-30) cc_final: 0.8598 (p0) REVERT: Dl 196 HIS cc_start: 0.9264 (m90) cc_final: 0.8979 (m90) REVERT: Dm 159 MET cc_start: 0.8514 (pmm) cc_final: 0.8161 (pmm) REVERT: Dm 214 ASP cc_start: 0.8977 (m-30) cc_final: 0.8728 (m-30) REVERT: Dm 218 HIS cc_start: 0.8530 (m90) cc_final: 0.8227 (m-70) REVERT: Dn 196 HIS cc_start: 0.9142 (m90) cc_final: 0.8703 (m170) REVERT: Do 196 HIS cc_start: 0.9300 (m-70) cc_final: 0.8935 (m-70) REVERT: Do 209 ASN cc_start: 0.8777 (m110) cc_final: 0.8474 (p0) REVERT: Dp 196 HIS cc_start: 0.8905 (m90) cc_final: 0.8406 (m90) REVERT: Dp 205 LEU cc_start: 0.8886 (tp) cc_final: 0.8576 (tp) REVERT: Dp 220 LEU cc_start: 0.9572 (mt) cc_final: 0.9180 (mp) REVERT: Dq 159 MET cc_start: 0.8840 (mmp) cc_final: 0.8583 (mmm) REVERT: Dr 196 HIS cc_start: 0.9167 (m90) cc_final: 0.8770 (m-70) REVERT: Dr 197 LEU cc_start: 0.9750 (mm) cc_final: 0.9495 (mm) REVERT: Dr 220 LEU cc_start: 0.8924 (mt) cc_final: 0.8619 (mp) REVERT: Ds 147 LEU cc_start: 0.9350 (mt) cc_final: 0.9032 (mt) REVERT: Ds 151 LYS cc_start: 0.9553 (ptpt) cc_final: 0.9326 (ptpt) REVERT: Ds 159 MET cc_start: 0.9133 (pmm) cc_final: 0.8888 (pmm) REVERT: Dt 126 PHE cc_start: 0.9385 (t80) cc_final: 0.8923 (t80) REVERT: Dt 128 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9213 (mt-10) REVERT: Dt 136 LEU cc_start: 0.9699 (mt) cc_final: 0.9175 (mt) REVERT: Dt 157 LEU cc_start: 0.9607 (tt) cc_final: 0.9344 (tp) REVERT: Du 147 LEU cc_start: 0.9458 (tt) cc_final: 0.8906 (mm) REVERT: Du 205 LEU cc_start: 0.8892 (tp) cc_final: 0.8599 (tp) REVERT: Dv 126 PHE cc_start: 0.9322 (t80) cc_final: 0.9055 (t80) REVERT: Dv 196 HIS cc_start: 0.9414 (m90) cc_final: 0.9120 (m90) REVERT: Dv 205 LEU cc_start: 0.8845 (tp) cc_final: 0.8610 (tp) REVERT: Dw 218 HIS cc_start: 0.8498 (m-70) cc_final: 0.8095 (m90) REVERT: Ca 416 THR cc_start: 0.8578 (p) cc_final: 0.8327 (p) REVERT: Cb 385 LEU cc_start: 0.7947 (tp) cc_final: 0.7384 (tp) REVERT: Cd 413 GLU cc_start: 0.7385 (tp30) cc_final: 0.6915 (tp30) REVERT: Cd 420 MET cc_start: 0.8066 (ttt) cc_final: 0.7650 (ttm) REVERT: Cf 413 GLU cc_start: 0.8500 (pt0) cc_final: 0.7859 (pt0) REVERT: Cf 420 MET cc_start: 0.8726 (ppp) cc_final: 0.8524 (ppp) REVERT: Ch 414 ASP cc_start: 0.7522 (t0) cc_final: 0.7270 (t0) REVERT: Ci 409 MET cc_start: 0.7003 (mmm) cc_final: 0.6610 (mmt) REVERT: Ci 413 GLU cc_start: 0.8554 (pt0) cc_final: 0.8134 (pt0) REVERT: Cj 385 LEU cc_start: 0.8172 (tp) cc_final: 0.7848 (mp) REVERT: Ck 413 GLU cc_start: 0.8975 (pt0) cc_final: 0.8312 (pt0) REVERT: Cn 242 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7915 (mt-10) REVERT: Cn 413 GLU cc_start: 0.8607 (pt0) cc_final: 0.8404 (pt0) REVERT: Cp 236 LYS cc_start: 0.9425 (pptt) cc_final: 0.9171 (pptt) REVERT: Cp 413 GLU cc_start: 0.7843 (tp30) cc_final: 0.7469 (tp30) REVERT: Cp 424 ASP cc_start: 0.7978 (p0) cc_final: 0.7641 (p0) REVERT: Cr 270 LEU cc_start: 0.8159 (mm) cc_final: 0.7517 (mm) REVERT: Cr 420 MET cc_start: 0.7788 (ptt) cc_final: 0.7056 (ppp) REVERT: Ct 253 LEU cc_start: 0.7872 (mt) cc_final: 0.7670 (mt) REVERT: Ct 385 LEU cc_start: 0.8143 (tp) cc_final: 0.7933 (mp) REVERT: Cu 270 LEU cc_start: 0.8096 (tp) cc_final: 0.7760 (tp) REVERT: Cu 416 THR cc_start: 0.8618 (p) cc_final: 0.8364 (p) REVERT: Cv 414 ASP cc_start: 0.8129 (t0) cc_final: 0.7561 (t70) REVERT: Cv 430 LEU cc_start: 0.8845 (tt) cc_final: 0.8450 (tt) REVERT: Cx 381 ASP cc_start: 0.7463 (m-30) cc_final: 0.7071 (m-30) REVERT: Cy 249 ILE cc_start: 0.9252 (mt) cc_final: 0.8777 (tp) REVERT: Cy 385 LEU cc_start: 0.7947 (tp) cc_final: 0.7666 (tp) REVERT: Cy 413 GLU cc_start: 0.8707 (pt0) cc_final: 0.8492 (pt0) REVERT: Eb 259 ASN cc_start: 0.8244 (p0) cc_final: 0.7715 (p0) REVERT: Eb 290 LYS cc_start: 0.8219 (pttp) cc_final: 0.7994 (pttp) REVERT: Ec 236 LYS cc_start: 0.8991 (pptt) cc_final: 0.8415 (pptt) REVERT: Ed 414 ASP cc_start: 0.7997 (t0) cc_final: 0.7654 (t0) REVERT: Ee 270 LEU cc_start: 0.8153 (mm) cc_final: 0.7951 (mm) REVERT: Ee 275 LYS cc_start: 0.8395 (pttm) cc_final: 0.8151 (ptpp) REVERT: Eg 259 ASN cc_start: 0.7927 (p0) cc_final: 0.7669 (p0) REVERT: Eg 414 ASP cc_start: 0.8143 (m-30) cc_final: 0.7605 (m-30) outliers start: 5 outliers final: 1 residues processed: 1184 average time/residue: 0.5220 time to fit residues: 1036.4659 Evaluate side-chains 835 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 834 time to evaluate : 5.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 237 optimal weight: 2.9990 chunk 636 optimal weight: 6.9990 chunk 139 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 707 optimal weight: 10.0000 chunk 587 optimal weight: 9.9990 chunk 327 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 233 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: De 131 ASN ** Dh 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 209 ASN ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dn 218 HIS ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dr 218 HIS Dt 218 HIS Du 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 365 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cd 246 GLN ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cg 297 GLN ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 365 ASN Ch 411 GLN ** Ci 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ci 274 ASN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cl 265 GLN ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cq 361 ASN ** Cq 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 411 GLN ** Ct 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 411 GLN ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cy 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 365 ASN ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ef 411 GLN ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 411 GLN ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.7855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 57796 Z= 0.257 Angle : 0.634 9.188 78238 Z= 0.333 Chirality : 0.042 0.162 9257 Planarity : 0.004 0.096 10442 Dihedral : 4.880 36.001 8031 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 25.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.10), residues: 7129 helix: 0.57 (0.11), residues: 2141 sheet: -0.94 (0.09), residues: 2998 loop : -0.84 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HISEb 263 PHE 0.021 0.002 PHECt 272 TYR 0.022 0.002 TYRCb 282 ARG 0.021 0.001 ARGcg 296 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1143 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Da 159 MET cc_start: 0.8895 (pmm) cc_final: 0.8605 (pmm) REVERT: Db 196 HIS cc_start: 0.9057 (m90) cc_final: 0.8625 (m-70) REVERT: Dc 173 SER cc_start: 0.8331 (m) cc_final: 0.8037 (t) REVERT: Dc 196 HIS cc_start: 0.9596 (m90) cc_final: 0.9357 (m90) REVERT: Dd 157 LEU cc_start: 0.8778 (pp) cc_final: 0.8496 (pp) REVERT: Dd 159 MET cc_start: 0.9191 (mmp) cc_final: 0.8648 (mmp) REVERT: De 131 ASN cc_start: 0.9418 (m110) cc_final: 0.8927 (t0) REVERT: Df 205 LEU cc_start: 0.6095 (tp) cc_final: 0.5486 (tp) REVERT: Dh 144 ILE cc_start: 0.9069 (mm) cc_final: 0.8850 (tp) REVERT: Dh 159 MET cc_start: 0.7013 (mmp) cc_final: 0.6692 (mmm) REVERT: Di 159 MET cc_start: 0.8356 (mmm) cc_final: 0.7202 (ptt) REVERT: Di 172 PRO cc_start: 0.8988 (Cg_endo) cc_final: 0.8590 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9090 (m-30) cc_final: 0.8539 (p0) REVERT: Dk 212 LEU cc_start: 0.9675 (tp) cc_final: 0.9474 (tp) REVERT: Dl 196 HIS cc_start: 0.9229 (m90) cc_final: 0.8902 (m90) REVERT: Dm 214 ASP cc_start: 0.9083 (m-30) cc_final: 0.8774 (m-30) REVERT: Dm 218 HIS cc_start: 0.8620 (m90) cc_final: 0.8369 (m-70) REVERT: Dn 196 HIS cc_start: 0.9098 (m90) cc_final: 0.8651 (m170) REVERT: Do 196 HIS cc_start: 0.9305 (m-70) cc_final: 0.8929 (m-70) REVERT: Do 209 ASN cc_start: 0.8844 (m110) cc_final: 0.8490 (p0) REVERT: Dp 136 LEU cc_start: 0.9755 (tt) cc_final: 0.9366 (mm) REVERT: Dp 205 LEU cc_start: 0.8894 (tp) cc_final: 0.8569 (tp) REVERT: Dq 159 MET cc_start: 0.8985 (mmp) cc_final: 0.8561 (mmp) REVERT: Dr 196 HIS cc_start: 0.9118 (m90) cc_final: 0.8733 (m-70) REVERT: Dr 197 LEU cc_start: 0.9743 (mm) cc_final: 0.9472 (mm) REVERT: Dr 218 HIS cc_start: 0.8876 (m90) cc_final: 0.8649 (m-70) REVERT: Ds 159 MET cc_start: 0.9109 (pmm) cc_final: 0.8770 (pmm) REVERT: Dt 126 PHE cc_start: 0.9402 (t80) cc_final: 0.8957 (t80) REVERT: Dt 128 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9215 (mt-10) REVERT: Dt 159 MET cc_start: 0.9144 (pmm) cc_final: 0.8349 (tpp) REVERT: Du 147 LEU cc_start: 0.9489 (tt) cc_final: 0.8881 (mt) REVERT: Du 205 LEU cc_start: 0.8945 (tp) cc_final: 0.8626 (tp) REVERT: Dv 126 PHE cc_start: 0.9319 (t80) cc_final: 0.9053 (t80) REVERT: Dv 136 LEU cc_start: 0.9720 (mt) cc_final: 0.9519 (mt) REVERT: Dv 139 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8962 (pm20) REVERT: Dv 178 VAL cc_start: 0.9576 (m) cc_final: 0.9366 (p) REVERT: Dv 186 LEU cc_start: 0.9109 (mp) cc_final: 0.8852 (mp) REVERT: Dv 196 HIS cc_start: 0.9453 (m90) cc_final: 0.9176 (m90) REVERT: Dv 205 LEU cc_start: 0.8954 (tp) cc_final: 0.8664 (tp) REVERT: Dw 218 HIS cc_start: 0.8520 (m-70) cc_final: 0.8159 (m90) REVERT: Cb 282 TYR cc_start: 0.7397 (m-10) cc_final: 0.7141 (m-10) REVERT: Cd 413 GLU cc_start: 0.7408 (tp30) cc_final: 0.6928 (tp30) REVERT: Cf 410 LYS cc_start: 0.9042 (ptpp) cc_final: 0.8652 (pttm) REVERT: Cf 413 GLU cc_start: 0.8512 (pt0) cc_final: 0.7856 (pt0) REVERT: cg 376 LYS cc_start: 0.8869 (pptt) cc_final: 0.8543 (pptt) REVERT: Ch 249 ILE cc_start: 0.9079 (mm) cc_final: 0.8469 (tp) REVERT: Ch 385 LEU cc_start: 0.8235 (mt) cc_final: 0.7905 (mp) REVERT: Ch 414 ASP cc_start: 0.7540 (t0) cc_final: 0.7261 (t0) REVERT: Ci 409 MET cc_start: 0.7017 (mmm) cc_final: 0.6692 (mmt) REVERT: Ci 413 GLU cc_start: 0.8559 (pt0) cc_final: 0.8186 (pt0) REVERT: Cj 385 LEU cc_start: 0.8073 (tp) cc_final: 0.7753 (mp) REVERT: Ck 413 GLU cc_start: 0.8970 (pt0) cc_final: 0.8194 (pt0) REVERT: Cp 236 LYS cc_start: 0.9413 (pptt) cc_final: 0.9188 (pptt) REVERT: Cp 424 ASP cc_start: 0.7823 (p0) cc_final: 0.7532 (p0) REVERT: Cq 270 LEU cc_start: 0.7866 (tp) cc_final: 0.7488 (tp) REVERT: Cr 270 LEU cc_start: 0.8309 (mm) cc_final: 0.8104 (tp) REVERT: Cr 420 MET cc_start: 0.7569 (ptt) cc_final: 0.6937 (ppp) REVERT: Cs 267 THR cc_start: 0.6002 (m) cc_final: 0.5747 (m) REVERT: Ct 385 LEU cc_start: 0.8448 (tp) cc_final: 0.8029 (mp) REVERT: Cu 270 LEU cc_start: 0.8113 (tp) cc_final: 0.7759 (tp) REVERT: Cu 413 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8012 (pm20) REVERT: Cv 414 ASP cc_start: 0.8280 (t0) cc_final: 0.7642 (t70) REVERT: Cx 253 LEU cc_start: 0.7703 (mt) cc_final: 0.7441 (mt) REVERT: Cx 381 ASP cc_start: 0.7638 (m-30) cc_final: 0.7238 (m-30) REVERT: Cy 249 ILE cc_start: 0.9200 (mt) cc_final: 0.8722 (tp) REVERT: Cy 385 LEU cc_start: 0.8087 (tp) cc_final: 0.7845 (tp) REVERT: Cy 430 LEU cc_start: 0.7908 (tp) cc_final: 0.7705 (tp) REVERT: Eb 250 GLU cc_start: 0.7389 (pm20) cc_final: 0.6973 (pm20) REVERT: Eb 259 ASN cc_start: 0.8261 (p0) cc_final: 0.7705 (p0) REVERT: Eb 407 ASP cc_start: 0.8243 (p0) cc_final: 0.7850 (p0) REVERT: Ec 236 LYS cc_start: 0.9006 (pptt) cc_final: 0.8424 (pptt) REVERT: Ed 414 ASP cc_start: 0.8000 (t0) cc_final: 0.7515 (t0) REVERT: Ee 252 ILE cc_start: 0.7280 (tp) cc_final: 0.7077 (tp) REVERT: Ee 270 LEU cc_start: 0.8263 (mm) cc_final: 0.8003 (mm) REVERT: Eg 259 ASN cc_start: 0.7563 (p0) cc_final: 0.7328 (p0) REVERT: Eg 267 THR cc_start: 0.6928 (t) cc_final: 0.6720 (t) outliers start: 7 outliers final: 2 residues processed: 1148 average time/residue: 0.5248 time to fit residues: 1012.7112 Evaluate side-chains 820 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 816 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 681 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 402 optimal weight: 0.9990 chunk 516 optimal weight: 3.9990 chunk 400 optimal weight: 7.9990 chunk 595 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 704 optimal weight: 0.7980 chunk 440 optimal weight: 0.9990 chunk 429 optimal weight: 8.9990 chunk 325 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Da 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dh 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 209 ASN Dl 218 HIS Dn 218 HIS ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dq 129 GLN ** Dt 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Dt 218 HIS Du 218 HIS Dw 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 365 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 365 ASN Ch 411 GLN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ci 365 ASN ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 277 GLN ** Cn 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cs 411 GLN ** Ct 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cx 274 ASN ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 297 GLN Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN Ea 277 GLN ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 365 ASN ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 57796 Z= 0.194 Angle : 0.610 10.094 78238 Z= 0.318 Chirality : 0.042 0.195 9257 Planarity : 0.004 0.090 10442 Dihedral : 4.692 35.309 8031 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.72 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.10), residues: 7129 helix: 0.69 (0.11), residues: 2141 sheet: -0.67 (0.10), residues: 2862 loop : -1.23 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HISCp 281 PHE 0.023 0.001 PHEDp 126 TYR 0.022 0.002 TYRFh 393 ARG 0.019 0.000 ARGCq 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1160 time to evaluate : 5.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Db 196 HIS cc_start: 0.9064 (m90) cc_final: 0.8639 (m-70) REVERT: Dc 173 SER cc_start: 0.8103 (m) cc_final: 0.7846 (t) REVERT: Dc 196 HIS cc_start: 0.9695 (m90) cc_final: 0.9420 (m90) REVERT: Dd 157 LEU cc_start: 0.8805 (pp) cc_final: 0.8495 (pp) REVERT: Dd 159 MET cc_start: 0.9168 (mmp) cc_final: 0.8694 (mmp) REVERT: De 125 GLN cc_start: 0.9247 (tm-30) cc_final: 0.8600 (mt0) REVERT: De 131 ASN cc_start: 0.9418 (m110) cc_final: 0.8918 (t0) REVERT: Df 205 LEU cc_start: 0.5769 (tp) cc_final: 0.5186 (tp) REVERT: Dh 144 ILE cc_start: 0.9023 (mm) cc_final: 0.8789 (tp) REVERT: Di 159 MET cc_start: 0.8346 (mmm) cc_final: 0.7144 (ptt) REVERT: Di 172 PRO cc_start: 0.8938 (Cg_endo) cc_final: 0.8551 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9031 (m-30) cc_final: 0.8534 (p0) REVERT: Dk 212 LEU cc_start: 0.9668 (tp) cc_final: 0.9454 (tp) REVERT: Dl 159 MET cc_start: 0.8041 (tpt) cc_final: 0.7535 (tpt) REVERT: Dl 196 HIS cc_start: 0.9204 (m90) cc_final: 0.8869 (m90) REVERT: Dm 159 MET cc_start: 0.8089 (pmm) cc_final: 0.7759 (pmm) REVERT: Dm 214 ASP cc_start: 0.9072 (m-30) cc_final: 0.8777 (m-30) REVERT: Dm 218 HIS cc_start: 0.8645 (m90) cc_final: 0.8394 (m-70) REVERT: Dn 196 HIS cc_start: 0.8983 (m90) cc_final: 0.8581 (m170) REVERT: Do 186 LEU cc_start: 0.8829 (tp) cc_final: 0.8116 (tp) REVERT: Do 196 HIS cc_start: 0.9245 (m-70) cc_final: 0.8854 (m-70) REVERT: Do 209 ASN cc_start: 0.8754 (m110) cc_final: 0.8453 (p0) REVERT: Dp 187 ASP cc_start: 0.9555 (t0) cc_final: 0.9337 (t70) REVERT: Dp 196 HIS cc_start: 0.8870 (m90) cc_final: 0.8286 (m90) REVERT: Dp 205 LEU cc_start: 0.8910 (tp) cc_final: 0.8665 (tp) REVERT: Dq 159 MET cc_start: 0.8904 (mmp) cc_final: 0.8507 (mmp) REVERT: Dr 196 HIS cc_start: 0.9073 (m90) cc_final: 0.8630 (m-70) REVERT: Dr 197 LEU cc_start: 0.9738 (mm) cc_final: 0.9427 (mm) REVERT: Dr 218 HIS cc_start: 0.8762 (m90) cc_final: 0.8529 (m-70) REVERT: Ds 147 LEU cc_start: 0.9455 (mt) cc_final: 0.9174 (mt) REVERT: Ds 151 LYS cc_start: 0.9464 (ptpt) cc_final: 0.9258 (ptpt) REVERT: Dt 126 PHE cc_start: 0.9385 (t80) cc_final: 0.9083 (t80) REVERT: Dt 157 LEU cc_start: 0.9491 (tt) cc_final: 0.9169 (tp) REVERT: Du 147 LEU cc_start: 0.9564 (tt) cc_final: 0.9038 (mm) REVERT: Du 205 LEU cc_start: 0.8962 (tp) cc_final: 0.8631 (tp) REVERT: Dv 126 PHE cc_start: 0.9241 (t80) cc_final: 0.8952 (t80) REVERT: Dv 186 LEU cc_start: 0.9130 (mp) cc_final: 0.8877 (mp) REVERT: Dv 196 HIS cc_start: 0.9433 (m90) cc_final: 0.9126 (m90) REVERT: Dv 197 LEU cc_start: 0.9820 (mm) cc_final: 0.9409 (pp) REVERT: Dv 205 LEU cc_start: 0.8926 (tp) cc_final: 0.8658 (tp) REVERT: Dw 218 HIS cc_start: 0.8002 (m90) cc_final: 0.7739 (m90) REVERT: Ca 271 ASP cc_start: 0.6143 (t0) cc_final: 0.5539 (t0) REVERT: Cb 366 TYR cc_start: 0.7140 (m-80) cc_final: 0.6852 (m-80) REVERT: Cd 413 GLU cc_start: 0.7452 (tp30) cc_final: 0.6904 (tp30) REVERT: Cd 416 THR cc_start: 0.8266 (p) cc_final: 0.7982 (p) REVERT: Cd 420 MET cc_start: 0.7665 (ttt) cc_final: 0.7039 (ttm) REVERT: Cf 274 ASN cc_start: 0.7690 (t0) cc_final: 0.7460 (t0) REVERT: Cf 413 GLU cc_start: 0.8435 (pt0) cc_final: 0.7793 (pt0) REVERT: cg 376 LYS cc_start: 0.8848 (pptt) cc_final: 0.8565 (pptt) REVERT: Ci 409 MET cc_start: 0.7066 (mmm) cc_final: 0.6805 (mmt) REVERT: Ci 413 GLU cc_start: 0.8492 (pt0) cc_final: 0.8156 (pt0) REVERT: Co 416 THR cc_start: 0.8769 (p) cc_final: 0.8541 (p) REVERT: Cp 236 LYS cc_start: 0.9419 (pptt) cc_final: 0.9134 (pptt) REVERT: Cp 410 LYS cc_start: 0.9251 (ptpp) cc_final: 0.8914 (ptpp) REVERT: Cp 424 ASP cc_start: 0.7734 (p0) cc_final: 0.7437 (p0) REVERT: Cr 420 MET cc_start: 0.7570 (ptt) cc_final: 0.7047 (ppp) REVERT: Cs 267 THR cc_start: 0.5932 (m) cc_final: 0.5709 (m) REVERT: Ct 385 LEU cc_start: 0.8426 (tp) cc_final: 0.8070 (mp) REVERT: Cu 270 LEU cc_start: 0.8066 (tp) cc_final: 0.7668 (tp) REVERT: Cv 385 LEU cc_start: 0.8333 (tp) cc_final: 0.8124 (tp) REVERT: Cv 414 ASP cc_start: 0.7956 (t0) cc_final: 0.7478 (t70) REVERT: Cw 413 GLU cc_start: 0.8095 (tp30) cc_final: 0.7836 (tp30) REVERT: Cx 253 LEU cc_start: 0.7800 (mt) cc_final: 0.7508 (mt) REVERT: Cx 381 ASP cc_start: 0.7464 (m-30) cc_final: 0.7063 (m-30) REVERT: Cy 249 ILE cc_start: 0.9216 (mt) cc_final: 0.8741 (tp) REVERT: Ea 366 TYR cc_start: 0.7018 (m-10) cc_final: 0.6610 (m-10) REVERT: Eb 259 ASN cc_start: 0.8175 (p0) cc_final: 0.7625 (p0) REVERT: Ec 236 LYS cc_start: 0.9030 (pptt) cc_final: 0.8409 (pptt) REVERT: Ec 385 LEU cc_start: 0.8777 (tp) cc_final: 0.8488 (pp) REVERT: Ed 414 ASP cc_start: 0.7950 (t0) cc_final: 0.7506 (t0) REVERT: Ee 236 LYS cc_start: 0.9242 (mptt) cc_final: 0.9002 (ptpp) REVERT: Ee 252 ILE cc_start: 0.7120 (tp) cc_final: 0.6877 (tp) REVERT: Ee 270 LEU cc_start: 0.8345 (mm) cc_final: 0.8088 (mm) REVERT: Eg 259 ASN cc_start: 0.7615 (p0) cc_final: 0.7364 (p0) outliers start: 0 outliers final: 0 residues processed: 1160 average time/residue: 0.5280 time to fit residues: 1029.0524 Evaluate side-chains 832 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 832 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 435 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 420 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 136 optimal weight: 40.0000 chunk 447 optimal weight: 5.9990 chunk 480 optimal weight: 9.9990 chunk 348 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 553 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Da 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** De 131 ASN Dh 133 GLN Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 209 ASN ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dn 218 HIS ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Du 218 HIS Dw 133 GLN ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 365 ASN ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cf 361 ASN cg 297 GLN ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 274 ASN Ch 365 ASN Ch 411 GLN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 359 GLN ** Co 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cr 246 GLN ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cx 408 GLN ** Cy 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 365 ASN Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.8123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 57796 Z= 0.186 Angle : 0.607 11.939 78238 Z= 0.316 Chirality : 0.042 0.210 9257 Planarity : 0.004 0.090 10442 Dihedral : 4.562 35.133 8031 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.67 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.10), residues: 7129 helix: 0.72 (0.11), residues: 2140 sheet: -0.56 (0.10), residues: 2862 loop : -1.12 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HISCn 374 PHE 0.024 0.001 PHEDp 126 TYR 0.038 0.002 TYRCk 282 ARG 0.013 0.000 ARGcg 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1138 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1138 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Db 196 HIS cc_start: 0.9048 (m90) cc_final: 0.8566 (m170) REVERT: Dc 173 SER cc_start: 0.8027 (m) cc_final: 0.7787 (t) REVERT: Dc 196 HIS cc_start: 0.9688 (m90) cc_final: 0.9420 (m90) REVERT: Dd 157 LEU cc_start: 0.8832 (pp) cc_final: 0.8523 (pp) REVERT: Dd 159 MET cc_start: 0.9186 (mmp) cc_final: 0.8778 (mmp) REVERT: De 125 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8568 (mt0) REVERT: De 131 ASN cc_start: 0.9521 (m-40) cc_final: 0.9104 (t0) REVERT: Df 132 TYR cc_start: 0.9111 (t80) cc_final: 0.8725 (t80) REVERT: Df 205 LEU cc_start: 0.5785 (tp) cc_final: 0.5184 (tp) REVERT: Di 159 MET cc_start: 0.8369 (mmm) cc_final: 0.7177 (ptt) REVERT: Di 172 PRO cc_start: 0.8972 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9000 (m-30) cc_final: 0.8591 (p0) REVERT: Dk 212 LEU cc_start: 0.9670 (tp) cc_final: 0.9469 (mm) REVERT: Dk 221 THR cc_start: 0.8072 (p) cc_final: 0.7842 (p) REVERT: Dl 196 HIS cc_start: 0.9193 (m90) cc_final: 0.8863 (m90) REVERT: Dm 159 MET cc_start: 0.8091 (pmm) cc_final: 0.7738 (pmm) REVERT: Dm 214 ASP cc_start: 0.9100 (m-30) cc_final: 0.8813 (m-30) REVERT: Dm 218 HIS cc_start: 0.8667 (m90) cc_final: 0.8391 (m-70) REVERT: Dn 186 LEU cc_start: 0.9560 (mm) cc_final: 0.9133 (tp) REVERT: Dn 196 HIS cc_start: 0.8977 (m90) cc_final: 0.8618 (m170) REVERT: Do 186 LEU cc_start: 0.8860 (tp) cc_final: 0.8214 (tp) REVERT: Do 196 HIS cc_start: 0.9243 (m-70) cc_final: 0.8840 (m-70) REVERT: Do 209 ASN cc_start: 0.8700 (m110) cc_final: 0.8434 (p0) REVERT: Dp 205 LEU cc_start: 0.8882 (tp) cc_final: 0.8627 (tp) REVERT: Dq 159 MET cc_start: 0.8864 (mmp) cc_final: 0.8482 (mmp) REVERT: Dr 196 HIS cc_start: 0.8994 (m90) cc_final: 0.8501 (m-70) REVERT: Dr 211 THR cc_start: 0.8535 (m) cc_final: 0.8307 (p) REVERT: Dr 218 HIS cc_start: 0.8745 (m90) cc_final: 0.8455 (m-70) REVERT: Ds 151 LYS cc_start: 0.9443 (ptpt) cc_final: 0.9171 (ptpt) REVERT: Ds 157 LEU cc_start: 0.9377 (mm) cc_final: 0.8886 (mm) REVERT: Ds 159 MET cc_start: 0.9179 (pmm) cc_final: 0.8796 (pmm) REVERT: Dt 126 PHE cc_start: 0.9408 (t80) cc_final: 0.9048 (t80) REVERT: Dt 157 LEU cc_start: 0.9449 (tt) cc_final: 0.9175 (tp) REVERT: Du 147 LEU cc_start: 0.9520 (tt) cc_final: 0.9137 (mm) REVERT: Du 205 LEU cc_start: 0.8897 (tp) cc_final: 0.8558 (tp) REVERT: Du 213 VAL cc_start: 0.9130 (m) cc_final: 0.8930 (t) REVERT: Dv 126 PHE cc_start: 0.9244 (t80) cc_final: 0.9009 (t80) REVERT: Dv 186 LEU cc_start: 0.9105 (mp) cc_final: 0.8858 (mp) REVERT: Dv 196 HIS cc_start: 0.9454 (m90) cc_final: 0.9148 (m90) REVERT: Dv 205 LEU cc_start: 0.8934 (tp) cc_final: 0.8629 (tp) REVERT: Cd 413 GLU cc_start: 0.7451 (tp30) cc_final: 0.6929 (tp30) REVERT: Cd 416 THR cc_start: 0.8298 (p) cc_final: 0.8066 (p) REVERT: Cd 420 MET cc_start: 0.7780 (ttt) cc_final: 0.7285 (ttm) REVERT: Ce 420 MET cc_start: 0.7911 (ppp) cc_final: 0.7069 (ppp) REVERT: Cf 413 GLU cc_start: 0.8422 (pt0) cc_final: 0.7794 (pt0) REVERT: Ch 249 ILE cc_start: 0.9061 (mm) cc_final: 0.8446 (tp) REVERT: Ci 409 MET cc_start: 0.7103 (mmm) cc_final: 0.6806 (mmt) REVERT: Ci 414 ASP cc_start: 0.8289 (m-30) cc_final: 0.7640 (m-30) REVERT: Cn 420 MET cc_start: 0.8699 (pmm) cc_final: 0.7712 (ppp) REVERT: Co 385 LEU cc_start: 0.8230 (tp) cc_final: 0.7975 (tp) REVERT: Cp 236 LYS cc_start: 0.9404 (pptt) cc_final: 0.9136 (pptt) REVERT: Cp 270 LEU cc_start: 0.8305 (mm) cc_final: 0.7702 (mm) REVERT: Cp 424 ASP cc_start: 0.7785 (p0) cc_final: 0.7453 (p0) REVERT: Cq 270 LEU cc_start: 0.7697 (tp) cc_final: 0.7492 (tp) REVERT: Cr 270 LEU cc_start: 0.8411 (mm) cc_final: 0.8057 (tp) REVERT: Cr 420 MET cc_start: 0.7321 (ptt) cc_final: 0.6965 (ppp) REVERT: Cs 267 THR cc_start: 0.5964 (m) cc_final: 0.5720 (m) REVERT: Cu 270 LEU cc_start: 0.8151 (tp) cc_final: 0.7766 (tp) REVERT: Cu 303 GLN cc_start: 0.6898 (pm20) cc_final: 0.6684 (pm20) REVERT: Cu 363 THR cc_start: 0.7467 (m) cc_final: 0.7195 (m) REVERT: Cv 267 THR cc_start: 0.6982 (t) cc_final: 0.6714 (t) REVERT: Cv 385 LEU cc_start: 0.8303 (tp) cc_final: 0.8069 (tp) REVERT: Cv 414 ASP cc_start: 0.8117 (t0) cc_final: 0.7499 (t70) REVERT: Cw 413 GLU cc_start: 0.7970 (tp30) cc_final: 0.7672 (tp30) REVERT: Cx 249 ILE cc_start: 0.8871 (tp) cc_final: 0.8548 (tp) REVERT: Cx 253 LEU cc_start: 0.7748 (mt) cc_final: 0.7238 (mt) REVERT: Cx 381 ASP cc_start: 0.7443 (m-30) cc_final: 0.7039 (m-30) REVERT: Cy 249 ILE cc_start: 0.9225 (mt) cc_final: 0.8755 (tp) REVERT: Cy 430 LEU cc_start: 0.7667 (tp) cc_final: 0.7456 (tp) REVERT: Ea 366 TYR cc_start: 0.6989 (m-10) cc_final: 0.6564 (m-10) REVERT: Eb 259 ASN cc_start: 0.8142 (p0) cc_final: 0.7626 (p0) REVERT: Ec 236 LYS cc_start: 0.9049 (pptt) cc_final: 0.8408 (pptt) REVERT: Ec 385 LEU cc_start: 0.8786 (tp) cc_final: 0.8464 (pp) REVERT: Ee 236 LYS cc_start: 0.9273 (mptt) cc_final: 0.9065 (ptpp) REVERT: Ee 252 ILE cc_start: 0.7267 (tp) cc_final: 0.7036 (tp) REVERT: Ee 270 LEU cc_start: 0.8246 (mm) cc_final: 0.8016 (mm) REVERT: Ee 420 MET cc_start: 0.7779 (ptm) cc_final: 0.7349 (ppp) REVERT: Eg 259 ASN cc_start: 0.7655 (p0) cc_final: 0.7362 (p0) outliers start: 0 outliers final: 0 residues processed: 1138 average time/residue: 0.5320 time to fit residues: 1020.8094 Evaluate side-chains 851 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 851 time to evaluate : 5.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 640 optimal weight: 10.0000 chunk 674 optimal weight: 7.9990 chunk 615 optimal weight: 2.9990 chunk 656 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 286 optimal weight: 4.9990 chunk 515 optimal weight: 2.9990 chunk 201 optimal weight: 50.0000 chunk 593 optimal weight: 0.6980 chunk 620 optimal weight: 6.9990 chunk 654 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Da 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dh 133 GLN Dh 218 HIS ** Di 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 209 ASN ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Du 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 359 GLN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 365 ASN ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cg 297 GLN ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 411 GLN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cj 365 ASN ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cp 365 ASN ** Cq 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cy 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 365 ASN Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 57796 Z= 0.203 Angle : 0.602 8.936 78238 Z= 0.315 Chirality : 0.042 0.183 9257 Planarity : 0.004 0.088 10442 Dihedral : 4.527 34.581 8031 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.65 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.10), residues: 7129 helix: 0.76 (0.11), residues: 2140 sheet: -0.47 (0.10), residues: 2828 loop : -0.96 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HISCn 374 PHE 0.023 0.002 PHEcg 237 TYR 0.021 0.002 TYRCn 282 ARG 0.012 0.000 ARGcg 296 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1114 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1114 time to evaluate : 5.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Db 196 HIS cc_start: 0.9089 (m90) cc_final: 0.8632 (m90) REVERT: Dc 173 SER cc_start: 0.7892 (m) cc_final: 0.7687 (t) REVERT: Dc 196 HIS cc_start: 0.9698 (m90) cc_final: 0.9404 (m90) REVERT: Dc 197 LEU cc_start: 0.9039 (tp) cc_final: 0.8837 (tp) REVERT: Dd 157 LEU cc_start: 0.8794 (pp) cc_final: 0.8540 (pp) REVERT: Dd 159 MET cc_start: 0.9156 (mmp) cc_final: 0.8694 (mmp) REVERT: De 125 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8565 (mt0) REVERT: De 131 ASN cc_start: 0.9520 (m-40) cc_final: 0.8932 (t0) REVERT: Df 159 MET cc_start: 0.9073 (pmm) cc_final: 0.8794 (tmm) REVERT: Df 205 LEU cc_start: 0.5877 (tp) cc_final: 0.5292 (tp) REVERT: Di 159 MET cc_start: 0.8370 (mmm) cc_final: 0.7216 (ptt) REVERT: Di 172 PRO cc_start: 0.8997 (Cg_endo) cc_final: 0.8694 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.9021 (m-30) cc_final: 0.8657 (p0) REVERT: Dk 221 THR cc_start: 0.8098 (p) cc_final: 0.7866 (p) REVERT: Dl 196 HIS cc_start: 0.9177 (m90) cc_final: 0.8780 (m90) REVERT: Dm 218 HIS cc_start: 0.8756 (m90) cc_final: 0.8454 (m-70) REVERT: Dn 196 HIS cc_start: 0.8907 (m90) cc_final: 0.8516 (m170) REVERT: Do 196 HIS cc_start: 0.9253 (m-70) cc_final: 0.8838 (m-70) REVERT: Do 209 ASN cc_start: 0.8711 (m110) cc_final: 0.8467 (p0) REVERT: Do 218 HIS cc_start: 0.9452 (t-90) cc_final: 0.9116 (t-90) REVERT: Dp 205 LEU cc_start: 0.8933 (tp) cc_final: 0.8673 (tp) REVERT: Dp 220 LEU cc_start: 0.9680 (mt) cc_final: 0.9461 (mp) REVERT: Dq 157 LEU cc_start: 0.9357 (pp) cc_final: 0.9122 (pp) REVERT: Dq 159 MET cc_start: 0.8836 (mmp) cc_final: 0.8431 (mmp) REVERT: Dr 136 LEU cc_start: 0.9683 (pp) cc_final: 0.9403 (pp) REVERT: Dr 157 LEU cc_start: 0.9081 (pp) cc_final: 0.8122 (pp) REVERT: Dr 196 HIS cc_start: 0.8870 (m90) cc_final: 0.8362 (m-70) REVERT: Dr 211 THR cc_start: 0.8553 (m) cc_final: 0.8274 (p) REVERT: Dr 218 HIS cc_start: 0.8747 (m90) cc_final: 0.8465 (m-70) REVERT: Ds 151 LYS cc_start: 0.9451 (ptpt) cc_final: 0.9183 (ptpt) REVERT: Ds 157 LEU cc_start: 0.9171 (mm) cc_final: 0.8780 (tp) REVERT: Dt 126 PHE cc_start: 0.9404 (t80) cc_final: 0.9051 (t80) REVERT: Dt 157 LEU cc_start: 0.9420 (tt) cc_final: 0.9128 (tp) REVERT: Du 147 LEU cc_start: 0.9574 (tt) cc_final: 0.9136 (mm) REVERT: Du 205 LEU cc_start: 0.8940 (tp) cc_final: 0.8614 (tp) REVERT: Du 213 VAL cc_start: 0.9108 (m) cc_final: 0.8712 (t) REVERT: Dv 126 PHE cc_start: 0.9254 (t80) cc_final: 0.9000 (t80) REVERT: Dv 178 VAL cc_start: 0.9597 (m) cc_final: 0.9385 (p) REVERT: Dv 186 LEU cc_start: 0.9108 (mp) cc_final: 0.8858 (mp) REVERT: Dv 196 HIS cc_start: 0.9454 (m90) cc_final: 0.9200 (m-70) REVERT: Dv 205 LEU cc_start: 0.8941 (tp) cc_final: 0.8651 (tp) REVERT: Dw 173 SER cc_start: 0.9026 (m) cc_final: 0.8670 (p) REVERT: Dw 218 HIS cc_start: 0.7958 (m90) cc_final: 0.7727 (m170) REVERT: Cd 413 GLU cc_start: 0.7564 (tp30) cc_final: 0.7073 (tp30) REVERT: Cd 416 THR cc_start: 0.8303 (p) cc_final: 0.8100 (p) REVERT: Cd 420 MET cc_start: 0.7850 (ttt) cc_final: 0.7415 (ttm) REVERT: Ce 420 MET cc_start: 0.7974 (ppp) cc_final: 0.7168 (ppp) REVERT: Cf 413 GLU cc_start: 0.8454 (pt0) cc_final: 0.7880 (pt0) REVERT: Ch 249 ILE cc_start: 0.9049 (mm) cc_final: 0.8470 (tp) REVERT: Ci 409 MET cc_start: 0.7220 (mmm) cc_final: 0.6841 (mmt) REVERT: Cj 299 ASN cc_start: 0.6583 (m-40) cc_final: 0.6260 (m-40) REVERT: Cm 414 ASP cc_start: 0.8097 (t70) cc_final: 0.7881 (t70) REVERT: Cp 236 LYS cc_start: 0.9379 (pptt) cc_final: 0.9129 (pptt) REVERT: Cp 270 LEU cc_start: 0.8810 (mm) cc_final: 0.8183 (mm) REVERT: Cp 381 ASP cc_start: 0.6583 (p0) cc_final: 0.6359 (p0) REVERT: Cp 424 ASP cc_start: 0.7772 (p0) cc_final: 0.7460 (p0) REVERT: Cr 270 LEU cc_start: 0.8668 (mm) cc_final: 0.7745 (mm) REVERT: Cr 420 MET cc_start: 0.7483 (ptt) cc_final: 0.7088 (ppp) REVERT: Cr 424 ASP cc_start: 0.7682 (p0) cc_final: 0.7173 (p0) REVERT: Cs 267 THR cc_start: 0.5989 (m) cc_final: 0.5750 (m) REVERT: Cu 270 LEU cc_start: 0.8154 (tp) cc_final: 0.7611 (tp) REVERT: Cv 385 LEU cc_start: 0.8364 (tp) cc_final: 0.8080 (tp) REVERT: Cv 414 ASP cc_start: 0.8120 (t0) cc_final: 0.7535 (t70) REVERT: Cw 413 GLU cc_start: 0.8040 (tp30) cc_final: 0.7776 (tp30) REVERT: Cx 249 ILE cc_start: 0.8832 (tp) cc_final: 0.8495 (tp) REVERT: Cx 253 LEU cc_start: 0.7719 (mt) cc_final: 0.7268 (mt) REVERT: Cx 381 ASP cc_start: 0.7486 (m-30) cc_final: 0.7212 (m-30) REVERT: Ea 366 TYR cc_start: 0.7198 (m-10) cc_final: 0.6921 (m-10) REVERT: Eb 259 ASN cc_start: 0.8210 (p0) cc_final: 0.7659 (p0) REVERT: Ec 236 LYS cc_start: 0.9075 (pptt) cc_final: 0.8381 (pptt) REVERT: Ec 385 LEU cc_start: 0.8826 (tp) cc_final: 0.8470 (pp) REVERT: Ee 236 LYS cc_start: 0.9270 (mptt) cc_final: 0.9031 (ptpp) REVERT: Ee 252 ILE cc_start: 0.7309 (tp) cc_final: 0.7109 (tp) REVERT: Ee 270 LEU cc_start: 0.8246 (mm) cc_final: 0.7983 (mm) REVERT: Ef 377 MET cc_start: 0.8283 (mpp) cc_final: 0.7387 (mpp) REVERT: Eg 259 ASN cc_start: 0.7699 (p0) cc_final: 0.7390 (p0) outliers start: 0 outliers final: 0 residues processed: 1114 average time/residue: 0.5283 time to fit residues: 989.0377 Evaluate side-chains 834 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 834 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 431 optimal weight: 2.9990 chunk 694 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 329 optimal weight: 10.0000 chunk 482 optimal weight: 2.9990 chunk 728 optimal weight: 0.7980 chunk 670 optimal weight: 0.9990 chunk 579 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 447 optimal weight: 1.9990 chunk 355 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Da 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dh 133 GLN Dh 218 HIS ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dl 209 ASN Dl 218 HIS ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dn 218 HIS ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Du 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 361 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cg 297 GLN ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ch 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 411 GLN ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cn 359 GLN Cn 374 HIS ** Co 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 361 ASN Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cq 281 HIS ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eb 281 HIS ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ed 365 ASN ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Eg 261 ASN ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.8390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 57796 Z= 0.174 Angle : 0.603 9.120 78238 Z= 0.312 Chirality : 0.042 0.228 9257 Planarity : 0.004 0.094 10442 Dihedral : 4.431 33.601 8031 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.48 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.10), residues: 7129 helix: 0.82 (0.11), residues: 2143 sheet: -0.17 (0.10), residues: 2646 loop : -1.40 (0.12), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HISCy 374 PHE 0.024 0.001 PHEcg 237 TYR 0.055 0.002 TYRCk 282 ARG 0.012 0.000 ARGcg 296 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14258 Ramachandran restraints generated. 7129 Oldfield, 0 Emsley, 7129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1136 time to evaluate : 5.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Db 151 LYS cc_start: 0.9404 (ptpp) cc_final: 0.9163 (mttm) REVERT: Db 196 HIS cc_start: 0.9066 (m90) cc_final: 0.8629 (m-70) REVERT: Dc 196 HIS cc_start: 0.9694 (m90) cc_final: 0.9390 (m90) REVERT: Dc 197 LEU cc_start: 0.9022 (tp) cc_final: 0.8811 (tp) REVERT: Dd 157 LEU cc_start: 0.8799 (pp) cc_final: 0.8561 (pp) REVERT: Dd 159 MET cc_start: 0.9155 (mmp) cc_final: 0.8592 (mmp) REVERT: De 125 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8553 (mt0) REVERT: De 131 ASN cc_start: 0.9535 (m-40) cc_final: 0.8972 (t0) REVERT: Df 159 MET cc_start: 0.9083 (pmm) cc_final: 0.8811 (tmm) REVERT: Df 184 ARG cc_start: 0.6554 (mmt90) cc_final: 0.6327 (tpt170) REVERT: Df 186 LEU cc_start: 0.7999 (mt) cc_final: 0.7711 (mt) REVERT: Df 205 LEU cc_start: 0.5746 (tp) cc_final: 0.5152 (tp) REVERT: Di 159 MET cc_start: 0.8359 (mmm) cc_final: 0.7225 (ptt) REVERT: Di 172 PRO cc_start: 0.9012 (Cg_endo) cc_final: 0.8685 (Cg_exo) REVERT: Di 187 ASP cc_start: 0.8975 (m-30) cc_final: 0.8611 (p0) REVERT: Dl 196 HIS cc_start: 0.9159 (m90) cc_final: 0.8714 (m90) REVERT: Dm 159 MET cc_start: 0.8448 (pmm) cc_final: 0.8062 (pmm) REVERT: Dm 214 ASP cc_start: 0.9321 (t0) cc_final: 0.8659 (p0) REVERT: Dm 218 HIS cc_start: 0.8812 (m90) cc_final: 0.8402 (m-70) REVERT: Dn 159 MET cc_start: 0.9157 (ptp) cc_final: 0.8921 (tpt) REVERT: Dn 196 HIS cc_start: 0.8922 (m90) cc_final: 0.8536 (m170) REVERT: Do 147 LEU cc_start: 0.9414 (tp) cc_final: 0.9212 (mt) REVERT: Do 186 LEU cc_start: 0.8303 (tp) cc_final: 0.7904 (tp) REVERT: Do 196 HIS cc_start: 0.9219 (m-70) cc_final: 0.8829 (m-70) REVERT: Do 218 HIS cc_start: 0.9412 (t-90) cc_final: 0.9179 (t-90) REVERT: Dp 205 LEU cc_start: 0.8904 (tp) cc_final: 0.8645 (tp) REVERT: Dp 220 LEU cc_start: 0.9721 (mt) cc_final: 0.9495 (mp) REVERT: Dq 157 LEU cc_start: 0.9368 (pp) cc_final: 0.9153 (pp) REVERT: Dq 159 MET cc_start: 0.8821 (mmp) cc_final: 0.8423 (mmp) REVERT: Dr 128 GLU cc_start: 0.9617 (tt0) cc_final: 0.9080 (pt0) REVERT: Dr 136 LEU cc_start: 0.9702 (pp) cc_final: 0.9415 (pp) REVERT: Dr 157 LEU cc_start: 0.8976 (pp) cc_final: 0.8704 (pp) REVERT: Dr 196 HIS cc_start: 0.8835 (m90) cc_final: 0.8585 (m90) REVERT: Dr 211 THR cc_start: 0.8492 (m) cc_final: 0.8259 (p) REVERT: Dr 218 HIS cc_start: 0.8718 (m90) cc_final: 0.8449 (m-70) REVERT: Ds 126 PHE cc_start: 0.9505 (t80) cc_final: 0.9298 (t80) REVERT: Ds 136 LEU cc_start: 0.9675 (mt) cc_final: 0.9394 (pp) REVERT: Ds 151 LYS cc_start: 0.9445 (ptpt) cc_final: 0.9175 (ptpt) REVERT: Ds 157 LEU cc_start: 0.9129 (mm) cc_final: 0.8727 (tp) REVERT: Dt 126 PHE cc_start: 0.9370 (t80) cc_final: 0.9071 (t80) REVERT: Dt 157 LEU cc_start: 0.9382 (tt) cc_final: 0.9097 (tp) REVERT: Du 139 GLU cc_start: 0.9614 (tt0) cc_final: 0.9371 (mt-10) REVERT: Du 147 LEU cc_start: 0.9560 (tt) cc_final: 0.9112 (mm) REVERT: Du 205 LEU cc_start: 0.8924 (tp) cc_final: 0.8576 (tp) REVERT: Du 213 VAL cc_start: 0.9082 (m) cc_final: 0.8733 (t) REVERT: Dv 178 VAL cc_start: 0.9575 (m) cc_final: 0.9362 (p) REVERT: Dv 186 LEU cc_start: 0.9091 (mp) cc_final: 0.8816 (mp) REVERT: Dv 196 HIS cc_start: 0.9484 (m90) cc_final: 0.9209 (m90) REVERT: Dv 205 LEU cc_start: 0.8820 (tp) cc_final: 0.8518 (tp) REVERT: Dw 173 SER cc_start: 0.9119 (m) cc_final: 0.8747 (p) REVERT: Dw 218 HIS cc_start: 0.7997 (m90) cc_final: 0.7767 (m170) REVERT: Cb 282 TYR cc_start: 0.7439 (m-10) cc_final: 0.6877 (m-10) REVERT: Cd 413 GLU cc_start: 0.7523 (tp30) cc_final: 0.7014 (tp30) REVERT: Cd 420 MET cc_start: 0.7762 (ttt) cc_final: 0.7339 (ttm) REVERT: Ce 420 MET cc_start: 0.7905 (ppp) cc_final: 0.7087 (ppp) REVERT: Cf 413 GLU cc_start: 0.8397 (pt0) cc_final: 0.7813 (pt0) REVERT: Ch 249 ILE cc_start: 0.9065 (mm) cc_final: 0.8446 (tp) REVERT: Ci 409 MET cc_start: 0.7223 (mmm) cc_final: 0.6865 (mmt) REVERT: Cj 299 ASN cc_start: 0.6622 (m-40) cc_final: 0.6366 (m110) REVERT: Cm 414 ASP cc_start: 0.8115 (t70) cc_final: 0.7891 (t70) REVERT: Cp 270 LEU cc_start: 0.8474 (mm) cc_final: 0.8016 (mm) REVERT: Cp 385 LEU cc_start: 0.8099 (pp) cc_final: 0.7871 (pp) REVERT: Cp 424 ASP cc_start: 0.7784 (p0) cc_final: 0.7521 (p0) REVERT: Cr 270 LEU cc_start: 0.8744 (mm) cc_final: 0.8513 (mm) REVERT: Cr 420 MET cc_start: 0.7371 (ptt) cc_final: 0.7056 (ppp) REVERT: Cr 424 ASP cc_start: 0.7721 (p0) cc_final: 0.7302 (p0) REVERT: Cu 270 LEU cc_start: 0.8112 (tp) cc_final: 0.7584 (tp) REVERT: Cu 303 GLN cc_start: 0.7025 (pm20) cc_final: 0.6767 (pm20) REVERT: Cv 385 LEU cc_start: 0.8257 (tp) cc_final: 0.7984 (tp) REVERT: Cv 414 ASP cc_start: 0.8031 (t0) cc_final: 0.7447 (t70) REVERT: Cw 413 GLU cc_start: 0.7989 (tp30) cc_final: 0.7757 (tp30) REVERT: Cx 249 ILE cc_start: 0.8821 (tp) cc_final: 0.8520 (tp) REVERT: Cx 253 LEU cc_start: 0.7552 (mt) cc_final: 0.7094 (mt) REVERT: Cy 236 LYS cc_start: 0.8984 (ptpp) cc_final: 0.8761 (ptpp) REVERT: Cy 430 LEU cc_start: 0.7519 (tp) cc_final: 0.7285 (tp) REVERT: Eb 259 ASN cc_start: 0.8129 (p0) cc_final: 0.7623 (p0) REVERT: Ec 236 LYS cc_start: 0.9060 (pptt) cc_final: 0.8401 (pptt) REVERT: Ec 385 LEU cc_start: 0.8742 (tp) cc_final: 0.8445 (pp) REVERT: Ee 236 LYS cc_start: 0.9245 (mptt) cc_final: 0.9037 (ptpp) REVERT: Ee 252 ILE cc_start: 0.7235 (tp) cc_final: 0.7017 (tp) REVERT: Ee 270 LEU cc_start: 0.8325 (mm) cc_final: 0.8040 (mm) REVERT: Ee 420 MET cc_start: 0.7464 (ptm) cc_final: 0.7127 (ppp) REVERT: Eg 259 ASN cc_start: 0.7674 (p0) cc_final: 0.7377 (p0) outliers start: 0 outliers final: 0 residues processed: 1136 average time/residue: 0.5255 time to fit residues: 1004.7873 Evaluate side-chains 841 residues out of total 6438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 841 time to evaluate : 5.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 731 random chunks: chunk 460 optimal weight: 6.9990 chunk 617 optimal weight: 1.9990 chunk 177 optimal weight: 3.9990 chunk 534 optimal weight: 0.9990 chunk 85 optimal weight: 6.9990 chunk 161 optimal weight: 50.0000 chunk 580 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 596 optimal weight: 3.9990 chunk 73 optimal weight: 0.0010 chunk 106 optimal weight: 6.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Da 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dg 131 ASN Dh 133 GLN Dh 218 HIS ** Dj 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dj 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dl 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dm 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Dp 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Dq 215 GLN Du 218 HIS ** Ca 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ca 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ca 365 ASN ** Ca 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cb 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cb 365 ASN ** Cb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cc 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cd 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ce 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cf 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** cg 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** cg 297 GLN ** cg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ch 411 GLN ** Ci 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ci 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cj 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ck 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cl 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cm 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cm 408 GLN ** Cn 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cn 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Co 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Co 374 HIS Co 408 GLN ** Co 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cp 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cq 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cr 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cs 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ct 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cu 246 GLN ** Cu 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cu 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cw 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cw 392 ASN ** Cx 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cx 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Cy 374 HIS Cy 411 GLN ** Cz 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Cz 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Cz 411 GLN ** Ea 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ea 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eb 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ec 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ed 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ee 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ef 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Eg 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Fh 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Fh 365 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.041192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.030222 restraints weight = 545290.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.031324 restraints weight = 335446.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.032158 restraints weight = 236272.913| |-----------------------------------------------------------------------------| r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.8592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 57796 Z= 0.225 Angle : 0.617 10.741 78238 Z= 0.324 Chirality : 0.042 0.214 9257 Planarity : 0.004 0.089 10442 Dihedral : 4.484 33.419 8031 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.10), residues: 7129 helix: 0.82 (0.11), residues: 2146 sheet: -0.15 (0.10), residues: 2605 loop : -1.28 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HISCn 374 PHE 0.022 0.002 PHEDp 126 TYR 0.032 0.002 TYRCn 282 ARG 0.013 0.000 ARGEg 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17010.19 seconds wall clock time: 298 minutes 0.79 seconds (17880.79 seconds total)