Starting phenix.real_space_refine on Sun Mar 17 14:18:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d5f_7797/03_2024/6d5f_7797.pdb" } resolution = 3.7 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= -0.001 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 672 5.49 5 S 312 5.16 5 C 48944 2.51 5 N 13376 2.21 5 O 16642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 79946 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "F" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "G" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "J" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "L" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "Q" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "S" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "T" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "W" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "X" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "Y" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "Z" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1486 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 12, 'TRANS': 181} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 13 Chain: "a" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "f" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "h" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "j" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "l" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "m" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "n" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "o" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "p" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "q" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "s" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "t" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "u" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "v" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "x" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "y" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1059 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 129} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 6888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 6888 Classifications: {'DNA': 336} Link IDs: {'rna3p': 335} Chain: "2" Number of atoms: 6888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 6888 Classifications: {'DNA': 336} Link IDs: {'rna3p': 335} Time building chain proxies: 29.21, per 1000 atoms: 0.37 Number of scatterers: 79946 At special positions: 0 Unit cell: (229.99, 231.08, 147.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 312 16.00 P 672 15.00 O 16642 8.00 N 13376 7.00 C 48944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 128 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 157 " distance=2.02 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 157 " distance=2.02 Simple disulfide: pdb=" SG CYS I 128 " - pdb=" SG CYS I 157 " distance=2.02 Simple disulfide: pdb=" SG CYS J 128 " - pdb=" SG CYS J 157 " distance=2.02 Simple disulfide: pdb=" SG CYS K 128 " - pdb=" SG CYS K 157 " distance=2.02 Simple disulfide: pdb=" SG CYS L 128 " - pdb=" SG CYS L 157 " distance=2.02 Simple disulfide: pdb=" SG CYS M 128 " - pdb=" SG CYS M 157 " distance=2.02 Simple disulfide: pdb=" SG CYS N 128 " - pdb=" SG CYS N 157 " distance=2.02 Simple disulfide: pdb=" SG CYS O 128 " - pdb=" SG CYS O 157 " distance=2.02 Simple disulfide: pdb=" SG CYS P 128 " - pdb=" SG CYS P 157 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 128 " - pdb=" SG CYS Q 157 " distance=2.02 Simple disulfide: pdb=" SG CYS R 128 " - pdb=" SG CYS R 157 " distance=2.02 Simple disulfide: pdb=" SG CYS S 128 " - pdb=" SG CYS S 157 " distance=2.02 Simple disulfide: pdb=" SG CYS T 128 " - pdb=" SG CYS T 157 " distance=2.02 Simple disulfide: pdb=" SG CYS U 128 " - pdb=" SG CYS U 157 " distance=2.02 Simple disulfide: pdb=" SG CYS V 128 " - pdb=" SG CYS V 157 " distance=2.02 Simple disulfide: pdb=" SG CYS W 128 " - pdb=" SG CYS W 157 " distance=2.02 Simple disulfide: pdb=" SG CYS X 128 " - pdb=" SG CYS X 157 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 128 " - pdb=" SG CYS Y 157 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 128 " - pdb=" SG CYS Z 157 " distance=2.02 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: 26.11 Conformation dependent library (CDL) restraints added in 8.7 seconds 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16016 Finding SS restraints... Secondary structure from input PDB file: 338 helices and 35 sheets defined 71.6% alpha, 2.1% beta 17 base pairs and 348 stacking pairs defined. Time for finding SS restraints: 19.25 Creating SS restraints... Processing helix chain 'A' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR A 35 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU A 47 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 98 Processing helix chain 'A' and resid 101 through 120 Processing helix chain 'A' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE A 192 " --> pdb=" O SER A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN B 23 " --> pdb=" O VAL B 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS B 34 " --> pdb=" O ASP B 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA B 38 " --> pdb=" O LYS B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU B 47 " --> pdb=" O GLY B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 98 Processing helix chain 'B' and resid 101 through 120 Processing helix chain 'B' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA B 186 " --> pdb=" O GLU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE B 192 " --> pdb=" O SER B 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET C 14 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN C 23 " --> pdb=" O VAL C 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP C 30 " --> pdb=" O GLY C 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS C 34 " --> pdb=" O ASP C 30 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR C 35 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA C 38 " --> pdb=" O LYS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 98 Processing helix chain 'C' and resid 101 through 120 Processing helix chain 'C' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA C 131 " --> pdb=" O SER C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA C 186 " --> pdb=" O GLU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 194 removed outlier: 3.606A pdb=" N ILE C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET D 14 " --> pdb=" O ASP D 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN D 23 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP D 30 " --> pdb=" O GLY D 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR D 35 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA D 38 " --> pdb=" O LYS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU D 47 " --> pdb=" O GLY D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 98 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'D' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE D 192 " --> pdb=" O SER D 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR E 24 " --> pdb=" O ARG E 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP E 27 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP E 30 " --> pdb=" O GLY E 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU E 47 " --> pdb=" O GLY E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 98 Processing helix chain 'E' and resid 101 through 120 Processing helix chain 'E' and resid 127 through 143 removed outlier: 3.537A pdb=" N ALA E 131 " --> pdb=" O SER E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 186 removed outlier: 3.525A pdb=" N ALA E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE E 192 " --> pdb=" O SER E 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR F 24 " --> pdb=" O ARG F 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY F 26 " --> pdb=" O LEU F 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP F 27 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP F 30 " --> pdb=" O GLY F 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR F 35 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA F 38 " --> pdb=" O LYS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 67 removed outlier: 4.257A pdb=" N LEU F 47 " --> pdb=" O GLY F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 98 Processing helix chain 'F' and resid 101 through 120 Processing helix chain 'F' and resid 127 through 143 removed outlier: 3.537A pdb=" N ALA F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET G 14 " --> pdb=" O ASP G 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN G 23 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR G 24 " --> pdb=" O ARG G 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP G 30 " --> pdb=" O GLY G 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA G 38 " --> pdb=" O LYS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU G 47 " --> pdb=" O GLY G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 98 Processing helix chain 'G' and resid 101 through 120 Processing helix chain 'G' and resid 127 through 143 removed outlier: 3.537A pdb=" N ALA G 131 " --> pdb=" O SER G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA G 186 " --> pdb=" O GLU G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 194 removed outlier: 3.606A pdb=" N ILE G 192 " --> pdb=" O SER G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET H 14 " --> pdb=" O ASP H 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN H 23 " --> pdb=" O VAL H 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR H 24 " --> pdb=" O ARG H 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY H 26 " --> pdb=" O LEU H 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP H 27 " --> pdb=" O GLN H 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR H 35 " --> pdb=" O GLU H 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA H 38 " --> pdb=" O LYS H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU H 47 " --> pdb=" O GLY H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'H' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA H 131 " --> pdb=" O SER H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA H 186 " --> pdb=" O GLU H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE H 192 " --> pdb=" O SER H 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET I 14 " --> pdb=" O ASP I 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN I 23 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP I 27 " --> pdb=" O GLN I 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP I 30 " --> pdb=" O GLY I 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS I 34 " --> pdb=" O ASP I 30 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR I 35 " --> pdb=" O GLU I 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA I 38 " --> pdb=" O LYS I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU I 47 " --> pdb=" O GLY I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 98 Processing helix chain 'I' and resid 101 through 120 Processing helix chain 'I' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA I 186 " --> pdb=" O GLU I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET J 14 " --> pdb=" O ASP J 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN J 23 " --> pdb=" O VAL J 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR J 24 " --> pdb=" O ARG J 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP J 27 " --> pdb=" O GLN J 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS J 34 " --> pdb=" O ASP J 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA J 38 " --> pdb=" O LYS J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU J 47 " --> pdb=" O GLY J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 98 Processing helix chain 'J' and resid 101 through 120 Processing helix chain 'J' and resid 127 through 143 removed outlier: 3.535A pdb=" N ALA J 131 " --> pdb=" O SER J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE J 192 " --> pdb=" O SER J 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET K 14 " --> pdb=" O ASP K 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN K 23 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR K 24 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY K 26 " --> pdb=" O LEU K 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP K 27 " --> pdb=" O GLN K 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP K 30 " --> pdb=" O GLY K 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS K 34 " --> pdb=" O ASP K 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR K 35 " --> pdb=" O GLU K 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA K 38 " --> pdb=" O LYS K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 67 removed outlier: 4.257A pdb=" N LEU K 47 " --> pdb=" O GLY K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 79 through 98 Processing helix chain 'K' and resid 101 through 120 Processing helix chain 'K' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA K 131 " --> pdb=" O SER K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA K 186 " --> pdb=" O GLU K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 removed outlier: 3.606A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET L 14 " --> pdb=" O ASP L 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN L 23 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR L 24 " --> pdb=" O ARG L 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP L 27 " --> pdb=" O GLN L 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP L 30 " --> pdb=" O GLY L 26 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS L 34 " --> pdb=" O ASP L 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR L 35 " --> pdb=" O GLU L 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA L 38 " --> pdb=" O LYS L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 67 removed outlier: 4.257A pdb=" N LEU L 47 " --> pdb=" O GLY L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 98 Processing helix chain 'L' and resid 101 through 120 Processing helix chain 'L' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA L 186 " --> pdb=" O GLU L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET M 14 " --> pdb=" O ASP M 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN M 23 " --> pdb=" O VAL M 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR M 24 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY M 26 " --> pdb=" O LEU M 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP M 27 " --> pdb=" O GLN M 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP M 30 " --> pdb=" O GLY M 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS M 34 " --> pdb=" O ASP M 30 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TYR M 35 " --> pdb=" O GLU M 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA M 38 " --> pdb=" O LYS M 34 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU M 47 " --> pdb=" O GLY M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 98 Processing helix chain 'M' and resid 101 through 120 Processing helix chain 'M' and resid 127 through 143 removed outlier: 3.535A pdb=" N ALA M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) Processing helix chain 'M' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA M 186 " --> pdb=" O GLU M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 194 removed outlier: 3.606A pdb=" N ILE M 192 " --> pdb=" O SER M 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN N 23 " --> pdb=" O VAL N 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR N 24 " --> pdb=" O ARG N 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY N 26 " --> pdb=" O LEU N 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP N 27 " --> pdb=" O GLN N 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS N 34 " --> pdb=" O ASP N 30 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR N 35 " --> pdb=" O GLU N 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA N 38 " --> pdb=" O LYS N 34 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU N 47 " --> pdb=" O GLY N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 98 Processing helix chain 'N' and resid 101 through 120 Processing helix chain 'N' and resid 127 through 143 removed outlier: 3.535A pdb=" N ALA N 131 " --> pdb=" O SER N 127 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA N 186 " --> pdb=" O GLU N 182 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE N 192 " --> pdb=" O SER N 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET O 14 " --> pdb=" O ASP O 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN O 23 " --> pdb=" O VAL O 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR O 24 " --> pdb=" O ARG O 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP O 27 " --> pdb=" O GLN O 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP O 30 " --> pdb=" O GLY O 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS O 34 " --> pdb=" O ASP O 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR O 35 " --> pdb=" O GLU O 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA O 38 " --> pdb=" O LYS O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU O 47 " --> pdb=" O GLY O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 98 Processing helix chain 'O' and resid 101 through 120 Processing helix chain 'O' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA O 131 " --> pdb=" O SER O 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA O 186 " --> pdb=" O GLU O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET P 14 " --> pdb=" O ASP P 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN P 23 " --> pdb=" O VAL P 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR P 24 " --> pdb=" O ARG P 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY P 26 " --> pdb=" O LEU P 22 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP P 27 " --> pdb=" O GLN P 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS P 34 " --> pdb=" O ASP P 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR P 35 " --> pdb=" O GLU P 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA P 38 " --> pdb=" O LYS P 34 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU P 47 " --> pdb=" O GLY P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 98 Processing helix chain 'P' and resid 101 through 120 Processing helix chain 'P' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA P 131 " --> pdb=" O SER P 127 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 186 removed outlier: 3.523A pdb=" N ALA P 186 " --> pdb=" O GLU P 182 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE P 192 " --> pdb=" O SER P 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET Q 14 " --> pdb=" O ASP Q 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN Q 23 " --> pdb=" O VAL Q 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR Q 24 " --> pdb=" O ARG Q 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY Q 26 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP Q 27 " --> pdb=" O GLN Q 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS Q 34 " --> pdb=" O ASP Q 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR Q 35 " --> pdb=" O GLU Q 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA Q 38 " --> pdb=" O LYS Q 34 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 98 Processing helix chain 'Q' and resid 101 through 120 Processing helix chain 'Q' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA Q 131 " --> pdb=" O SER Q 127 " (cutoff:3.500A) Processing helix chain 'Q' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA Q 186 " --> pdb=" O GLU Q 182 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET R 14 " --> pdb=" O ASP R 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN R 23 " --> pdb=" O VAL R 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY R 26 " --> pdb=" O LEU R 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP R 30 " --> pdb=" O GLY R 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS R 34 " --> pdb=" O ASP R 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA R 38 " --> pdb=" O LYS R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 98 Processing helix chain 'R' and resid 101 through 120 Processing helix chain 'R' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA R 131 " --> pdb=" O SER R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA R 186 " --> pdb=" O GLU R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 194 removed outlier: 3.606A pdb=" N ILE R 192 " --> pdb=" O SER R 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET S 14 " --> pdb=" O ASP S 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN S 23 " --> pdb=" O VAL S 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR S 24 " --> pdb=" O ARG S 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY S 26 " --> pdb=" O LEU S 22 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP S 27 " --> pdb=" O GLN S 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N LYS S 34 " --> pdb=" O ASP S 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR S 35 " --> pdb=" O GLU S 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA S 38 " --> pdb=" O LYS S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU S 47 " --> pdb=" O GLY S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 98 Processing helix chain 'S' and resid 101 through 120 Processing helix chain 'S' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA S 131 " --> pdb=" O SER S 127 " (cutoff:3.500A) Processing helix chain 'S' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA S 186 " --> pdb=" O GLU S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE S 192 " --> pdb=" O SER S 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET T 14 " --> pdb=" O ASP T 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN T 23 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR T 24 " --> pdb=" O ARG T 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY T 26 " --> pdb=" O LEU T 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP T 27 " --> pdb=" O GLN T 23 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP T 30 " --> pdb=" O GLY T 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS T 34 " --> pdb=" O ASP T 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR T 35 " --> pdb=" O GLU T 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA T 38 " --> pdb=" O LYS T 34 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU T 47 " --> pdb=" O GLY T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 79 through 98 Processing helix chain 'T' and resid 101 through 120 Processing helix chain 'T' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA T 131 " --> pdb=" O SER T 127 " (cutoff:3.500A) Processing helix chain 'T' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA T 186 " --> pdb=" O GLU T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE T 192 " --> pdb=" O SER T 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET U 14 " --> pdb=" O ASP U 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN U 23 " --> pdb=" O VAL U 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY U 26 " --> pdb=" O LEU U 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP U 27 " --> pdb=" O GLN U 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP U 30 " --> pdb=" O GLY U 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS U 34 " --> pdb=" O ASP U 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR U 35 " --> pdb=" O GLU U 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA U 38 " --> pdb=" O LYS U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 67 removed outlier: 4.257A pdb=" N LEU U 47 " --> pdb=" O GLY U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 79 through 98 Processing helix chain 'U' and resid 101 through 120 Processing helix chain 'U' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA U 131 " --> pdb=" O SER U 127 " (cutoff:3.500A) Processing helix chain 'U' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA U 186 " --> pdb=" O GLU U 182 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE U 192 " --> pdb=" O SER U 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET V 14 " --> pdb=" O ASP V 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN V 23 " --> pdb=" O VAL V 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR V 24 " --> pdb=" O ARG V 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY V 26 " --> pdb=" O LEU V 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP V 27 " --> pdb=" O GLN V 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP V 30 " --> pdb=" O GLY V 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS V 34 " --> pdb=" O ASP V 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR V 35 " --> pdb=" O GLU V 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA V 38 " --> pdb=" O LYS V 34 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU V 47 " --> pdb=" O GLY V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 79 through 98 Processing helix chain 'V' and resid 101 through 120 Processing helix chain 'V' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA V 131 " --> pdb=" O SER V 127 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA V 186 " --> pdb=" O GLU V 182 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE V 192 " --> pdb=" O SER V 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET W 14 " --> pdb=" O ASP W 10 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN W 23 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR W 24 " --> pdb=" O ARG W 20 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N GLY W 26 " --> pdb=" O LEU W 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP W 27 " --> pdb=" O GLN W 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP W 30 " --> pdb=" O GLY W 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS W 34 " --> pdb=" O ASP W 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR W 35 " --> pdb=" O GLU W 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA W 38 " --> pdb=" O LYS W 34 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU W 47 " --> pdb=" O GLY W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 98 Processing helix chain 'W' and resid 101 through 120 Processing helix chain 'W' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA W 131 " --> pdb=" O SER W 127 " (cutoff:3.500A) Processing helix chain 'W' and resid 179 through 186 removed outlier: 3.525A pdb=" N ALA W 186 " --> pdb=" O GLU W 182 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE W 192 " --> pdb=" O SER W 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 42 removed outlier: 3.556A pdb=" N MET X 14 " --> pdb=" O ASP X 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN X 23 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY X 26 " --> pdb=" O LEU X 22 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP X 27 " --> pdb=" O GLN X 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP X 30 " --> pdb=" O GLY X 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS X 34 " --> pdb=" O ASP X 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR X 35 " --> pdb=" O GLU X 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA X 38 " --> pdb=" O LYS X 34 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 79 through 98 Processing helix chain 'X' and resid 101 through 120 Processing helix chain 'X' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA X 131 " --> pdb=" O SER X 127 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 186 removed outlier: 3.524A pdb=" N ALA X 186 " --> pdb=" O GLU X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE X 192 " --> pdb=" O SER X 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET Y 14 " --> pdb=" O ASP Y 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN Y 23 " --> pdb=" O VAL Y 19 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR Y 24 " --> pdb=" O ARG Y 20 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLY Y 26 " --> pdb=" O LEU Y 22 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP Y 27 " --> pdb=" O GLN Y 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP Y 30 " --> pdb=" O GLY Y 26 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS Y 34 " --> pdb=" O ASP Y 30 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR Y 35 " --> pdb=" O GLU Y 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA Y 38 " --> pdb=" O LYS Y 34 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 67 removed outlier: 4.257A pdb=" N LEU Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 98 Processing helix chain 'Y' and resid 101 through 120 Processing helix chain 'Y' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA Y 131 " --> pdb=" O SER Y 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 179 through 186 removed outlier: 3.524A pdb=" N ALA Y 186 " --> pdb=" O GLU Y 182 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE Y 192 " --> pdb=" O SER Y 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 42 removed outlier: 3.555A pdb=" N MET Z 14 " --> pdb=" O ASP Z 10 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN Z 23 " --> pdb=" O VAL Z 19 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N THR Z 24 " --> pdb=" O ARG Z 20 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY Z 26 " --> pdb=" O LEU Z 22 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASP Z 27 " --> pdb=" O GLN Z 23 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP Z 30 " --> pdb=" O GLY Z 26 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS Z 34 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N TYR Z 35 " --> pdb=" O GLU Z 31 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA Z 38 " --> pdb=" O LYS Z 34 " (cutoff:3.500A) Processing helix chain 'Z' and resid 43 through 67 removed outlier: 4.258A pdb=" N LEU Z 47 " --> pdb=" O GLY Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 98 Processing helix chain 'Z' and resid 101 through 120 Processing helix chain 'Z' and resid 127 through 143 removed outlier: 3.536A pdb=" N ALA Z 131 " --> pdb=" O SER Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 180 through 186 removed outlier: 3.525A pdb=" N ALA Z 186 " --> pdb=" O GLU Z 182 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 194 removed outlier: 3.607A pdb=" N ILE Z 192 " --> pdb=" O SER Z 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA a 13 " --> pdb=" O THR a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 20 through 39 removed outlier: 4.048A pdb=" N ASN a 30 " --> pdb=" O THR a 26 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS a 33 " --> pdb=" O LYS a 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL a 37 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN a 38 " --> pdb=" O ASP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA a 52 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Proline residue: a 55 - end of helix removed outlier: 3.696A pdb=" N GLY a 61 " --> pdb=" O LEU a 57 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 83 Processing helix chain 'a' and resid 86 through 104 removed outlier: 5.010A pdb=" N ARG a 92 " --> pdb=" O GLU a 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE a 95 " --> pdb=" O LYS a 91 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA b 13 " --> pdb=" O THR b 9 " (cutoff:3.500A) Processing helix chain 'b' and resid 20 through 39 removed outlier: 4.048A pdb=" N ASN b 30 " --> pdb=" O THR b 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS b 33 " --> pdb=" O LYS b 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL b 37 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN b 38 " --> pdb=" O ASP b 34 " (cutoff:3.500A) Processing helix chain 'b' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA b 52 " --> pdb=" O VAL b 48 " (cutoff:3.500A) Proline residue: b 55 - end of helix removed outlier: 3.696A pdb=" N GLY b 61 " --> pdb=" O LEU b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 83 Processing helix chain 'b' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG b 92 " --> pdb=" O GLU b 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE b 95 " --> pdb=" O LYS b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU b 113 " --> pdb=" O ALA b 109 " (cutoff:3.500A) Processing helix chain 'c' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA c 13 " --> pdb=" O THR c 9 " (cutoff:3.500A) Processing helix chain 'c' and resid 20 through 39 removed outlier: 4.046A pdb=" N ASN c 30 " --> pdb=" O THR c 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS c 33 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL c 37 " --> pdb=" O LYS c 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN c 38 " --> pdb=" O ASP c 34 " (cutoff:3.500A) Processing helix chain 'c' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA c 52 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Proline residue: c 55 - end of helix removed outlier: 3.696A pdb=" N GLY c 61 " --> pdb=" O LEU c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 83 Processing helix chain 'c' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE c 95 " --> pdb=" O LYS c 91 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU c 113 " --> pdb=" O ALA c 109 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA d 13 " --> pdb=" O THR d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN d 30 " --> pdb=" O THR d 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS d 33 " --> pdb=" O LYS d 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL d 37 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN d 38 " --> pdb=" O ASP d 34 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA d 52 " --> pdb=" O VAL d 48 " (cutoff:3.500A) Proline residue: d 55 - end of helix removed outlier: 3.696A pdb=" N GLY d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 83 Processing helix chain 'd' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG d 92 " --> pdb=" O GLU d 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE d 95 " --> pdb=" O LYS d 91 " (cutoff:3.500A) Processing helix chain 'd' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU d 113 " --> pdb=" O ALA d 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA e 13 " --> pdb=" O THR e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN e 30 " --> pdb=" O THR e 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS e 33 " --> pdb=" O LYS e 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL e 37 " --> pdb=" O LYS e 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN e 38 " --> pdb=" O ASP e 34 " (cutoff:3.500A) Processing helix chain 'e' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA e 52 " --> pdb=" O VAL e 48 " (cutoff:3.500A) Proline residue: e 55 - end of helix removed outlier: 3.696A pdb=" N GLY e 61 " --> pdb=" O LEU e 57 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 83 Processing helix chain 'e' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG e 92 " --> pdb=" O GLU e 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE e 95 " --> pdb=" O LYS e 91 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'f' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA f 13 " --> pdb=" O THR f 9 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN f 30 " --> pdb=" O THR f 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS f 33 " --> pdb=" O LYS f 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL f 37 " --> pdb=" O LYS f 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN f 38 " --> pdb=" O ASP f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA f 52 " --> pdb=" O VAL f 48 " (cutoff:3.500A) Proline residue: f 55 - end of helix removed outlier: 3.697A pdb=" N GLY f 61 " --> pdb=" O LEU f 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 83 Processing helix chain 'f' and resid 86 through 104 removed outlier: 5.008A pdb=" N ARG f 92 " --> pdb=" O GLU f 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE f 95 " --> pdb=" O LYS f 91 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU f 113 " --> pdb=" O ALA f 109 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA g 13 " --> pdb=" O THR g 9 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN g 30 " --> pdb=" O THR g 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS g 33 " --> pdb=" O LYS g 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL g 37 " --> pdb=" O LYS g 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN g 38 " --> pdb=" O ASP g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Proline residue: g 55 - end of helix removed outlier: 3.696A pdb=" N GLY g 61 " --> pdb=" O LEU g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 66 through 83 Processing helix chain 'g' and resid 86 through 104 removed outlier: 5.008A pdb=" N ARG g 92 " --> pdb=" O GLU g 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE g 95 " --> pdb=" O LYS g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU g 113 " --> pdb=" O ALA g 109 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA h 13 " --> pdb=" O THR h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS h 33 " --> pdb=" O LYS h 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL h 37 " --> pdb=" O LYS h 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN h 38 " --> pdb=" O ASP h 34 " (cutoff:3.500A) Processing helix chain 'h' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA h 52 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Proline residue: h 55 - end of helix removed outlier: 3.697A pdb=" N GLY h 61 " --> pdb=" O LEU h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 66 through 83 Processing helix chain 'h' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG h 92 " --> pdb=" O GLU h 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE h 95 " --> pdb=" O LYS h 91 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU h 113 " --> pdb=" O ALA h 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA i 13 " --> pdb=" O THR i 9 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 39 removed outlier: 4.048A pdb=" N ASN i 30 " --> pdb=" O THR i 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS i 33 " --> pdb=" O LYS i 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL i 37 " --> pdb=" O LYS i 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN i 38 " --> pdb=" O ASP i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA i 52 " --> pdb=" O VAL i 48 " (cutoff:3.500A) Proline residue: i 55 - end of helix removed outlier: 3.697A pdb=" N GLY i 61 " --> pdb=" O LEU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 66 through 83 Processing helix chain 'i' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE i 95 " --> pdb=" O LYS i 91 " (cutoff:3.500A) Processing helix chain 'i' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU i 113 " --> pdb=" O ALA i 109 " (cutoff:3.500A) Processing helix chain 'j' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA j 13 " --> pdb=" O THR j 9 " (cutoff:3.500A) Processing helix chain 'j' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN j 30 " --> pdb=" O THR j 26 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS j 33 " --> pdb=" O LYS j 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL j 37 " --> pdb=" O LYS j 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN j 38 " --> pdb=" O ASP j 34 " (cutoff:3.500A) Processing helix chain 'j' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA j 52 " --> pdb=" O VAL j 48 " (cutoff:3.500A) Proline residue: j 55 - end of helix removed outlier: 3.696A pdb=" N GLY j 61 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing helix chain 'j' and resid 66 through 83 Processing helix chain 'j' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG j 92 " --> pdb=" O GLU j 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE j 95 " --> pdb=" O LYS j 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU j 113 " --> pdb=" O ALA j 109 " (cutoff:3.500A) Processing helix chain 'k' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA k 13 " --> pdb=" O THR k 9 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN k 30 " --> pdb=" O THR k 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS k 33 " --> pdb=" O LYS k 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL k 37 " --> pdb=" O LYS k 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN k 38 " --> pdb=" O ASP k 34 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA k 52 " --> pdb=" O VAL k 48 " (cutoff:3.500A) Proline residue: k 55 - end of helix removed outlier: 3.695A pdb=" N GLY k 61 " --> pdb=" O LEU k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 66 through 83 Processing helix chain 'k' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG k 92 " --> pdb=" O GLU k 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE k 95 " --> pdb=" O LYS k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU k 113 " --> pdb=" O ALA k 109 " (cutoff:3.500A) Processing helix chain 'l' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA l 13 " --> pdb=" O THR l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN l 30 " --> pdb=" O THR l 26 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS l 33 " --> pdb=" O LYS l 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL l 37 " --> pdb=" O LYS l 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN l 38 " --> pdb=" O ASP l 34 " (cutoff:3.500A) Processing helix chain 'l' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA l 52 " --> pdb=" O VAL l 48 " (cutoff:3.500A) Proline residue: l 55 - end of helix removed outlier: 3.696A pdb=" N GLY l 61 " --> pdb=" O LEU l 57 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 83 Processing helix chain 'l' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG l 92 " --> pdb=" O GLU l 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE l 95 " --> pdb=" O LYS l 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU l 113 " --> pdb=" O ALA l 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA m 13 " --> pdb=" O THR m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN m 30 " --> pdb=" O THR m 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS m 33 " --> pdb=" O LYS m 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL m 37 " --> pdb=" O LYS m 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA m 52 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Proline residue: m 55 - end of helix removed outlier: 3.696A pdb=" N GLY m 61 " --> pdb=" O LEU m 57 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 83 Processing helix chain 'm' and resid 86 through 104 removed outlier: 5.010A pdb=" N ARG m 92 " --> pdb=" O GLU m 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE m 95 " --> pdb=" O LYS m 91 " (cutoff:3.500A) Processing helix chain 'm' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU m 113 " --> pdb=" O ALA m 109 " (cutoff:3.500A) Processing helix chain 'n' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA n 13 " --> pdb=" O THR n 9 " (cutoff:3.500A) Processing helix chain 'n' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN n 30 " --> pdb=" O THR n 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS n 33 " --> pdb=" O LYS n 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL n 37 " --> pdb=" O LYS n 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN n 38 " --> pdb=" O ASP n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA n 52 " --> pdb=" O VAL n 48 " (cutoff:3.500A) Proline residue: n 55 - end of helix removed outlier: 3.695A pdb=" N GLY n 61 " --> pdb=" O LEU n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 66 through 83 Processing helix chain 'n' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG n 92 " --> pdb=" O GLU n 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE n 95 " --> pdb=" O LYS n 91 " (cutoff:3.500A) Processing helix chain 'n' and resid 107 through 118 removed outlier: 4.488A pdb=" N GLU n 113 " --> pdb=" O ALA n 109 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA o 13 " --> pdb=" O THR o 9 " (cutoff:3.500A) Processing helix chain 'o' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN o 30 " --> pdb=" O THR o 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS o 33 " --> pdb=" O LYS o 29 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL o 37 " --> pdb=" O LYS o 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN o 38 " --> pdb=" O ASP o 34 " (cutoff:3.500A) Processing helix chain 'o' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA o 52 " --> pdb=" O VAL o 48 " (cutoff:3.500A) Proline residue: o 55 - end of helix removed outlier: 3.696A pdb=" N GLY o 61 " --> pdb=" O LEU o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 66 through 83 Processing helix chain 'o' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG o 92 " --> pdb=" O GLU o 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE o 95 " --> pdb=" O LYS o 91 " (cutoff:3.500A) Processing helix chain 'o' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA p 13 " --> pdb=" O THR p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN p 30 " --> pdb=" O THR p 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS p 33 " --> pdb=" O LYS p 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL p 37 " --> pdb=" O LYS p 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN p 38 " --> pdb=" O ASP p 34 " (cutoff:3.500A) Processing helix chain 'p' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA p 52 " --> pdb=" O VAL p 48 " (cutoff:3.500A) Proline residue: p 55 - end of helix removed outlier: 3.697A pdb=" N GLY p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing helix chain 'p' and resid 66 through 83 Processing helix chain 'p' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG p 92 " --> pdb=" O GLU p 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE p 95 " --> pdb=" O LYS p 91 " (cutoff:3.500A) Processing helix chain 'p' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU p 113 " --> pdb=" O ALA p 109 " (cutoff:3.500A) Processing helix chain 'q' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA q 13 " --> pdb=" O THR q 9 " (cutoff:3.500A) Processing helix chain 'q' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN q 30 " --> pdb=" O THR q 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS q 33 " --> pdb=" O LYS q 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL q 37 " --> pdb=" O LYS q 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN q 38 " --> pdb=" O ASP q 34 " (cutoff:3.500A) Processing helix chain 'q' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Proline residue: q 55 - end of helix removed outlier: 3.697A pdb=" N GLY q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 83 Processing helix chain 'q' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG q 92 " --> pdb=" O GLU q 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE q 95 " --> pdb=" O LYS q 91 " (cutoff:3.500A) Processing helix chain 'q' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU q 113 " --> pdb=" O ALA q 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA r 13 " --> pdb=" O THR r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN r 30 " --> pdb=" O THR r 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS r 33 " --> pdb=" O LYS r 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL r 37 " --> pdb=" O LYS r 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN r 38 " --> pdb=" O ASP r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA r 52 " --> pdb=" O VAL r 48 " (cutoff:3.500A) Proline residue: r 55 - end of helix removed outlier: 3.697A pdb=" N GLY r 61 " --> pdb=" O LEU r 57 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 83 Processing helix chain 'r' and resid 86 through 104 removed outlier: 5.010A pdb=" N ARG r 92 " --> pdb=" O GLU r 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE r 95 " --> pdb=" O LYS r 91 " (cutoff:3.500A) Processing helix chain 'r' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU r 113 " --> pdb=" O ALA r 109 " (cutoff:3.500A) Processing helix chain 's' and resid 9 through 20 removed outlier: 3.841A pdb=" N ALA s 13 " --> pdb=" O THR s 9 " (cutoff:3.500A) Processing helix chain 's' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN s 30 " --> pdb=" O THR s 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS s 33 " --> pdb=" O LYS s 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL s 37 " --> pdb=" O LYS s 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN s 38 " --> pdb=" O ASP s 34 " (cutoff:3.500A) Processing helix chain 's' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA s 52 " --> pdb=" O VAL s 48 " (cutoff:3.500A) Proline residue: s 55 - end of helix removed outlier: 3.696A pdb=" N GLY s 61 " --> pdb=" O LEU s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 66 through 83 Processing helix chain 's' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG s 92 " --> pdb=" O GLU s 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE s 95 " --> pdb=" O LYS s 91 " (cutoff:3.500A) Processing helix chain 's' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU s 113 " --> pdb=" O ALA s 109 " (cutoff:3.500A) Processing helix chain 't' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA t 13 " --> pdb=" O THR t 9 " (cutoff:3.500A) Processing helix chain 't' and resid 20 through 39 removed outlier: 4.048A pdb=" N ASN t 30 " --> pdb=" O THR t 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS t 33 " --> pdb=" O LYS t 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL t 37 " --> pdb=" O LYS t 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN t 38 " --> pdb=" O ASP t 34 " (cutoff:3.500A) Processing helix chain 't' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA t 52 " --> pdb=" O VAL t 48 " (cutoff:3.500A) Proline residue: t 55 - end of helix removed outlier: 3.695A pdb=" N GLY t 61 " --> pdb=" O LEU t 57 " (cutoff:3.500A) Processing helix chain 't' and resid 66 through 83 Processing helix chain 't' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG t 92 " --> pdb=" O GLU t 88 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE t 95 " --> pdb=" O LYS t 91 " (cutoff:3.500A) Processing helix chain 't' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU t 113 " --> pdb=" O ALA t 109 " (cutoff:3.500A) Processing helix chain 'u' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA u 13 " --> pdb=" O THR u 9 " (cutoff:3.500A) Processing helix chain 'u' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN u 30 " --> pdb=" O THR u 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS u 33 " --> pdb=" O LYS u 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL u 37 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN u 38 " --> pdb=" O ASP u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA u 52 " --> pdb=" O VAL u 48 " (cutoff:3.500A) Proline residue: u 55 - end of helix removed outlier: 3.697A pdb=" N GLY u 61 " --> pdb=" O LEU u 57 " (cutoff:3.500A) Processing helix chain 'u' and resid 66 through 83 Processing helix chain 'u' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG u 92 " --> pdb=" O GLU u 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE u 95 " --> pdb=" O LYS u 91 " (cutoff:3.500A) Processing helix chain 'u' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU u 113 " --> pdb=" O ALA u 109 " (cutoff:3.500A) Processing helix chain 'v' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA v 13 " --> pdb=" O THR v 9 " (cutoff:3.500A) Processing helix chain 'v' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN v 30 " --> pdb=" O THR v 26 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS v 33 " --> pdb=" O LYS v 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL v 37 " --> pdb=" O LYS v 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN v 38 " --> pdb=" O ASP v 34 " (cutoff:3.500A) Processing helix chain 'v' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA v 52 " --> pdb=" O VAL v 48 " (cutoff:3.500A) Proline residue: v 55 - end of helix removed outlier: 3.696A pdb=" N GLY v 61 " --> pdb=" O LEU v 57 " (cutoff:3.500A) Processing helix chain 'v' and resid 66 through 83 Processing helix chain 'v' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG v 92 " --> pdb=" O GLU v 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE v 95 " --> pdb=" O LYS v 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU v 113 " --> pdb=" O ALA v 109 " (cutoff:3.500A) Processing helix chain 'w' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA w 13 " --> pdb=" O THR w 9 " (cutoff:3.500A) Processing helix chain 'w' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN w 30 " --> pdb=" O THR w 26 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS w 33 " --> pdb=" O LYS w 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL w 37 " --> pdb=" O LYS w 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN w 38 " --> pdb=" O ASP w 34 " (cutoff:3.500A) Processing helix chain 'w' and resid 40 through 61 removed outlier: 4.047A pdb=" N ALA w 52 " --> pdb=" O VAL w 48 " (cutoff:3.500A) Proline residue: w 55 - end of helix removed outlier: 3.696A pdb=" N GLY w 61 " --> pdb=" O LEU w 57 " (cutoff:3.500A) Processing helix chain 'w' and resid 66 through 83 Processing helix chain 'w' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG w 92 " --> pdb=" O GLU w 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE w 95 " --> pdb=" O LYS w 91 " (cutoff:3.500A) Processing helix chain 'w' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU w 113 " --> pdb=" O ALA w 109 " (cutoff:3.500A) Processing helix chain 'x' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA x 13 " --> pdb=" O THR x 9 " (cutoff:3.500A) Processing helix chain 'x' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN x 30 " --> pdb=" O THR x 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS x 33 " --> pdb=" O LYS x 29 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL x 37 " --> pdb=" O LYS x 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN x 38 " --> pdb=" O ASP x 34 " (cutoff:3.500A) Processing helix chain 'x' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA x 52 " --> pdb=" O VAL x 48 " (cutoff:3.500A) Proline residue: x 55 - end of helix removed outlier: 3.696A pdb=" N GLY x 61 " --> pdb=" O LEU x 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 66 through 83 Processing helix chain 'x' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG x 92 " --> pdb=" O GLU x 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE x 95 " --> pdb=" O LYS x 91 " (cutoff:3.500A) Processing helix chain 'x' and resid 107 through 118 removed outlier: 4.489A pdb=" N GLU x 113 " --> pdb=" O ALA x 109 " (cutoff:3.500A) Processing helix chain 'y' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA y 13 " --> pdb=" O THR y 9 " (cutoff:3.500A) Processing helix chain 'y' and resid 20 through 39 removed outlier: 4.047A pdb=" N ASN y 30 " --> pdb=" O THR y 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS y 33 " --> pdb=" O LYS y 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL y 37 " --> pdb=" O LYS y 33 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN y 38 " --> pdb=" O ASP y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA y 52 " --> pdb=" O VAL y 48 " (cutoff:3.500A) Proline residue: y 55 - end of helix removed outlier: 3.696A pdb=" N GLY y 61 " --> pdb=" O LEU y 57 " (cutoff:3.500A) Processing helix chain 'y' and resid 66 through 83 Processing helix chain 'y' and resid 86 through 104 removed outlier: 5.010A pdb=" N ARG y 92 " --> pdb=" O GLU y 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE y 95 " --> pdb=" O LYS y 91 " (cutoff:3.500A) Processing helix chain 'y' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU y 113 " --> pdb=" O ALA y 109 " (cutoff:3.500A) Processing helix chain 'z' and resid 9 through 20 removed outlier: 3.842A pdb=" N ALA z 13 " --> pdb=" O THR z 9 " (cutoff:3.500A) Processing helix chain 'z' and resid 20 through 39 removed outlier: 4.046A pdb=" N ASN z 30 " --> pdb=" O THR z 26 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS z 33 " --> pdb=" O LYS z 29 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL z 37 " --> pdb=" O LYS z 33 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN z 38 " --> pdb=" O ASP z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 61 removed outlier: 4.046A pdb=" N ALA z 52 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Proline residue: z 55 - end of helix removed outlier: 3.695A pdb=" N GLY z 61 " --> pdb=" O LEU z 57 " (cutoff:3.500A) Processing helix chain 'z' and resid 66 through 83 Processing helix chain 'z' and resid 86 through 104 removed outlier: 5.009A pdb=" N ARG z 92 " --> pdb=" O GLU z 88 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE z 95 " --> pdb=" O LYS z 91 " (cutoff:3.500A) Processing helix chain 'z' and resid 107 through 118 removed outlier: 4.490A pdb=" N GLU z 113 " --> pdb=" O ALA z 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 151 Processing sheet with id=AA2, first strand: chain 'B' and resid 148 through 151 Processing sheet with id=AA3, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AA4, first strand: chain 'D' and resid 148 through 151 Processing sheet with id=AA5, first strand: chain 'E' and resid 148 through 151 Processing sheet with id=AA6, first strand: chain 'F' and resid 148 through 151 Processing sheet with id=AA7, first strand: chain 'G' and resid 148 through 151 Processing sheet with id=AA8, first strand: chain 'H' and resid 148 through 151 Processing sheet with id=AA9, first strand: chain 'I' and resid 148 through 151 Processing sheet with id=AB1, first strand: chain 'J' and resid 148 through 151 Processing sheet with id=AB2, first strand: chain 'J' and resid 178 through 179 removed outlier: 6.409A pdb=" N ALA J 178 " --> pdb=" O ILE y 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 148 through 151 Processing sheet with id=AB4, first strand: chain 'L' and resid 148 through 151 Processing sheet with id=AB5, first strand: chain 'L' and resid 178 through 179 removed outlier: 6.220A pdb=" N ALA L 178 " --> pdb=" O ILE w 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'M' and resid 148 through 151 Processing sheet with id=AB7, first strand: chain 'N' and resid 148 through 151 Processing sheet with id=AB8, first strand: chain 'N' and resid 178 through 179 removed outlier: 6.220A pdb=" N ALA N 178 " --> pdb=" O ILE u 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'O' and resid 148 through 151 Processing sheet with id=AC1, first strand: chain 'P' and resid 148 through 151 Processing sheet with id=AC2, first strand: chain 'P' and resid 178 through 179 removed outlier: 6.317A pdb=" N ALA P 178 " --> pdb=" O ILE s 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'Q' and resid 148 through 151 Processing sheet with id=AC4, first strand: chain 'R' and resid 148 through 151 Processing sheet with id=AC5, first strand: chain 'R' and resid 178 through 179 removed outlier: 6.250A pdb=" N ALA R 178 " --> pdb=" O ILE q 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'S' and resid 148 through 151 Processing sheet with id=AC7, first strand: chain 'T' and resid 148 through 151 Processing sheet with id=AC8, first strand: chain 'T' and resid 178 through 179 removed outlier: 6.290A pdb=" N ALA T 178 " --> pdb=" O ILE o 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'U' and resid 148 through 151 Processing sheet with id=AD1, first strand: chain 'V' and resid 148 through 151 Processing sheet with id=AD2, first strand: chain 'V' and resid 178 through 179 removed outlier: 6.399A pdb=" N ALA V 178 " --> pdb=" O ILE m 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'W' and resid 148 through 151 Processing sheet with id=AD4, first strand: chain 'X' and resid 148 through 151 Processing sheet with id=AD5, first strand: chain 'X' and resid 178 through 179 removed outlier: 6.246A pdb=" N ALA X 178 " --> pdb=" O ILE k 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'Y' and resid 148 through 151 Processing sheet with id=AD7, first strand: chain 'Z' and resid 148 through 151 Processing sheet with id=AD8, first strand: chain 'Z' and resid 178 through 179 removed outlier: 6.250A pdb=" N ALA Z 178 " --> pdb=" O ILE i 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 4125 hydrogen bonds defined for protein. 12297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 348 stacking parallelities Total time for adding SS restraints: 27.61 Time building geometry restraints manager: 28.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 12226 1.31 - 1.44: 24552 1.44 - 1.56: 44180 1.56 - 1.68: 1342 1.68 - 1.81: 572 Bond restraints: 82872 Sorted by residual: bond pdb=" CG1 ILE d 68 " pdb=" CD1 ILE d 68 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CG1 ILE o 68 " pdb=" CD1 ILE o 68 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CG1 ILE n 68 " pdb=" CD1 ILE n 68 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CG1 ILE m 68 " pdb=" CD1 ILE m 68 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 bond pdb=" CG1 ILE u 68 " pdb=" CD1 ILE u 68 " ideal model delta sigma weight residual 1.513 1.372 0.141 3.90e-02 6.57e+02 1.31e+01 ... (remaining 82867 not shown) Histogram of bond angle deviations from ideal: 99.34 - 106.27: 5859 106.27 - 113.20: 44360 113.20 - 120.14: 32721 120.14 - 127.07: 30176 127.07 - 134.01: 2148 Bond angle restraints: 115264 Sorted by residual: angle pdb=" N ALA Y 33 " pdb=" CA ALA Y 33 " pdb=" C ALA Y 33 " ideal model delta sigma weight residual 111.33 116.61 -5.28 1.21e+00 6.83e-01 1.90e+01 angle pdb=" N ALA A 33 " pdb=" CA ALA A 33 " pdb=" C ALA A 33 " ideal model delta sigma weight residual 111.33 116.60 -5.27 1.21e+00 6.83e-01 1.90e+01 angle pdb=" N ALA B 33 " pdb=" CA ALA B 33 " pdb=" C ALA B 33 " ideal model delta sigma weight residual 111.33 116.60 -5.27 1.21e+00 6.83e-01 1.90e+01 angle pdb=" N ALA C 33 " pdb=" CA ALA C 33 " pdb=" C ALA C 33 " ideal model delta sigma weight residual 111.33 116.59 -5.26 1.21e+00 6.83e-01 1.89e+01 angle pdb=" N ALA Z 33 " pdb=" CA ALA Z 33 " pdb=" C ALA Z 33 " ideal model delta sigma weight residual 111.33 116.57 -5.24 1.21e+00 6.83e-01 1.88e+01 ... (remaining 115259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.48: 42092 14.48 - 28.97: 4134 28.97 - 43.45: 1699 43.45 - 57.93: 1007 57.93 - 72.42: 128 Dihedral angle restraints: 49060 sinusoidal: 24230 harmonic: 24830 Sorted by residual: dihedral pdb=" CA ASN p 82 " pdb=" C ASN p 82 " pdb=" N THR p 83 " pdb=" CA THR p 83 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN o 82 " pdb=" C ASN o 82 " pdb=" N THR o 83 " pdb=" CA THR o 83 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ASN q 82 " pdb=" C ASN q 82 " pdb=" N THR q 83 " pdb=" CA THR q 83 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 49057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 8608 0.051 - 0.103: 3259 0.103 - 0.154: 1141 0.154 - 0.206: 77 0.206 - 0.257: 29 Chirality restraints: 13114 Sorted by residual: chirality pdb=" CB ILE Z 88 " pdb=" CA ILE Z 88 " pdb=" CG1 ILE Z 88 " pdb=" CG2 ILE Z 88 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE X 88 " pdb=" CA ILE X 88 " pdb=" CG1 ILE X 88 " pdb=" CG2 ILE X 88 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE V 88 " pdb=" CA ILE V 88 " pdb=" CG1 ILE V 88 " pdb=" CG2 ILE V 88 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 13111 not shown) Planarity restraints: 12372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP w 56 " -0.016 2.00e-02 2.50e+03 1.30e-02 4.23e+00 pdb=" CG TRP w 56 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP w 56 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP w 56 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP w 56 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP w 56 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP w 56 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP w 56 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP w 56 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP w 56 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP t 56 " 0.017 2.00e-02 2.50e+03 1.30e-02 4.20e+00 pdb=" CG TRP t 56 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP t 56 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP t 56 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP t 56 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP t 56 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP t 56 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP t 56 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP t 56 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP t 56 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP m 56 " 0.016 2.00e-02 2.50e+03 1.29e-02 4.19e+00 pdb=" CG TRP m 56 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP m 56 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP m 56 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP m 56 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP m 56 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP m 56 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 56 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 56 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP m 56 " 0.003 2.00e-02 2.50e+03 ... (remaining 12369 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 3226 2.69 - 3.24: 74177 3.24 - 3.79: 131803 3.79 - 4.35: 172530 4.35 - 4.90: 276706 Nonbonded interactions: 658442 Sorted by model distance: nonbonded pdb=" OH TYR A 29 " pdb=" O2 DT 1 175 " model vdw 2.134 2.440 nonbonded pdb=" OH TYR Z 29 " pdb=" O2 DT 1 19 " model vdw 2.168 2.440 nonbonded pdb=" OH TYR C 29 " pdb=" O2 DT 1 187 " model vdw 2.173 2.440 nonbonded pdb=" OH TYR J 29 " pdb=" O2 DT 1 115 " model vdw 2.183 2.440 nonbonded pdb=" OH TYR I 29 " pdb=" O2 DT 1 223 " model vdw 2.185 2.440 ... (remaining 658437 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 '1' selection = chain '2' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'u' selection = chain 'v' selection = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 14.240 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 166.550 Find NCS groups from input model: 4.010 Set up NCS constraints: 1.000 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 192.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.010 0.141 82872 Z= 0.598 Angle : 1.047 11.289 115264 Z= 0.601 Chirality : 0.060 0.257 13114 Planarity : 0.008 0.045 12372 Dihedral : 15.576 72.417 32966 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.36 % Favored : 91.33 % Rotamer: Outliers : 0.37 % Allowed : 3.31 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.38 (0.07), residues: 8346 helix: -2.54 (0.05), residues: 5512 sheet: -1.46 (0.28), residues: 312 loop : -3.53 (0.10), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP k 56 HIS 0.011 0.004 HIS G 48 PHE 0.032 0.004 PHE X 176 TYR 0.023 0.003 TYR v 70 ARG 0.011 0.002 ARG k 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2106 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 2080 time to evaluate : 5.854 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 25 MET cc_start: 0.9292 (mtp) cc_final: 0.9048 (mtm) REVERT: A 39 ASN cc_start: 0.9067 (m-40) cc_final: 0.8851 (m-40) REVERT: A 163 SER cc_start: 0.9176 (p) cc_final: 0.8946 (m) REVERT: A 168 VAL cc_start: 0.9160 (t) cc_final: 0.8931 (p) REVERT: B 168 VAL cc_start: 0.9121 (t) cc_final: 0.8766 (p) REVERT: C 75 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8368 (pp) REVERT: D 75 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8453 (pp) REVERT: E 146 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7445 (mt-10) REVERT: E 168 VAL cc_start: 0.9067 (t) cc_final: 0.8822 (p) REVERT: F 75 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8844 (pp) REVERT: F 163 SER cc_start: 0.9045 (p) cc_final: 0.8842 (m) REVERT: H 75 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8527 (pp) REVERT: H 151 GLU cc_start: 0.7395 (pt0) cc_final: 0.6966 (pt0) REVERT: H 163 SER cc_start: 0.9237 (p) cc_final: 0.9037 (m) REVERT: I 25 MET cc_start: 0.9238 (mtp) cc_final: 0.8730 (mtm) REVERT: I 75 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8423 (pp) REVERT: I 168 VAL cc_start: 0.9120 (t) cc_final: 0.8831 (p) REVERT: J 115 MET cc_start: 0.8259 (mmm) cc_final: 0.7930 (mmm) REVERT: J 151 GLU cc_start: 0.7489 (pt0) cc_final: 0.7247 (pm20) REVERT: K 75 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8456 (pp) REVERT: K 137 SER cc_start: 0.9288 (t) cc_final: 0.8953 (m) REVERT: M 57 TYR cc_start: 0.8093 (m-10) cc_final: 0.7883 (m-10) REVERT: M 75 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8232 (pp) REVERT: N 163 SER cc_start: 0.8936 (p) cc_final: 0.8699 (m) REVERT: P 66 ILE cc_start: 0.9112 (mm) cc_final: 0.8846 (mt) REVERT: P 75 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8592 (pp) REVERT: R 25 MET cc_start: 0.9213 (mtp) cc_final: 0.8921 (mtp) REVERT: R 66 ILE cc_start: 0.9115 (mm) cc_final: 0.8790 (mt) REVERT: T 14 MET cc_start: 0.8375 (mtt) cc_final: 0.8102 (mtm) REVERT: T 75 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8664 (pp) REVERT: T 94 LYS cc_start: 0.9115 (ttpt) cc_final: 0.8784 (tttt) REVERT: U 14 MET cc_start: 0.8305 (mtt) cc_final: 0.8094 (mtp) REVERT: U 151 GLU cc_start: 0.7542 (pt0) cc_final: 0.7335 (pm20) REVERT: V 159 VAL cc_start: 0.9109 (t) cc_final: 0.8802 (p) REVERT: V 185 GLN cc_start: 0.5764 (mm-40) cc_final: 0.4779 (mm-40) REVERT: W 151 GLU cc_start: 0.7718 (pt0) cc_final: 0.7405 (pm20) REVERT: X 66 ILE cc_start: 0.9025 (mm) cc_final: 0.8802 (mt) REVERT: X 114 THR cc_start: 0.9086 (m) cc_final: 0.8832 (t) REVERT: X 151 GLU cc_start: 0.7408 (pt0) cc_final: 0.7199 (pt0) REVERT: Y 14 MET cc_start: 0.8241 (mtt) cc_final: 0.7974 (mtp) REVERT: Y 136 ASN cc_start: 0.9010 (m-40) cc_final: 0.8807 (m-40) REVERT: Y 151 GLU cc_start: 0.7825 (pt0) cc_final: 0.7607 (pt0) REVERT: Y 168 VAL cc_start: 0.9160 (t) cc_final: 0.8879 (p) REVERT: Y 185 GLN cc_start: 0.6203 (mm-40) cc_final: 0.5221 (mm-40) REVERT: Z 66 ILE cc_start: 0.9094 (mm) cc_final: 0.8788 (mt) REVERT: Z 75 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8381 (pp) REVERT: Z 98 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7659 (mt-10) REVERT: Z 115 MET cc_start: 0.8198 (mmm) cc_final: 0.7917 (mmm) REVERT: b 101 TYR cc_start: 0.9033 (m-80) cc_final: 0.8604 (m-80) REVERT: b 129 ILE cc_start: 0.9210 (mt) cc_final: 0.9000 (mt) REVERT: c 8 ILE cc_start: 0.9155 (tt) cc_final: 0.8913 (mt) REVERT: e 8 ILE cc_start: 0.9072 (tt) cc_final: 0.8838 (mt) REVERT: e 73 LEU cc_start: 0.9339 (tp) cc_final: 0.9034 (tt) REVERT: e 101 TYR cc_start: 0.9180 (m-80) cc_final: 0.8961 (m-80) REVERT: g 8 ILE cc_start: 0.8895 (tt) cc_final: 0.8447 (mt) REVERT: h 101 TYR cc_start: 0.9091 (m-80) cc_final: 0.8889 (m-80) REVERT: h 129 ILE cc_start: 0.9254 (mt) cc_final: 0.8965 (mt) REVERT: i 8 ILE cc_start: 0.9193 (tt) cc_final: 0.8873 (mt) REVERT: i 58 ASN cc_start: 0.8789 (t0) cc_final: 0.8507 (t0) REVERT: i 73 LEU cc_start: 0.9394 (tp) cc_final: 0.9166 (tt) REVERT: i 129 ILE cc_start: 0.9075 (mt) cc_final: 0.8871 (mt) REVERT: j 129 ILE cc_start: 0.8981 (mt) cc_final: 0.8572 (mt) REVERT: k 8 ILE cc_start: 0.9057 (tt) cc_final: 0.8738 (mt) REVERT: k 133 MET cc_start: 0.7979 (tpt) cc_final: 0.7776 (tpt) REVERT: m 8 ILE cc_start: 0.8901 (tt) cc_final: 0.8607 (mt) REVERT: m 36 VAL cc_start: 0.9098 (t) cc_final: 0.8854 (p) REVERT: m 58 ASN cc_start: 0.8404 (t0) cc_final: 0.7927 (t0) REVERT: m 129 ILE cc_start: 0.9051 (mt) cc_final: 0.8812 (mt) REVERT: n 15 THR cc_start: 0.9155 (m) cc_final: 0.8778 (p) REVERT: n 58 ASN cc_start: 0.8914 (t0) cc_final: 0.8522 (t0) REVERT: n 117 TYR cc_start: 0.8715 (t80) cc_final: 0.8169 (t80) REVERT: n 129 ILE cc_start: 0.9129 (mt) cc_final: 0.8803 (mt) REVERT: o 19 VAL cc_start: 0.9543 (p) cc_final: 0.9204 (m) REVERT: o 38 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8744 (mm-40) REVERT: o 58 ASN cc_start: 0.8887 (t0) cc_final: 0.8506 (t0) REVERT: p 43 MET cc_start: 0.8260 (ttp) cc_final: 0.8048 (ttm) REVERT: p 58 ASN cc_start: 0.8888 (t0) cc_final: 0.8514 (t0) REVERT: p 73 LEU cc_start: 0.9421 (tp) cc_final: 0.9200 (tp) REVERT: p 110 MET cc_start: 0.8203 (mmt) cc_final: 0.7823 (mmt) REVERT: q 8 ILE cc_start: 0.8928 (tt) cc_final: 0.8499 (mt) REVERT: q 58 ASN cc_start: 0.8864 (t0) cc_final: 0.8236 (t0) REVERT: r 58 ASN cc_start: 0.8996 (t0) cc_final: 0.8697 (t0) REVERT: r 101 TYR cc_start: 0.9161 (m-80) cc_final: 0.8899 (m-80) REVERT: r 129 ILE cc_start: 0.9043 (mt) cc_final: 0.8820 (mt) REVERT: s 38 GLN cc_start: 0.9226 (mm-40) cc_final: 0.8971 (mm-40) REVERT: t 8 ILE cc_start: 0.9181 (tt) cc_final: 0.8840 (mt) REVERT: t 58 ASN cc_start: 0.8835 (t0) cc_final: 0.8455 (t0) REVERT: u 8 ILE cc_start: 0.9060 (tt) cc_final: 0.8705 (mt) REVERT: v 8 ILE cc_start: 0.9115 (tt) cc_final: 0.8648 (mt) REVERT: v 58 ASN cc_start: 0.9014 (t0) cc_final: 0.8770 (t0) REVERT: v 101 TYR cc_start: 0.9041 (m-80) cc_final: 0.8690 (m-80) REVERT: w 73 LEU cc_start: 0.9388 (tp) cc_final: 0.9151 (tt) REVERT: x 8 ILE cc_start: 0.9145 (tt) cc_final: 0.8938 (mt) REVERT: x 58 ASN cc_start: 0.8969 (t0) cc_final: 0.8728 (t0) REVERT: x 123 SER cc_start: 0.9415 (p) cc_final: 0.9211 (t) REVERT: y 15 THR cc_start: 0.8575 (m) cc_final: 0.8246 (t) REVERT: y 101 TYR cc_start: 0.9301 (m-80) cc_final: 0.8705 (m-80) REVERT: z 15 THR cc_start: 0.9208 (m) cc_final: 0.8942 (t) REVERT: z 101 TYR cc_start: 0.9207 (m-80) cc_final: 0.8994 (m-80) outliers start: 26 outliers final: 2 residues processed: 2106 average time/residue: 0.7071 time to fit residues: 2564.3395 Evaluate side-chains 1467 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1455 time to evaluate : 6.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Z residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 758 optimal weight: 5.9990 chunk 680 optimal weight: 1.9990 chunk 377 optimal weight: 20.0000 chunk 232 optimal weight: 3.9990 chunk 459 optimal weight: 0.9980 chunk 363 optimal weight: 0.9990 chunk 703 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 427 optimal weight: 2.9990 chunk 523 optimal weight: 0.9990 chunk 815 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN B 52 ASN C 52 ASN D 52 ASN E 52 ASN F 52 ASN G 52 ASN H 52 ASN I 52 ASN J 52 ASN K 52 ASN L 52 ASN L 60 ASN M 52 ASN N 52 ASN N 60 ASN O 52 ASN P 60 ASN P 108 ASN Q 52 ASN R 52 ASN S 52 ASN T 52 ASN U 52 ASN V 42 ASN V 52 ASN W 52 ASN X 52 ASN Y 52 ASN Z 52 ASN a 25 GLN a 41 ASN a 44 ASN a 65 ASN b 25 GLN b 41 ASN b 44 ASN b 50 ASN c 25 GLN c 41 ASN c 44 ASN c 50 ASN c 65 ASN c 132 ASN d 25 GLN d 41 ASN d 44 ASN d 50 ASN d 65 ASN d 75 ASN d 132 ASN ** e 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 41 ASN e 44 ASN e 65 ASN f 25 GLN f 41 ASN f 44 ASN f 50 ASN ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 41 ASN g 44 ASN ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 41 ASN h 44 ASN h 65 ASN i 25 GLN i 41 ASN i 44 ASN j 25 GLN j 41 ASN j 44 ASN j 50 ASN k 25 GLN k 41 ASN k 44 ASN ** k 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 41 ASN l 44 ASN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 75 ASN l 132 ASN m 25 GLN m 41 ASN m 44 ASN n 25 GLN n 41 ASN n 44 ASN n 65 ASN n 132 ASN ** o 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 41 ASN o 44 ASN o 65 ASN p 25 GLN p 41 ASN p 44 ASN p 65 ASN p 132 ASN q 25 GLN q 41 ASN q 44 ASN r 25 GLN r 41 ASN r 44 ASN ** r 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 25 GLN s 41 ASN s 44 ASN s 65 ASN t 25 GLN t 41 ASN t 44 ASN ** t 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 41 ASN u 44 ASN ** u 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 25 GLN v 41 ASN v 44 ASN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 GLN w 41 ASN w 44 ASN ** w 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 132 ASN x 25 GLN x 41 ASN x 44 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 25 GLN y 41 ASN y 44 ASN y 50 ASN ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 41 ASN z 44 ASN Total number of N/Q/H flips: 126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 82872 Z= 0.215 Angle : 0.629 9.832 115264 Z= 0.357 Chirality : 0.039 0.215 13114 Planarity : 0.005 0.037 12372 Dihedral : 17.375 75.515 17208 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.88 % Allowed : 10.21 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.08), residues: 8346 helix: -1.12 (0.06), residues: 5486 sheet: -1.05 (0.29), residues: 312 loop : -3.01 (0.11), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP d 102 HIS 0.004 0.001 HIS D 48 PHE 0.015 0.002 PHE T 176 TYR 0.018 0.001 TYR Y 122 ARG 0.007 0.001 ARG S 153 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1841 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1637 time to evaluate : 5.951 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8716 (mt) REVERT: A 114 THR cc_start: 0.9296 (m) cc_final: 0.8985 (t) REVERT: A 151 GLU cc_start: 0.7121 (tp30) cc_final: 0.6762 (mm-30) REVERT: A 154 GLU cc_start: 0.6399 (mp0) cc_final: 0.6051 (mp0) REVERT: A 168 VAL cc_start: 0.9137 (t) cc_final: 0.8739 (p) REVERT: B 154 GLU cc_start: 0.7305 (mp0) cc_final: 0.6800 (mp0) REVERT: C 75 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8067 (pp) REVERT: C 95 TYR cc_start: 0.8817 (m-80) cc_final: 0.8570 (m-80) REVERT: D 75 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8395 (pp) REVERT: D 104 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7172 (mt-10) REVERT: E 95 TYR cc_start: 0.8996 (m-80) cc_final: 0.8795 (m-80) REVERT: E 97 ASN cc_start: 0.8343 (t0) cc_final: 0.8096 (t0) REVERT: E 114 THR cc_start: 0.9301 (m) cc_final: 0.9044 (t) REVERT: F 75 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8529 (pp) REVERT: F 114 THR cc_start: 0.9245 (m) cc_final: 0.8975 (t) REVERT: F 168 VAL cc_start: 0.9251 (t) cc_final: 0.8833 (p) REVERT: G 20 ARG cc_start: 0.9116 (ttp-170) cc_final: 0.8886 (ttp80) REVERT: G 125 ARG cc_start: 0.8681 (ttt180) cc_final: 0.8463 (ttt180) REVERT: G 154 GLU cc_start: 0.6851 (mp0) cc_final: 0.6410 (mp0) REVERT: H 75 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8305 (pp) REVERT: H 88 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.8847 (mt) REVERT: H 114 THR cc_start: 0.9234 (m) cc_final: 0.9027 (t) REVERT: H 151 GLU cc_start: 0.7386 (pt0) cc_final: 0.6821 (pt0) REVERT: I 25 MET cc_start: 0.9048 (mtp) cc_final: 0.8776 (mtm) REVERT: I 75 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8314 (pp) REVERT: I 97 ASN cc_start: 0.8367 (t0) cc_final: 0.8075 (t0) REVERT: I 114 THR cc_start: 0.9297 (m) cc_final: 0.9018 (t) REVERT: I 152 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6713 (tm-30) REVERT: J 95 TYR cc_start: 0.8875 (m-80) cc_final: 0.8591 (m-80) REVERT: J 114 THR cc_start: 0.9152 (m) cc_final: 0.8949 (t) REVERT: J 151 GLU cc_start: 0.7492 (pt0) cc_final: 0.7255 (pm20) REVERT: K 75 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8379 (pp) REVERT: K 114 THR cc_start: 0.9279 (m) cc_final: 0.9056 (t) REVERT: K 154 GLU cc_start: 0.6546 (mp0) cc_final: 0.6301 (mp0) REVERT: K 168 VAL cc_start: 0.9216 (t) cc_final: 0.8886 (p) REVERT: M 64 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7796 (mm-30) REVERT: M 75 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8204 (pp) REVERT: N 77 TYR cc_start: 0.8671 (m-80) cc_final: 0.8403 (m-80) REVERT: N 95 TYR cc_start: 0.8824 (m-80) cc_final: 0.8468 (m-80) REVERT: N 97 ASN cc_start: 0.8055 (t0) cc_final: 0.7791 (t0) REVERT: N 154 GLU cc_start: 0.6409 (mp0) cc_final: 0.5993 (mp0) REVERT: O 95 TYR cc_start: 0.8980 (m-80) cc_final: 0.8702 (m-80) REVERT: P 66 ILE cc_start: 0.8949 (mm) cc_final: 0.8684 (mt) REVERT: P 75 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8512 (pp) REVERT: P 114 THR cc_start: 0.9262 (m) cc_final: 0.9058 (t) REVERT: Q 64 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7548 (mm-30) REVERT: Q 151 GLU cc_start: 0.7481 (pm20) cc_final: 0.7278 (pm20) REVERT: Q 152 GLU cc_start: 0.6689 (tm-30) cc_final: 0.6479 (tm-30) REVERT: R 25 MET cc_start: 0.9169 (mtp) cc_final: 0.8825 (mtp) REVERT: R 95 TYR cc_start: 0.8779 (m-80) cc_final: 0.8392 (m-80) REVERT: R 151 GLU cc_start: 0.7617 (pm20) cc_final: 0.7217 (pm20) REVERT: R 152 GLU cc_start: 0.6672 (tm-30) cc_final: 0.6428 (tm-30) REVERT: S 149 GLU cc_start: 0.7758 (pt0) cc_final: 0.7552 (pt0) REVERT: S 152 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6155 (tm-30) REVERT: T 75 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8554 (pp) REVERT: T 152 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6165 (tm-30) REVERT: T 154 GLU cc_start: 0.6832 (mp0) cc_final: 0.6390 (mp0) REVERT: T 185 GLN cc_start: 0.5815 (mm-40) cc_final: 0.4639 (mm-40) REVERT: U 64 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7747 (mm-30) REVERT: U 95 TYR cc_start: 0.8991 (m-80) cc_final: 0.8753 (m-80) REVERT: U 114 THR cc_start: 0.9391 (m) cc_final: 0.9054 (t) REVERT: U 120 ASN cc_start: 0.7960 (p0) cc_final: 0.7741 (p0) REVERT: U 151 GLU cc_start: 0.7607 (pt0) cc_final: 0.7265 (pm20) REVERT: V 31 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7280 (mt-10) REVERT: V 95 TYR cc_start: 0.8840 (m-80) cc_final: 0.8321 (m-80) REVERT: V 168 VAL cc_start: 0.9024 (t) cc_final: 0.8787 (p) REVERT: V 185 GLN cc_start: 0.6089 (mm-40) cc_final: 0.5200 (mm-40) REVERT: X 66 ILE cc_start: 0.8842 (mm) cc_final: 0.8609 (mt) REVERT: X 95 TYR cc_start: 0.8946 (m-80) cc_final: 0.8298 (m-80) REVERT: Y 49 MET cc_start: 0.6678 (mmp) cc_final: 0.6439 (mmp) REVERT: Y 120 ASN cc_start: 0.7924 (p0) cc_final: 0.7659 (p0) REVERT: Y 121 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8885 (mt) REVERT: Y 151 GLU cc_start: 0.7701 (pt0) cc_final: 0.7409 (pt0) REVERT: Y 168 VAL cc_start: 0.9291 (t) cc_final: 0.8973 (p) REVERT: Z 75 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8375 (pp) REVERT: Z 115 MET cc_start: 0.8159 (mmm) cc_final: 0.7950 (mmm) REVERT: b 35 MET cc_start: 0.8752 (mtp) cc_final: 0.8044 (mpp) REVERT: b 82 ASN cc_start: 0.8583 (p0) cc_final: 0.8382 (p0) REVERT: b 129 ILE cc_start: 0.9130 (mt) cc_final: 0.8874 (mt) REVERT: c 8 ILE cc_start: 0.8981 (tt) cc_final: 0.8753 (mt) REVERT: c 18 SER cc_start: 0.9379 (m) cc_final: 0.9139 (m) REVERT: c 35 MET cc_start: 0.8747 (mtp) cc_final: 0.8145 (mpp) REVERT: e 8 ILE cc_start: 0.8933 (tt) cc_final: 0.8699 (mt) REVERT: f 35 MET cc_start: 0.8737 (mtp) cc_final: 0.8199 (mpp) REVERT: f 82 ASN cc_start: 0.8694 (p0) cc_final: 0.8480 (p0) REVERT: f 110 MET cc_start: 0.8327 (mmt) cc_final: 0.7825 (mmt) REVERT: g 8 ILE cc_start: 0.8978 (tt) cc_final: 0.8578 (mt) REVERT: g 83 THR cc_start: 0.8726 (t) cc_final: 0.8485 (t) REVERT: h 35 MET cc_start: 0.8537 (mtt) cc_final: 0.8284 (mpp) REVERT: h 101 TYR cc_start: 0.8903 (m-80) cc_final: 0.8637 (m-80) REVERT: h 129 ILE cc_start: 0.9143 (mt) cc_final: 0.8809 (mt) REVERT: i 8 ILE cc_start: 0.9156 (tt) cc_final: 0.8887 (mt) REVERT: i 69 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7791 (tt) REVERT: i 115 MET cc_start: 0.8840 (mmm) cc_final: 0.8595 (mmm) REVERT: i 129 ILE cc_start: 0.8975 (mt) cc_final: 0.8723 (mt) REVERT: j 132 ASN cc_start: 0.7311 (t0) cc_final: 0.7096 (t0) REVERT: k 8 ILE cc_start: 0.9064 (tt) cc_final: 0.8709 (mt) REVERT: k 82 ASN cc_start: 0.8645 (p0) cc_final: 0.8388 (p0) REVERT: l 51 GLN cc_start: 0.8287 (tt0) cc_final: 0.8069 (tt0) REVERT: l 101 TYR cc_start: 0.8911 (m-80) cc_final: 0.8698 (m-80) REVERT: m 8 ILE cc_start: 0.8863 (tt) cc_final: 0.8559 (mt) REVERT: m 35 MET cc_start: 0.8837 (mtp) cc_final: 0.8231 (mpp) REVERT: m 77 TYR cc_start: 0.8885 (t80) cc_final: 0.8596 (t80) REVERT: m 129 ILE cc_start: 0.9041 (mt) cc_final: 0.8733 (mt) REVERT: n 35 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8559 (mpp) REVERT: n 101 TYR cc_start: 0.8909 (m-80) cc_final: 0.8641 (m-80) REVERT: n 117 TYR cc_start: 0.8606 (t80) cc_final: 0.8050 (t80) REVERT: n 129 ILE cc_start: 0.9091 (mt) cc_final: 0.8755 (mt) REVERT: o 58 ASN cc_start: 0.8581 (t0) cc_final: 0.7973 (t0) REVERT: o 81 LEU cc_start: 0.8833 (mt) cc_final: 0.8631 (mt) REVERT: o 82 ASN cc_start: 0.8551 (p0) cc_final: 0.8120 (p0) REVERT: p 8 ILE cc_start: 0.9324 (tt) cc_final: 0.8996 (mt) REVERT: p 58 ASN cc_start: 0.8823 (t0) cc_final: 0.8333 (t0) REVERT: p 101 TYR cc_start: 0.8995 (m-80) cc_final: 0.8720 (m-80) REVERT: p 110 MET cc_start: 0.8247 (mmt) cc_final: 0.7917 (mmt) REVERT: q 8 ILE cc_start: 0.8882 (tt) cc_final: 0.8508 (mt) REVERT: r 58 ASN cc_start: 0.8768 (t0) cc_final: 0.8380 (t0) REVERT: r 101 TYR cc_start: 0.9053 (m-80) cc_final: 0.8428 (m-80) REVERT: r 129 ILE cc_start: 0.8898 (mt) cc_final: 0.8681 (mt) REVERT: s 69 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7629 (tt) REVERT: s 101 TYR cc_start: 0.9097 (m-80) cc_final: 0.8801 (m-80) REVERT: t 8 ILE cc_start: 0.9110 (tt) cc_final: 0.8824 (mt) REVERT: u 8 ILE cc_start: 0.9050 (tt) cc_final: 0.8813 (mt) REVERT: u 35 MET cc_start: 0.8848 (mtp) cc_final: 0.8010 (mpp) REVERT: u 82 ASN cc_start: 0.8494 (p0) cc_final: 0.8214 (p0) REVERT: u 101 TYR cc_start: 0.9130 (m-80) cc_final: 0.8876 (m-80) REVERT: v 8 ILE cc_start: 0.8999 (tt) cc_final: 0.8605 (mt) REVERT: v 15 THR cc_start: 0.9286 (m) cc_final: 0.9071 (p) REVERT: w 128 TYR cc_start: 0.9070 (m-80) cc_final: 0.8620 (m-80) REVERT: x 35 MET cc_start: 0.8733 (mtp) cc_final: 0.8527 (mtp) REVERT: x 58 ASN cc_start: 0.8822 (t0) cc_final: 0.8300 (t0) REVERT: y 82 ASN cc_start: 0.8363 (p0) cc_final: 0.7934 (p0) REVERT: z 35 MET cc_start: 0.8635 (OUTLIER) cc_final: 0.8432 (mtp) REVERT: z 43 MET cc_start: 0.8054 (ttm) cc_final: 0.7833 (ttm) REVERT: z 69 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8147 (tt) REVERT: z 115 MET cc_start: 0.8786 (mmt) cc_final: 0.8574 (mmm) outliers start: 204 outliers final: 98 residues processed: 1767 average time/residue: 0.7293 time to fit residues: 2228.7212 Evaluate side-chains 1537 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 1421 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain K residue 66 ILE Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain M residue 66 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 191 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 133 SER Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 114 THR Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain T residue 66 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 96 SER Chi-restraints excluded: chain T residue 163 SER Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain V residue 66 ILE Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 116 THR Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 191 GLU Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 123 SER Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 65 ASN Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain e residue 123 SER Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain h residue 65 ASN Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain l residue 130 ILE Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 35 MET Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 65 ASN Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 65 ASN Chi-restraints excluded: chain p residue 130 ILE Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 65 ASN Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 130 ILE Chi-restraints excluded: chain w residue 130 ILE Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain z residue 35 MET Chi-restraints excluded: chain z residue 51 GLN Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 453 optimal weight: 7.9990 chunk 253 optimal weight: 4.9990 chunk 678 optimal weight: 2.9990 chunk 555 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 816 optimal weight: 3.9990 chunk 882 optimal weight: 7.9990 chunk 727 optimal weight: 4.9990 chunk 810 optimal weight: 6.9990 chunk 278 optimal weight: 9.9990 chunk 655 optimal weight: 0.5980 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 39 ASN F 60 ASN H 60 ASN L 181 GLN N 60 ASN R 60 ASN V 42 ASN X 39 ASN a 65 ASN d 25 GLN ** e 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 GLN ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 50 ASN ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 65 ASN p 25 GLN p 132 ASN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 25 GLN ** t 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 132 ASN v 132 ASN w 50 ASN w 65 ASN w 82 ASN w 132 ASN ** x 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 82872 Z= 0.252 Angle : 0.625 11.193 115264 Z= 0.354 Chirality : 0.040 0.245 13114 Planarity : 0.004 0.049 12372 Dihedral : 17.071 73.508 17206 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.34 % Favored : 92.64 % Rotamer: Outliers : 3.42 % Allowed : 12.75 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.09), residues: 8346 helix: -0.32 (0.06), residues: 5486 sheet: -0.43 (0.29), residues: 312 loop : -2.64 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 142 HIS 0.006 0.002 HIS L 48 PHE 0.014 0.002 PHE L 176 TYR 0.018 0.001 TYR y 46 ARG 0.012 0.001 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1493 time to evaluate : 5.878 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8872 (mt) REVERT: A 136 ASN cc_start: 0.9214 (m-40) cc_final: 0.8918 (m-40) REVERT: A 151 GLU cc_start: 0.7303 (tp30) cc_final: 0.6724 (mp0) REVERT: A 152 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6731 (tm-30) REVERT: A 154 GLU cc_start: 0.6279 (mp0) cc_final: 0.6073 (mp0) REVERT: A 168 VAL cc_start: 0.9167 (t) cc_final: 0.8806 (p) REVERT: B 152 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6402 (tm-30) REVERT: B 154 GLU cc_start: 0.7096 (mp0) cc_final: 0.6724 (mp0) REVERT: C 75 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8182 (pp) REVERT: C 151 GLU cc_start: 0.6767 (tp30) cc_final: 0.6030 (mp0) REVERT: C 152 GLU cc_start: 0.6904 (tm-30) cc_final: 0.6222 (tm-30) REVERT: D 75 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8510 (pp) REVERT: E 152 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6783 (tm-30) REVERT: F 75 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8749 (pp) REVERT: F 154 GLU cc_start: 0.7330 (mp0) cc_final: 0.6692 (mp0) REVERT: G 120 ASN cc_start: 0.8299 (p0) cc_final: 0.8068 (p0) REVERT: H 75 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8436 (pp) REVERT: H 88 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8933 (mt) REVERT: I 25 MET cc_start: 0.9003 (mtp) cc_final: 0.8624 (mtm) REVERT: I 75 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8522 (pp) REVERT: I 88 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8415 (mt) REVERT: I 115 MET cc_start: 0.8529 (mmm) cc_final: 0.8272 (tpt) REVERT: I 152 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6891 (tm-30) REVERT: I 168 VAL cc_start: 0.9320 (t) cc_final: 0.9011 (p) REVERT: J 95 TYR cc_start: 0.8991 (m-80) cc_final: 0.8668 (m-80) REVERT: J 115 MET cc_start: 0.8210 (tpt) cc_final: 0.7888 (tpt) REVERT: J 151 GLU cc_start: 0.7603 (pt0) cc_final: 0.7356 (pm20) REVERT: J 152 GLU cc_start: 0.7099 (tm-30) cc_final: 0.6521 (tm-30) REVERT: K 75 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8486 (pp) REVERT: K 98 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8073 (mt-10) REVERT: K 152 GLU cc_start: 0.6779 (tm-30) cc_final: 0.6443 (tm-30) REVERT: K 154 GLU cc_start: 0.6977 (mp0) cc_final: 0.6694 (mp0) REVERT: K 168 VAL cc_start: 0.9240 (t) cc_final: 0.8915 (p) REVERT: M 64 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7854 (mm-30) REVERT: M 75 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8505 (pp) REVERT: M 115 MET cc_start: 0.8344 (mmm) cc_final: 0.8121 (tpt) REVERT: M 152 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6646 (tm-30) REVERT: N 95 TYR cc_start: 0.8923 (m-80) cc_final: 0.8546 (m-80) REVERT: N 97 ASN cc_start: 0.8047 (t0) cc_final: 0.7755 (t0) REVERT: O 168 VAL cc_start: 0.9261 (t) cc_final: 0.8975 (p) REVERT: P 66 ILE cc_start: 0.9019 (mm) cc_final: 0.8786 (mt) REVERT: P 75 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8535 (pp) REVERT: P 88 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8985 (mt) REVERT: P 151 GLU cc_start: 0.7426 (pm20) cc_final: 0.7169 (pm20) REVERT: Q 64 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7672 (mm-30) REVERT: Q 151 GLU cc_start: 0.7519 (pm20) cc_final: 0.7222 (pm20) REVERT: Q 152 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6562 (tm-30) REVERT: Q 154 GLU cc_start: 0.5844 (mp0) cc_final: 0.5602 (mp0) REVERT: R 97 ASN cc_start: 0.8149 (t0) cc_final: 0.7882 (t0) REVERT: R 168 VAL cc_start: 0.9219 (t) cc_final: 0.8818 (p) REVERT: S 88 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8481 (mt) REVERT: S 152 GLU cc_start: 0.6855 (tm-30) cc_final: 0.5959 (tm-30) REVERT: T 75 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8735 (pp) REVERT: T 86 MET cc_start: 0.7935 (ttm) cc_final: 0.7732 (mtt) REVERT: T 151 GLU cc_start: 0.7697 (pm20) cc_final: 0.7431 (pm20) REVERT: T 152 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: T 154 GLU cc_start: 0.6951 (mp0) cc_final: 0.6264 (mp0) REVERT: T 168 VAL cc_start: 0.9203 (t) cc_final: 0.8846 (p) REVERT: T 185 GLN cc_start: 0.5856 (mm-40) cc_final: 0.4607 (mm-40) REVERT: U 86 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7392 (ttp) REVERT: U 95 TYR cc_start: 0.9091 (m-80) cc_final: 0.8809 (m-80) REVERT: U 120 ASN cc_start: 0.8051 (p0) cc_final: 0.7621 (p0) REVERT: U 151 GLU cc_start: 0.7674 (pt0) cc_final: 0.7406 (pm20) REVERT: U 168 VAL cc_start: 0.9212 (t) cc_final: 0.8941 (p) REVERT: V 31 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7298 (mt-10) REVERT: V 88 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8600 (mt) REVERT: V 97 ASN cc_start: 0.8326 (t0) cc_final: 0.8121 (t0) REVERT: V 129 GLU cc_start: 0.7253 (mp0) cc_final: 0.7038 (mp0) REVERT: V 168 VAL cc_start: 0.9022 (t) cc_final: 0.8794 (p) REVERT: V 185 GLN cc_start: 0.6218 (mm-40) cc_final: 0.5055 (mm-40) REVERT: W 75 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8481 (pp) REVERT: W 152 GLU cc_start: 0.6920 (tm-30) cc_final: 0.6604 (tm-30) REVERT: X 88 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8691 (mt) REVERT: Y 114 THR cc_start: 0.9275 (m) cc_final: 0.9011 (t) REVERT: Y 115 MET cc_start: 0.8341 (mmm) cc_final: 0.8056 (tpt) REVERT: Y 151 GLU cc_start: 0.7736 (pt0) cc_final: 0.7476 (pt0) REVERT: Y 168 VAL cc_start: 0.9278 (t) cc_final: 0.8954 (p) REVERT: Z 66 ILE cc_start: 0.9027 (mm) cc_final: 0.8819 (mt) REVERT: Z 75 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8655 (pp) REVERT: Z 88 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8753 (mt) REVERT: Z 97 ASN cc_start: 0.7948 (t0) cc_final: 0.7676 (t0) REVERT: b 82 ASN cc_start: 0.8471 (p0) cc_final: 0.7899 (p0) REVERT: b 129 ILE cc_start: 0.9128 (mt) cc_final: 0.8871 (mt) REVERT: c 8 ILE cc_start: 0.9030 (tt) cc_final: 0.8696 (mt) REVERT: c 35 MET cc_start: 0.8404 (mtp) cc_final: 0.7839 (mpp) REVERT: d 110 MET cc_start: 0.8349 (mmt) cc_final: 0.8137 (mmt) REVERT: e 8 ILE cc_start: 0.9057 (tt) cc_final: 0.8790 (mt) REVERT: g 8 ILE cc_start: 0.9066 (tt) cc_final: 0.8699 (mt) REVERT: h 8 ILE cc_start: 0.9158 (tt) cc_final: 0.8955 (mt) REVERT: h 51 GLN cc_start: 0.8458 (tt0) cc_final: 0.8250 (tt0) REVERT: h 115 MET cc_start: 0.8823 (mmm) cc_final: 0.8314 (mmm) REVERT: h 129 ILE cc_start: 0.9184 (mt) cc_final: 0.8893 (mt) REVERT: i 8 ILE cc_start: 0.9273 (tt) cc_final: 0.8988 (mt) REVERT: i 115 MET cc_start: 0.9058 (mmm) cc_final: 0.8552 (mmm) REVERT: i 129 ILE cc_start: 0.9089 (mt) cc_final: 0.8847 (mt) REVERT: k 8 ILE cc_start: 0.9144 (tt) cc_final: 0.8899 (mt) REVERT: k 82 ASN cc_start: 0.8628 (p0) cc_final: 0.8329 (p0) REVERT: l 8 ILE cc_start: 0.9132 (tt) cc_final: 0.8905 (mt) REVERT: l 58 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8522 (t0) REVERT: m 35 MET cc_start: 0.8735 (mtp) cc_final: 0.8093 (mpp) REVERT: n 35 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8515 (mpp) REVERT: p 8 ILE cc_start: 0.9360 (tt) cc_final: 0.9073 (mt) REVERT: p 58 ASN cc_start: 0.8879 (t0) cc_final: 0.8514 (t0) REVERT: p 101 TYR cc_start: 0.9068 (m-80) cc_final: 0.8718 (m-80) REVERT: p 110 MET cc_start: 0.8287 (mmt) cc_final: 0.7898 (mmt) REVERT: q 8 ILE cc_start: 0.9069 (tt) cc_final: 0.8681 (mt) REVERT: q 35 MET cc_start: 0.8829 (mtp) cc_final: 0.8618 (mtp) REVERT: q 133 MET cc_start: 0.7723 (tpp) cc_final: 0.7470 (tpt) REVERT: r 82 ASN cc_start: 0.8220 (p0) cc_final: 0.7936 (p0) REVERT: r 101 TYR cc_start: 0.9055 (m-80) cc_final: 0.8483 (m-80) REVERT: r 129 ILE cc_start: 0.8961 (mt) cc_final: 0.8709 (mt) REVERT: s 58 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8353 (t0) REVERT: s 69 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7720 (tt) REVERT: s 101 TYR cc_start: 0.9167 (m-80) cc_final: 0.8929 (m-80) REVERT: t 8 ILE cc_start: 0.9176 (tt) cc_final: 0.8812 (mt) REVERT: u 8 ILE cc_start: 0.9104 (tt) cc_final: 0.8845 (mt) REVERT: u 101 TYR cc_start: 0.9184 (m-80) cc_final: 0.8937 (m-80) REVERT: v 8 ILE cc_start: 0.9126 (tt) cc_final: 0.8744 (mt) REVERT: v 35 MET cc_start: 0.8429 (mtt) cc_final: 0.8193 (mtm) REVERT: x 35 MET cc_start: 0.8750 (mtp) cc_final: 0.8528 (mtp) REVERT: x 58 ASN cc_start: 0.8970 (t0) cc_final: 0.8530 (t0) REVERT: x 110 MET cc_start: 0.8534 (mmt) cc_final: 0.8283 (mmt) REVERT: z 69 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8162 (tt) REVERT: z 101 TYR cc_start: 0.8944 (m-80) cc_final: 0.8674 (m-80) outliers start: 242 outliers final: 134 residues processed: 1630 average time/residue: 0.7242 time to fit residues: 2062.6561 Evaluate side-chains 1532 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1372 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 96 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 181 GLN Chi-restraints excluded: chain L residue 187 LYS Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 121 LEU Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain P residue 37 ILE Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 96 SER Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 191 GLU Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 86 MET Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 75 LEU Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 116 THR Chi-restraints excluded: chain W residue 191 GLU Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain Z residue 12 LEU Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 191 GLU Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 80 VAL Chi-restraints excluded: chain a residue 123 SER Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 125 THR Chi-restraints excluded: chain d residue 123 SER Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain e residue 123 SER Chi-restraints excluded: chain f residue 80 VAL Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 123 SER Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain m residue 123 SER Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 35 MET Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 80 VAL Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 62 VAL Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 62 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 36 VAL Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain q residue 125 THR Chi-restraints excluded: chain r residue 80 VAL Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 36 VAL Chi-restraints excluded: chain v residue 43 MET Chi-restraints excluded: chain w residue 48 VAL Chi-restraints excluded: chain w residue 82 ASN Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain w residue 130 ILE Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 807 optimal weight: 0.9980 chunk 614 optimal weight: 0.9980 chunk 423 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 389 optimal weight: 7.9990 chunk 548 optimal weight: 1.9990 chunk 819 optimal weight: 0.9980 chunk 868 optimal weight: 6.9990 chunk 428 optimal weight: 7.9990 chunk 777 optimal weight: 9.9990 chunk 233 optimal weight: 8.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN D 120 ASN L 60 ASN L 181 GLN N 60 ASN R 60 ASN ** W 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 108 ASN a 50 ASN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 ASN ** d 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 25 GLN e 50 ASN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 25 GLN g 25 GLN ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 25 GLN h 50 ASN i 50 ASN ** i 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 132 ASN m 50 ASN ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 65 ASN o 25 GLN o 50 ASN ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 25 GLN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 50 ASN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 50 ASN s 65 ASN t 25 GLN ** t 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 132 ASN ** u 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 ASN w 65 ASN ** y 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 25 GLN z 50 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 82872 Z= 0.203 Angle : 0.579 11.079 115264 Z= 0.329 Chirality : 0.038 0.149 13114 Planarity : 0.003 0.038 12372 Dihedral : 16.831 73.155 17206 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.29 % Allowed : 15.17 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.09), residues: 8346 helix: 0.20 (0.07), residues: 5590 sheet: -0.23 (0.29), residues: 312 loop : -2.31 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 102 HIS 0.003 0.001 HIS L 48 PHE 0.013 0.002 PHE Y 54 TYR 0.018 0.001 TYR y 128 ARG 0.004 0.000 ARG J 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1698 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1465 time to evaluate : 5.985 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8792 (mt) REVERT: A 115 MET cc_start: 0.8163 (mmm) cc_final: 0.7824 (tpt) REVERT: A 120 ASN cc_start: 0.8000 (p0) cc_final: 0.7542 (p0) REVERT: A 151 GLU cc_start: 0.7175 (tp30) cc_final: 0.6857 (mm-30) REVERT: A 168 VAL cc_start: 0.9155 (t) cc_final: 0.8797 (p) REVERT: C 75 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8277 (pp) REVERT: C 95 TYR cc_start: 0.8740 (m-80) cc_final: 0.8422 (m-80) REVERT: D 75 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8624 (pp) REVERT: D 88 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.8923 (mt) REVERT: D 120 ASN cc_start: 0.8505 (p0) cc_final: 0.7866 (p0) REVERT: E 95 TYR cc_start: 0.8982 (m-80) cc_final: 0.8693 (m-80) REVERT: E 152 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6299 (tm-30) REVERT: F 75 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8761 (pp) REVERT: F 120 ASN cc_start: 0.8689 (p0) cc_final: 0.8433 (p0) REVERT: F 168 VAL cc_start: 0.9247 (t) cc_final: 0.8825 (p) REVERT: G 120 ASN cc_start: 0.8038 (p0) cc_final: 0.7759 (p0) REVERT: G 152 GLU cc_start: 0.6575 (tm-30) cc_final: 0.6078 (tm-30) REVERT: G 154 GLU cc_start: 0.6343 (mp0) cc_final: 0.6003 (mp0) REVERT: H 75 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8495 (pp) REVERT: H 88 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.8892 (mt) REVERT: H 152 GLU cc_start: 0.7252 (tm-30) cc_final: 0.6573 (tm-30) REVERT: I 75 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8598 (pp) REVERT: I 152 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6694 (tm-30) REVERT: J 95 TYR cc_start: 0.8934 (m-80) cc_final: 0.8533 (m-80) REVERT: J 115 MET cc_start: 0.8253 (tpt) cc_final: 0.7893 (tpt) REVERT: J 151 GLU cc_start: 0.7638 (pt0) cc_final: 0.7355 (pm20) REVERT: J 152 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6622 (tm-30) REVERT: J 154 GLU cc_start: 0.6148 (mp0) cc_final: 0.5831 (mp0) REVERT: K 31 GLU cc_start: 0.7704 (tt0) cc_final: 0.7489 (mt-10) REVERT: K 75 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8588 (pp) REVERT: K 88 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8524 (mt) REVERT: K 98 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7983 (mt-10) REVERT: K 152 GLU cc_start: 0.6697 (tm-30) cc_final: 0.6192 (tm-30) REVERT: K 154 GLU cc_start: 0.6771 (mp0) cc_final: 0.6481 (mp0) REVERT: K 168 VAL cc_start: 0.9278 (t) cc_final: 0.8985 (p) REVERT: L 88 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.8874 (mt) REVERT: L 152 GLU cc_start: 0.6736 (tm-30) cc_final: 0.6264 (tm-30) REVERT: M 64 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7966 (mm-30) REVERT: M 75 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8621 (pp) REVERT: M 152 GLU cc_start: 0.6596 (tm-30) cc_final: 0.6195 (tm-30) REVERT: N 95 TYR cc_start: 0.8902 (m-80) cc_final: 0.8502 (m-80) REVERT: N 97 ASN cc_start: 0.7966 (t0) cc_final: 0.7705 (t0) REVERT: O 95 TYR cc_start: 0.8900 (m-80) cc_final: 0.8524 (m-80) REVERT: O 168 VAL cc_start: 0.9283 (t) cc_final: 0.9020 (p) REVERT: P 52 ASN cc_start: 0.7786 (m-40) cc_final: 0.7585 (m110) REVERT: P 57 TYR cc_start: 0.9049 (m-10) cc_final: 0.8725 (m-80) REVERT: P 66 ILE cc_start: 0.8999 (mm) cc_final: 0.8757 (mt) REVERT: P 75 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8557 (pp) REVERT: Q 151 GLU cc_start: 0.7498 (pm20) cc_final: 0.7184 (pm20) REVERT: Q 152 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6317 (tm-30) REVERT: Q 154 GLU cc_start: 0.5905 (mp0) cc_final: 0.5695 (mp0) REVERT: R 97 ASN cc_start: 0.8086 (t0) cc_final: 0.7702 (t0) REVERT: R 120 ASN cc_start: 0.8612 (p0) cc_final: 0.8160 (p0) REVERT: R 185 GLN cc_start: 0.6160 (mm-40) cc_final: 0.5869 (mm-40) REVERT: S 88 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8439 (mt) REVERT: S 152 GLU cc_start: 0.6799 (tm-30) cc_final: 0.6171 (tm-30) REVERT: T 75 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8696 (pp) REVERT: T 86 MET cc_start: 0.7859 (ttm) cc_final: 0.7657 (mtt) REVERT: T 152 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: T 168 VAL cc_start: 0.9165 (t) cc_final: 0.8810 (p) REVERT: T 185 GLN cc_start: 0.5907 (mm-40) cc_final: 0.4615 (mm-40) REVERT: U 95 TYR cc_start: 0.9025 (m-80) cc_final: 0.8674 (m-80) REVERT: U 120 ASN cc_start: 0.7889 (p0) cc_final: 0.7453 (p0) REVERT: U 151 GLU cc_start: 0.7668 (pt0) cc_final: 0.7454 (pm20) REVERT: U 168 VAL cc_start: 0.9227 (t) cc_final: 0.8974 (p) REVERT: V 88 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8633 (mt) REVERT: V 97 ASN cc_start: 0.8334 (t0) cc_final: 0.8056 (t0) REVERT: V 185 GLN cc_start: 0.6232 (mm-40) cc_final: 0.5156 (mm-40) REVERT: W 88 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8757 (mt) REVERT: X 88 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8786 (mt) REVERT: Y 115 MET cc_start: 0.8399 (mmm) cc_final: 0.8057 (tpt) REVERT: Y 168 VAL cc_start: 0.9306 (t) cc_final: 0.8991 (p) REVERT: Z 66 ILE cc_start: 0.8987 (mm) cc_final: 0.8777 (mt) REVERT: Z 75 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8792 (pp) REVERT: Z 88 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8725 (mt) REVERT: a 36 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8478 (t) REVERT: a 122 LYS cc_start: 0.6806 (ptmt) cc_final: 0.5658 (mttt) REVERT: b 82 ASN cc_start: 0.8241 (p0) cc_final: 0.7648 (p0) REVERT: c 8 ILE cc_start: 0.8973 (tt) cc_final: 0.8597 (mt) REVERT: c 35 MET cc_start: 0.8363 (mtp) cc_final: 0.7769 (mpp) REVERT: c 82 ASN cc_start: 0.8356 (p0) cc_final: 0.8018 (p0) REVERT: e 8 ILE cc_start: 0.8947 (tt) cc_final: 0.8638 (mt) REVERT: f 110 MET cc_start: 0.8394 (mmt) cc_final: 0.7893 (mmt) REVERT: g 8 ILE cc_start: 0.9108 (tt) cc_final: 0.8717 (mt) REVERT: h 8 ILE cc_start: 0.9135 (tt) cc_final: 0.8912 (mt) REVERT: h 51 GLN cc_start: 0.8441 (tt0) cc_final: 0.8237 (tt0) REVERT: h 62 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8833 (m) REVERT: h 115 MET cc_start: 0.8962 (mmm) cc_final: 0.8611 (mmm) REVERT: i 8 ILE cc_start: 0.9266 (tt) cc_final: 0.8921 (mt) REVERT: i 115 MET cc_start: 0.8927 (mmm) cc_final: 0.8293 (mmm) REVERT: j 62 VAL cc_start: 0.9017 (p) cc_final: 0.8777 (m) REVERT: k 8 ILE cc_start: 0.9115 (tt) cc_final: 0.8808 (mt) REVERT: k 79 LYS cc_start: 0.8728 (tttm) cc_final: 0.8486 (tttm) REVERT: k 82 ASN cc_start: 0.8530 (p0) cc_final: 0.8274 (p0) REVERT: l 58 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8445 (t0) REVERT: m 35 MET cc_start: 0.8758 (mtp) cc_final: 0.8031 (mpp) REVERT: p 8 ILE cc_start: 0.9327 (tt) cc_final: 0.9036 (mt) REVERT: p 58 ASN cc_start: 0.8858 (t0) cc_final: 0.8524 (t0) REVERT: p 101 TYR cc_start: 0.8985 (m-80) cc_final: 0.8746 (m-80) REVERT: p 110 MET cc_start: 0.8196 (mmt) cc_final: 0.7905 (mmt) REVERT: p 129 ILE cc_start: 0.9081 (mt) cc_final: 0.8764 (mt) REVERT: q 8 ILE cc_start: 0.9090 (tt) cc_final: 0.8691 (mt) REVERT: q 129 ILE cc_start: 0.9121 (mt) cc_final: 0.8903 (mt) REVERT: r 62 VAL cc_start: 0.8943 (p) cc_final: 0.8722 (m) REVERT: r 82 ASN cc_start: 0.8366 (p0) cc_final: 0.8097 (p0) REVERT: r 129 ILE cc_start: 0.8931 (mt) cc_final: 0.8689 (mt) REVERT: s 58 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (t0) REVERT: s 69 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7516 (tt) REVERT: t 8 ILE cc_start: 0.9101 (tt) cc_final: 0.8736 (mt) REVERT: t 33 LYS cc_start: 0.8592 (mtmm) cc_final: 0.7297 (mmtt) REVERT: t 101 TYR cc_start: 0.8900 (m-80) cc_final: 0.8563 (m-80) REVERT: u 8 ILE cc_start: 0.9006 (tt) cc_final: 0.8576 (mt) REVERT: u 35 MET cc_start: 0.8896 (mtp) cc_final: 0.8116 (mpp) REVERT: u 101 TYR cc_start: 0.9131 (m-80) cc_final: 0.8905 (m-80) REVERT: v 8 ILE cc_start: 0.9102 (tt) cc_final: 0.8709 (mt) REVERT: v 35 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8218 (mtm) REVERT: v 110 MET cc_start: 0.8474 (mmt) cc_final: 0.8198 (mmt) REVERT: x 33 LYS cc_start: 0.8758 (mtmm) cc_final: 0.7546 (mmtt) REVERT: x 58 ASN cc_start: 0.8981 (t0) cc_final: 0.8448 (t0) REVERT: x 110 MET cc_start: 0.8585 (mmt) cc_final: 0.8340 (mmt) REVERT: y 35 MET cc_start: 0.8705 (mtp) cc_final: 0.7826 (mpp) REVERT: y 113 GLU cc_start: 0.8073 (tp30) cc_final: 0.7736 (tp30) REVERT: z 69 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8113 (tt) outliers start: 233 outliers final: 134 residues processed: 1606 average time/residue: 0.6986 time to fit residues: 1941.4314 Evaluate side-chains 1537 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1375 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 187 LYS Chi-restraints excluded: chain M residue 14 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 163 SER Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 191 GLU Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 116 THR Chi-restraints excluded: chain W residue 191 GLU Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 185 GLN Chi-restraints excluded: chain Y residue 191 GLU Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 THR Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 80 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 80 VAL Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 51 GLN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 123 SER Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain s residue 65 ASN Chi-restraints excluded: chain s residue 69 LEU Chi-restraints excluded: chain s residue 106 LEU Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain t residue 132 ASN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 81 LEU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 82 ASN Chi-restraints excluded: chain w residue 65 ASN Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 83 THR Chi-restraints excluded: chain w residue 130 ILE Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 122 LYS Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 722 optimal weight: 0.5980 chunk 492 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 646 optimal weight: 2.9990 chunk 358 optimal weight: 0.7980 chunk 740 optimal weight: 8.9990 chunk 600 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 443 optimal weight: 8.9990 chunk 779 optimal weight: 0.5980 chunk 219 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN J 60 ASN L 60 ASN L 181 GLN N 60 ASN R 60 ASN X 42 ASN Y 136 ASN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN j 132 ASN l 50 ASN ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 65 ASN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 50 ASN s 65 ASN t 50 ASN t 65 ASN ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 82 ASN x 50 ASN ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.3915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 82872 Z= 0.191 Angle : 0.573 11.169 115264 Z= 0.324 Chirality : 0.038 0.168 13114 Planarity : 0.003 0.037 12372 Dihedral : 16.736 71.543 17206 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.55 % Allowed : 15.84 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.09), residues: 8346 helix: 0.44 (0.07), residues: 5616 sheet: -0.14 (0.29), residues: 312 loop : -2.11 (0.13), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP x 102 HIS 0.003 0.001 HIS H 48 PHE 0.020 0.001 PHE L 54 TYR 0.017 0.001 TYR t 117 ARG 0.006 0.000 ARG W 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1451 time to evaluate : 5.924 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8817 (mt) REVERT: A 115 MET cc_start: 0.8394 (mmm) cc_final: 0.8027 (tpt) REVERT: A 120 ASN cc_start: 0.7894 (p0) cc_final: 0.7459 (p0) REVERT: A 152 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6602 (tm-30) REVERT: A 168 VAL cc_start: 0.9173 (t) cc_final: 0.8812 (p) REVERT: C 75 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8262 (pp) REVERT: C 95 TYR cc_start: 0.8742 (m-80) cc_final: 0.8363 (m-80) REVERT: C 152 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6479 (tm-30) REVERT: D 75 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8671 (pp) REVERT: D 120 ASN cc_start: 0.8216 (p0) cc_final: 0.7529 (p0) REVERT: E 25 MET cc_start: 0.8846 (mmm) cc_final: 0.8566 (mmm) REVERT: E 95 TYR cc_start: 0.9006 (m-80) cc_final: 0.8640 (m-80) REVERT: E 152 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6277 (tm-30) REVERT: F 75 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8808 (pp) REVERT: F 120 ASN cc_start: 0.8584 (p0) cc_final: 0.8012 (p0) REVERT: F 168 VAL cc_start: 0.9234 (t) cc_final: 0.8838 (p) REVERT: G 51 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7895 (mt-10) REVERT: G 152 GLU cc_start: 0.6585 (tm-30) cc_final: 0.5604 (tm-30) REVERT: H 57 TYR cc_start: 0.8826 (m-10) cc_final: 0.8609 (m-10) REVERT: H 75 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8565 (pp) REVERT: H 88 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.8921 (mt) REVERT: H 152 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6421 (tm-30) REVERT: I 152 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6717 (tm-30) REVERT: I 168 VAL cc_start: 0.9364 (t) cc_final: 0.9087 (p) REVERT: J 95 TYR cc_start: 0.8920 (m-80) cc_final: 0.8442 (m-10) REVERT: J 115 MET cc_start: 0.8316 (tpt) cc_final: 0.7930 (tpt) REVERT: J 151 GLU cc_start: 0.7650 (pt0) cc_final: 0.7397 (pm20) REVERT: J 152 GLU cc_start: 0.6812 (tm-30) cc_final: 0.6505 (tm-30) REVERT: J 154 GLU cc_start: 0.6468 (mp0) cc_final: 0.6184 (mp0) REVERT: K 31 GLU cc_start: 0.7683 (tt0) cc_final: 0.7469 (mt-10) REVERT: K 75 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8672 (pp) REVERT: K 88 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8464 (mt) REVERT: K 152 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6093 (tm-30) REVERT: K 168 VAL cc_start: 0.9267 (t) cc_final: 0.8983 (p) REVERT: L 88 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.8861 (mt) REVERT: L 120 ASN cc_start: 0.7745 (p0) cc_final: 0.6936 (p0) REVERT: L 152 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6193 (tm-30) REVERT: M 75 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8670 (pp) REVERT: M 152 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6074 (tm-30) REVERT: M 168 VAL cc_start: 0.9166 (t) cc_final: 0.8933 (p) REVERT: N 95 TYR cc_start: 0.8878 (m-80) cc_final: 0.8430 (m-80) REVERT: N 97 ASN cc_start: 0.7942 (t0) cc_final: 0.7725 (t0) REVERT: O 95 TYR cc_start: 0.8894 (m-80) cc_final: 0.8537 (m-80) REVERT: O 168 VAL cc_start: 0.9311 (t) cc_final: 0.9071 (p) REVERT: P 57 TYR cc_start: 0.9110 (m-10) cc_final: 0.8748 (m-80) REVERT: P 66 ILE cc_start: 0.8991 (mm) cc_final: 0.8761 (mt) REVERT: P 75 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8586 (pp) REVERT: Q 151 GLU cc_start: 0.7464 (pm20) cc_final: 0.7182 (pm20) REVERT: Q 152 GLU cc_start: 0.6722 (tm-30) cc_final: 0.6203 (tm-30) REVERT: R 97 ASN cc_start: 0.8028 (t0) cc_final: 0.7700 (t0) REVERT: R 120 ASN cc_start: 0.8379 (p0) cc_final: 0.8019 (p0) REVERT: R 185 GLN cc_start: 0.6152 (mm-40) cc_final: 0.5827 (mm-40) REVERT: S 88 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8451 (mt) REVERT: S 152 GLU cc_start: 0.6726 (tm-30) cc_final: 0.6044 (tm-30) REVERT: S 191 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: T 75 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8809 (pp) REVERT: T 152 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: T 154 GLU cc_start: 0.6757 (mp0) cc_final: 0.6270 (mp0) REVERT: T 163 SER cc_start: 0.8932 (OUTLIER) cc_final: 0.8716 (m) REVERT: T 168 VAL cc_start: 0.9182 (t) cc_final: 0.8824 (p) REVERT: U 95 TYR cc_start: 0.9016 (m-80) cc_final: 0.8644 (m-80) REVERT: U 115 MET cc_start: 0.8698 (tpp) cc_final: 0.8035 (tpt) REVERT: U 151 GLU cc_start: 0.7675 (pt0) cc_final: 0.7443 (pm20) REVERT: U 168 VAL cc_start: 0.9229 (t) cc_final: 0.8985 (p) REVERT: V 31 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7099 (mt-10) REVERT: V 88 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8688 (mt) REVERT: V 97 ASN cc_start: 0.8311 (t0) cc_final: 0.8004 (t0) REVERT: V 185 GLN cc_start: 0.6228 (mm-40) cc_final: 0.5210 (mm-40) REVERT: W 88 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8707 (mt) REVERT: X 88 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8770 (mt) REVERT: Y 60 ASN cc_start: 0.8453 (m-40) cc_final: 0.8166 (m-40) REVERT: Y 151 GLU cc_start: 0.7710 (pt0) cc_final: 0.7508 (pt0) REVERT: Y 168 VAL cc_start: 0.9308 (t) cc_final: 0.9032 (p) REVERT: Z 66 ILE cc_start: 0.8996 (mm) cc_final: 0.8780 (mt) REVERT: Z 88 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8762 (mt) REVERT: Z 97 ASN cc_start: 0.7908 (t0) cc_final: 0.7619 (t0) REVERT: a 122 LYS cc_start: 0.6846 (ptmt) cc_final: 0.5836 (mttt) REVERT: b 35 MET cc_start: 0.8396 (mtp) cc_final: 0.7852 (mpp) REVERT: b 82 ASN cc_start: 0.8172 (p0) cc_final: 0.7614 (p0) REVERT: c 35 MET cc_start: 0.8257 (mtp) cc_final: 0.7651 (mpp) REVERT: c 82 ASN cc_start: 0.8342 (p0) cc_final: 0.7992 (p0) REVERT: c 122 LYS cc_start: 0.7139 (OUTLIER) cc_final: 0.5585 (mttt) REVERT: d 122 LYS cc_start: 0.6844 (ptmt) cc_final: 0.5638 (mttt) REVERT: e 8 ILE cc_start: 0.8908 (tt) cc_final: 0.8609 (mt) REVERT: f 62 VAL cc_start: 0.9026 (p) cc_final: 0.8825 (m) REVERT: f 82 ASN cc_start: 0.8465 (p0) cc_final: 0.7959 (p0) REVERT: f 110 MET cc_start: 0.8375 (mmt) cc_final: 0.7932 (mmt) REVERT: g 8 ILE cc_start: 0.9108 (tt) cc_final: 0.8731 (mt) REVERT: h 51 GLN cc_start: 0.8422 (tt0) cc_final: 0.8216 (tt0) REVERT: i 8 ILE cc_start: 0.9238 (tt) cc_final: 0.8887 (mt) REVERT: i 115 MET cc_start: 0.8959 (mmm) cc_final: 0.8382 (mmm) REVERT: k 8 ILE cc_start: 0.9141 (tt) cc_final: 0.8826 (mt) REVERT: k 79 LYS cc_start: 0.8731 (tttm) cc_final: 0.8407 (tttm) REVERT: k 82 ASN cc_start: 0.8564 (p0) cc_final: 0.8245 (p0) REVERT: m 35 MET cc_start: 0.8704 (mtp) cc_final: 0.7981 (mpp) REVERT: n 110 MET cc_start: 0.8352 (mmt) cc_final: 0.8002 (mmt) REVERT: o 58 ASN cc_start: 0.8511 (t0) cc_final: 0.7881 (t0) REVERT: p 8 ILE cc_start: 0.9296 (tt) cc_final: 0.8991 (mt) REVERT: p 58 ASN cc_start: 0.8907 (t0) cc_final: 0.8591 (t0) REVERT: p 101 TYR cc_start: 0.8947 (m-80) cc_final: 0.8730 (m-80) REVERT: p 129 ILE cc_start: 0.9075 (mt) cc_final: 0.8791 (mt) REVERT: q 8 ILE cc_start: 0.9012 (tt) cc_final: 0.8635 (mt) REVERT: q 69 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7850 (tt) REVERT: r 129 ILE cc_start: 0.8967 (mt) cc_final: 0.8763 (mt) REVERT: s 58 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8220 (t0) REVERT: t 8 ILE cc_start: 0.9081 (tt) cc_final: 0.8711 (mt) REVERT: t 33 LYS cc_start: 0.8551 (mtmm) cc_final: 0.7283 (mmtt) REVERT: t 115 MET cc_start: 0.8778 (mmm) cc_final: 0.8517 (mmm) REVERT: u 8 ILE cc_start: 0.9016 (tt) cc_final: 0.8569 (mt) REVERT: v 8 ILE cc_start: 0.9059 (tt) cc_final: 0.8716 (mt) REVERT: v 35 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8252 (mtm) REVERT: v 110 MET cc_start: 0.8563 (mmt) cc_final: 0.8290 (mmt) REVERT: x 33 LYS cc_start: 0.8636 (mtmm) cc_final: 0.7429 (mmtt) REVERT: x 58 ASN cc_start: 0.8994 (t0) cc_final: 0.8449 (t0) REVERT: y 35 MET cc_start: 0.8656 (mtp) cc_final: 0.7787 (mpp) REVERT: y 113 GLU cc_start: 0.8126 (tp30) cc_final: 0.7759 (tp30) REVERT: z 69 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (tt) outliers start: 251 outliers final: 151 residues processed: 1614 average time/residue: 0.6962 time to fit residues: 1950.8756 Evaluate side-chains 1570 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1394 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 191 GLU Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain M residue 14 MET Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 191 GLU Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 163 SER Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 66 ILE Chi-restraints excluded: chain W residue 88 ILE Chi-restraints excluded: chain W residue 116 THR Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 174 THR Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain Y residue 66 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Y residue 191 GLU Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 88 ILE Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain Z residue 174 THR Chi-restraints excluded: chain Z residue 187 LYS Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 122 LYS Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 122 LYS Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 69 LEU Chi-restraints excluded: chain f residue 80 VAL Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 62 VAL Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain m residue 130 ILE Chi-restraints excluded: chain n residue 62 VAL Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 80 VAL Chi-restraints excluded: chain n residue 82 ASN Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 82 ASN Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 19 VAL Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain s residue 65 ASN Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 125 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain w residue 130 ILE Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 292 optimal weight: 20.0000 chunk 781 optimal weight: 10.0000 chunk 171 optimal weight: 30.0000 chunk 509 optimal weight: 0.8980 chunk 214 optimal weight: 10.0000 chunk 868 optimal weight: 7.9990 chunk 721 optimal weight: 8.9990 chunk 402 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 456 optimal weight: 30.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 42 ASN F 60 ASN H 60 ASN J 42 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 48 HIS N 52 ASN N 60 ASN O 108 ASN P 52 ASN R 60 ASN V 42 ASN V 120 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN a 25 GLN a 65 ASN b 25 GLN b 65 ASN c 25 GLN ** c 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 ASN e 25 GLN e 65 ASN f 25 GLN g 25 GLN g 65 ASN h 25 GLN i 25 GLN j 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN k 25 GLN ** k 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 65 ASN m 25 GLN ** m 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 25 GLN o 25 GLN o 65 ASN p 25 GLN p 65 ASN q 25 GLN r 25 GLN s 25 GLN s 65 ASN t 25 GLN v 25 GLN v 65 ASN w 25 GLN w 65 ASN w 132 ASN x 25 GLN x 65 ASN y 25 GLN ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 25 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 82872 Z= 0.438 Angle : 0.737 11.341 115264 Z= 0.410 Chirality : 0.048 0.201 13114 Planarity : 0.004 0.045 12372 Dihedral : 17.229 77.991 17202 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.44 % Favored : 92.52 % Rotamer: Outliers : 4.98 % Allowed : 15.89 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.09), residues: 8346 helix: 0.21 (0.07), residues: 5564 sheet: -0.25 (0.28), residues: 312 loop : -2.20 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 92 HIS 0.009 0.003 HIS G 48 PHE 0.029 0.002 PHE L 89 TYR 0.026 0.002 TYR c 46 ARG 0.006 0.001 ARG s 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1819 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 1467 time to evaluate : 6.106 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.8883 (mt) REVERT: A 104 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7835 (mp0) REVERT: A 136 ASN cc_start: 0.9210 (m-40) cc_final: 0.8873 (m-40) REVERT: A 152 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7141 (tm-30) REVERT: A 168 VAL cc_start: 0.9305 (t) cc_final: 0.8966 (p) REVERT: B 103 ASN cc_start: 0.8809 (p0) cc_final: 0.8573 (p0) REVERT: B 120 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8787 (p0) REVERT: C 75 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8521 (pp) REVERT: C 152 GLU cc_start: 0.7310 (tm-30) cc_final: 0.6898 (tm-30) REVERT: D 75 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8775 (pp) REVERT: D 88 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9093 (mt) REVERT: D 108 ASN cc_start: 0.8995 (m-40) cc_final: 0.8692 (m110) REVERT: D 120 ASN cc_start: 0.8833 (p0) cc_final: 0.8228 (p0) REVERT: E 152 GLU cc_start: 0.7731 (tm-30) cc_final: 0.6792 (tm-30) REVERT: E 154 GLU cc_start: 0.6909 (mp0) cc_final: 0.6657 (mp0) REVERT: E 168 VAL cc_start: 0.9303 (t) cc_final: 0.9065 (p) REVERT: F 75 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8920 (pp) REVERT: F 88 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9001 (mt) REVERT: F 151 GLU cc_start: 0.7181 (pm20) cc_final: 0.6898 (pm20) REVERT: G 152 GLU cc_start: 0.7098 (tm-30) cc_final: 0.6601 (tm-30) REVERT: H 57 TYR cc_start: 0.8982 (m-10) cc_final: 0.8628 (m-10) REVERT: H 75 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8711 (pp) REVERT: H 88 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9068 (mt) REVERT: H 152 GLU cc_start: 0.7595 (tm-30) cc_final: 0.6978 (tm-30) REVERT: H 154 GLU cc_start: 0.7046 (mp0) cc_final: 0.6761 (mp0) REVERT: I 88 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8718 (mt) REVERT: I 115 MET cc_start: 0.8543 (tpt) cc_final: 0.8332 (tpt) REVERT: I 152 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7127 (tm-30) REVERT: I 168 VAL cc_start: 0.9466 (t) cc_final: 0.9190 (p) REVERT: J 151 GLU cc_start: 0.7725 (pt0) cc_final: 0.7346 (pm20) REVERT: J 152 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6569 (tm-30) REVERT: J 154 GLU cc_start: 0.6597 (mp0) cc_final: 0.6225 (mp0) REVERT: K 75 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8825 (pp) REVERT: K 88 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8637 (mt) REVERT: K 152 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6670 (tm-30) REVERT: L 88 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.8999 (mt) REVERT: L 120 ASN cc_start: 0.8319 (p0) cc_final: 0.7560 (p0) REVERT: M 25 MET cc_start: 0.8579 (mtt) cc_final: 0.8327 (mtt) REVERT: M 75 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8698 (pp) REVERT: M 115 MET cc_start: 0.8590 (tpt) cc_final: 0.8275 (tpt) REVERT: M 152 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6595 (tm-30) REVERT: M 168 VAL cc_start: 0.9222 (t) cc_final: 0.8941 (p) REVERT: N 97 ASN cc_start: 0.8387 (t0) cc_final: 0.7713 (t0) REVERT: N 104 GLU cc_start: 0.7541 (mp0) cc_final: 0.7239 (mp0) REVERT: N 108 ASN cc_start: 0.9024 (m-40) cc_final: 0.8243 (m110) REVERT: O 152 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6665 (tm-30) REVERT: O 168 VAL cc_start: 0.9338 (t) cc_final: 0.9093 (p) REVERT: P 57 TYR cc_start: 0.9178 (m-10) cc_final: 0.8822 (m-80) REVERT: P 75 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8843 (pp) REVERT: P 120 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8795 (p0) REVERT: P 125 ARG cc_start: 0.9076 (ttp80) cc_final: 0.8861 (ttp-170) REVERT: Q 25 MET cc_start: 0.8860 (mtt) cc_final: 0.8628 (mtt) REVERT: Q 87 LYS cc_start: 0.8364 (mttt) cc_final: 0.7812 (mtmt) REVERT: Q 152 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6911 (tm-30) REVERT: Q 154 GLU cc_start: 0.6331 (mp0) cc_final: 0.6096 (mp0) REVERT: R 97 ASN cc_start: 0.8370 (t0) cc_final: 0.7934 (t0) REVERT: R 104 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7654 (mp0) REVERT: R 152 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6828 (tm-30) REVERT: R 168 VAL cc_start: 0.9314 (OUTLIER) cc_final: 0.8935 (p) REVERT: R 185 GLN cc_start: 0.6266 (mm-40) cc_final: 0.5782 (mm-40) REVERT: S 88 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8705 (mt) REVERT: S 152 GLU cc_start: 0.7034 (tm-30) cc_final: 0.6562 (tm-30) REVERT: T 75 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8753 (pp) REVERT: T 152 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6441 (tm-30) REVERT: T 163 SER cc_start: 0.9041 (OUTLIER) cc_final: 0.8818 (m) REVERT: U 88 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8741 (mt) REVERT: U 151 GLU cc_start: 0.7638 (pt0) cc_final: 0.7397 (pm20) REVERT: V 31 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7343 (mt-10) REVERT: V 88 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8850 (mt) REVERT: V 168 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8882 (p) REVERT: V 185 GLN cc_start: 0.6288 (mm-40) cc_final: 0.5055 (mm-40) REVERT: X 88 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8834 (mt) REVERT: X 152 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: Y 87 LYS cc_start: 0.8337 (mttt) cc_final: 0.8064 (mtpp) REVERT: Y 88 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8776 (mt) REVERT: Y 120 ASN cc_start: 0.9177 (p0) cc_final: 0.8716 (p0) REVERT: Y 168 VAL cc_start: 0.9362 (t) cc_final: 0.9021 (p) REVERT: Z 97 ASN cc_start: 0.7998 (t0) cc_final: 0.7682 (t0) REVERT: a 70 TYR cc_start: 0.9061 (m-80) cc_final: 0.8858 (m-80) REVERT: a 115 MET cc_start: 0.8297 (mmm) cc_final: 0.8020 (mmm) REVERT: a 122 LYS cc_start: 0.7139 (ptmt) cc_final: 0.6029 (mttt) REVERT: b 101 TYR cc_start: 0.9115 (m-80) cc_final: 0.8690 (m-80) REVERT: c 8 ILE cc_start: 0.9339 (tt) cc_final: 0.8982 (mt) REVERT: c 35 MET cc_start: 0.8687 (mtp) cc_final: 0.8052 (mpp) REVERT: d 8 ILE cc_start: 0.9193 (tt) cc_final: 0.8844 (mt) REVERT: e 8 ILE cc_start: 0.9185 (tt) cc_final: 0.8965 (mt) REVERT: f 62 VAL cc_start: 0.9277 (p) cc_final: 0.9077 (m) REVERT: f 110 MET cc_start: 0.8481 (mmt) cc_final: 0.8035 (mmt) REVERT: i 8 ILE cc_start: 0.9324 (tt) cc_final: 0.9010 (mt) REVERT: l 8 ILE cc_start: 0.9121 (tt) cc_final: 0.8841 (mt) REVERT: l 58 ASN cc_start: 0.8905 (OUTLIER) cc_final: 0.8581 (t0) REVERT: m 8 ILE cc_start: 0.9078 (tt) cc_final: 0.8847 (mt) REVERT: m 36 VAL cc_start: 0.9404 (OUTLIER) cc_final: 0.9193 (p) REVERT: m 77 TYR cc_start: 0.9070 (t80) cc_final: 0.8790 (t80) REVERT: n 110 MET cc_start: 0.8443 (mmt) cc_final: 0.8191 (mmt) REVERT: n 117 TYR cc_start: 0.8690 (t80) cc_final: 0.7898 (t80) REVERT: n 129 ILE cc_start: 0.9197 (mt) cc_final: 0.8937 (mt) REVERT: p 8 ILE cc_start: 0.9355 (tt) cc_final: 0.8987 (mt) REVERT: p 58 ASN cc_start: 0.8954 (t0) cc_final: 0.8616 (t0) REVERT: p 110 MET cc_start: 0.8607 (mmt) cc_final: 0.8355 (tpp) REVERT: p 129 ILE cc_start: 0.9213 (mt) cc_final: 0.8976 (mt) REVERT: q 8 ILE cc_start: 0.9123 (tt) cc_final: 0.8897 (mt) REVERT: r 58 ASN cc_start: 0.8966 (t0) cc_final: 0.8430 (t0) REVERT: r 101 TYR cc_start: 0.9170 (m-80) cc_final: 0.8641 (m-80) REVERT: r 129 ILE cc_start: 0.9102 (mt) cc_final: 0.8873 (mt) REVERT: s 8 ILE cc_start: 0.9188 (tt) cc_final: 0.8957 (mt) REVERT: s 58 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8370 (t0) REVERT: s 133 MET cc_start: 0.8144 (tpt) cc_final: 0.7918 (tpt) REVERT: t 8 ILE cc_start: 0.9179 (tt) cc_final: 0.8881 (mt) REVERT: t 115 MET cc_start: 0.8819 (mmm) cc_final: 0.8593 (mmm) REVERT: u 8 ILE cc_start: 0.9159 (tt) cc_final: 0.8844 (mt) REVERT: v 8 ILE cc_start: 0.9148 (tt) cc_final: 0.8766 (mt) REVERT: v 14 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8731 (mt) REVERT: v 35 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8126 (mtm) REVERT: w 93 LEU cc_start: 0.9317 (mt) cc_final: 0.9113 (mp) REVERT: x 58 ASN cc_start: 0.9145 (t0) cc_final: 0.8514 (t0) REVERT: y 8 ILE cc_start: 0.8863 (tt) cc_final: 0.8565 (mt) REVERT: y 113 GLU cc_start: 0.8122 (tp30) cc_final: 0.7790 (tp30) REVERT: z 69 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8327 (tt) outliers start: 352 outliers final: 206 residues processed: 1721 average time/residue: 0.7008 time to fit residues: 2107.8223 Evaluate side-chains 1590 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1351 time to evaluate : 5.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 133 SER Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 96 SER Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 124 THR Chi-restraints excluded: chain J residue 159 VAL Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 193 ILE Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 30 ASP Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 116 THR Chi-restraints excluded: chain N residue 145 VAL Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 193 ILE Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 86 MET Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 96 SER Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 96 SER Chi-restraints excluded: chain P residue 116 THR Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 133 SER Chi-restraints excluded: chain P residue 174 THR Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 145 VAL Chi-restraints excluded: chain T residue 149 GLU Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 163 SER Chi-restraints excluded: chain T residue 172 SER Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 74 ASP Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 96 SER Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 174 THR Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain V residue 193 ILE Chi-restraints excluded: chain W residue 96 SER Chi-restraints excluded: chain W residue 116 THR Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain W residue 191 GLU Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 152 GLU Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain Y residue 24 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain a residue 48 VAL Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 51 GLN Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain c residue 125 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 65 ASN Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 48 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 65 ASN Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 36 VAL Chi-restraints excluded: chain f residue 69 LEU Chi-restraints excluded: chain f residue 80 VAL Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 124 THR Chi-restraints excluded: chain i residue 48 VAL Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 80 VAL Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 132 ASN Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 35 MET Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain m residue 36 VAL Chi-restraints excluded: chain m residue 48 VAL Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 80 VAL Chi-restraints excluded: chain n residue 83 THR Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 51 GLN Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 123 SER Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 69 LEU Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 58 ASN Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 36 VAL Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 62 VAL Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 123 SER Chi-restraints excluded: chain u residue 125 THR Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 125 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 48 VAL Chi-restraints excluded: chain w residue 65 ASN Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 65 ASN Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 62 VAL Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain y residue 125 THR Chi-restraints excluded: chain z residue 36 VAL Chi-restraints excluded: chain z residue 51 GLN Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 837 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 495 optimal weight: 2.9990 chunk 634 optimal weight: 1.9990 chunk 491 optimal weight: 0.9990 chunk 731 optimal weight: 0.7980 chunk 485 optimal weight: 1.9990 chunk 865 optimal weight: 5.9990 chunk 541 optimal weight: 5.9990 chunk 527 optimal weight: 0.9980 chunk 399 optimal weight: 20.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 108 ASN B 136 ASN C 136 ASN D 60 ASN D 136 ASN J 42 ASN L 60 ASN N 48 HIS N 60 ASN P 52 ASN R 60 ASN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 42 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN a 25 GLN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 25 GLN b 65 ASN c 25 GLN d 25 GLN d 65 ASN e 25 GLN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 25 GLN h 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN k 25 GLN k 50 ASN k 132 ASN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 65 ASN ** m 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 25 GLN ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 82 ASN q 25 GLN ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** r 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 25 GLN s 65 ASN ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 50 ASN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 25 GLN ** w 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 25 GLN x 132 ASN ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 ASN z 25 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 82872 Z= 0.191 Angle : 0.604 11.164 115264 Z= 0.340 Chirality : 0.039 0.254 13114 Planarity : 0.003 0.036 12372 Dihedral : 16.917 73.026 17202 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.25 % Allowed : 18.35 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.09), residues: 8346 helix: 0.50 (0.07), residues: 5590 sheet: -0.26 (0.29), residues: 312 loop : -2.18 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 56 HIS 0.003 0.001 HIS B 48 PHE 0.018 0.001 PHE S 54 TYR 0.025 0.001 TYR b 117 ARG 0.006 0.000 ARG W 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1698 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1468 time to evaluate : 6.009 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8799 (mt) REVERT: A 115 MET cc_start: 0.8442 (mmm) cc_final: 0.8088 (tpt) REVERT: A 120 ASN cc_start: 0.8085 (p0) cc_final: 0.7733 (p0) REVERT: A 152 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6849 (tm-30) REVERT: A 168 VAL cc_start: 0.9205 (t) cc_final: 0.8881 (p) REVERT: B 152 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6746 (tm-30) REVERT: C 75 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8383 (pp) REVERT: C 95 TYR cc_start: 0.8741 (m-80) cc_final: 0.8362 (m-80) REVERT: C 104 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7843 (mp0) REVERT: C 152 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6503 (tm-30) REVERT: C 154 GLU cc_start: 0.6893 (mp0) cc_final: 0.6599 (mp0) REVERT: D 75 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8782 (pp) REVERT: D 88 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.8993 (mt) REVERT: D 120 ASN cc_start: 0.8332 (p0) cc_final: 0.7620 (p0) REVERT: E 25 MET cc_start: 0.8954 (mmm) cc_final: 0.8602 (mmm) REVERT: E 95 TYR cc_start: 0.8985 (m-80) cc_final: 0.8671 (m-80) REVERT: E 152 GLU cc_start: 0.7348 (tm-30) cc_final: 0.6353 (tm-30) REVERT: F 75 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8879 (pp) REVERT: F 120 ASN cc_start: 0.8589 (p0) cc_final: 0.8034 (p0) REVERT: F 125 ARG cc_start: 0.8944 (ttp-170) cc_final: 0.8721 (ttp-170) REVERT: G 120 ASN cc_start: 0.8030 (p0) cc_final: 0.7521 (p0) REVERT: G 152 GLU cc_start: 0.6786 (tm-30) cc_final: 0.6240 (tm-30) REVERT: H 75 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8639 (pp) REVERT: H 88 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8862 (mt) REVERT: H 104 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7747 (mp0) REVERT: H 115 MET cc_start: 0.8458 (mmm) cc_final: 0.8197 (tpt) REVERT: H 152 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6718 (tm-30) REVERT: I 88 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8435 (mt) REVERT: I 152 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6781 (tm-30) REVERT: I 168 VAL cc_start: 0.9408 (t) cc_final: 0.9132 (p) REVERT: J 77 TYR cc_start: 0.8595 (m-80) cc_final: 0.8391 (m-80) REVERT: J 95 TYR cc_start: 0.8940 (m-80) cc_final: 0.8593 (m-80) REVERT: J 151 GLU cc_start: 0.7687 (pt0) cc_final: 0.7376 (pm20) REVERT: J 152 GLU cc_start: 0.6835 (tm-30) cc_final: 0.6121 (tm-30) REVERT: J 154 GLU cc_start: 0.6555 (mp0) cc_final: 0.6213 (mp0) REVERT: J 163 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.8990 (m) REVERT: K 88 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8563 (mt) REVERT: K 152 GLU cc_start: 0.6677 (tm-30) cc_final: 0.6120 (tm-30) REVERT: K 154 GLU cc_start: 0.6935 (mp0) cc_final: 0.6644 (mp0) REVERT: K 168 VAL cc_start: 0.9327 (t) cc_final: 0.9057 (p) REVERT: L 88 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.8891 (mt) REVERT: L 120 ASN cc_start: 0.7767 (p0) cc_final: 0.7003 (p0) REVERT: L 152 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6315 (tm-30) REVERT: M 75 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8680 (pp) REVERT: M 152 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6326 (tm-30) REVERT: M 187 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8027 (mttm) REVERT: N 95 TYR cc_start: 0.8877 (m-80) cc_final: 0.8480 (m-80) REVERT: N 97 ASN cc_start: 0.8065 (t0) cc_final: 0.7665 (t0) REVERT: O 152 GLU cc_start: 0.6621 (tm-30) cc_final: 0.6364 (tm-30) REVERT: O 168 VAL cc_start: 0.9317 (t) cc_final: 0.9095 (p) REVERT: P 57 TYR cc_start: 0.9160 (m-10) cc_final: 0.8797 (m-80) REVERT: P 75 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8716 (pp) REVERT: Q 152 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6443 (tm-30) REVERT: R 97 ASN cc_start: 0.8158 (t0) cc_final: 0.7549 (t0) REVERT: R 120 ASN cc_start: 0.8400 (p0) cc_final: 0.7540 (p0) REVERT: S 88 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8544 (mt) REVERT: S 191 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7220 (tt0) REVERT: T 75 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8847 (pp) REVERT: T 152 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6207 (tm-30) REVERT: T 163 SER cc_start: 0.9015 (OUTLIER) cc_final: 0.8808 (m) REVERT: T 168 VAL cc_start: 0.9174 (t) cc_final: 0.8840 (p) REVERT: U 151 GLU cc_start: 0.7696 (pt0) cc_final: 0.7441 (pm20) REVERT: V 31 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7198 (mt-10) REVERT: V 88 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8568 (mt) REVERT: V 120 ASN cc_start: 0.8218 (p0) cc_final: 0.7949 (p0) REVERT: V 185 GLN cc_start: 0.6179 (mm-40) cc_final: 0.5115 (mm-40) REVERT: W 168 VAL cc_start: 0.9213 (t) cc_final: 0.8885 (p) REVERT: X 88 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8660 (mt) REVERT: Y 149 GLU cc_start: 0.7982 (pt0) cc_final: 0.7651 (pm20) REVERT: Y 168 VAL cc_start: 0.9324 (t) cc_final: 0.9029 (p) REVERT: Z 97 ASN cc_start: 0.7931 (t0) cc_final: 0.7685 (t0) REVERT: a 65 ASN cc_start: 0.8899 (OUTLIER) cc_final: 0.8507 (t0) REVERT: c 82 ASN cc_start: 0.8384 (p0) cc_final: 0.8043 (p0) REVERT: c 122 LYS cc_start: 0.7007 (ptmt) cc_final: 0.5501 (mttt) REVERT: d 122 LYS cc_start: 0.6644 (ptmt) cc_final: 0.5540 (mttt) REVERT: e 8 ILE cc_start: 0.8968 (tt) cc_final: 0.8625 (mt) REVERT: f 110 MET cc_start: 0.8376 (mmt) cc_final: 0.7971 (mmt) REVERT: f 117 TYR cc_start: 0.8773 (t80) cc_final: 0.8426 (t80) REVERT: g 8 ILE cc_start: 0.9105 (tt) cc_final: 0.8765 (mt) REVERT: g 35 MET cc_start: 0.8632 (mtp) cc_final: 0.8309 (mtp) REVERT: h 122 LYS cc_start: 0.7259 (ptmt) cc_final: 0.6879 (ptmt) REVERT: h 129 ILE cc_start: 0.9175 (mt) cc_final: 0.8878 (mt) REVERT: j 110 MET cc_start: 0.8672 (mmt) cc_final: 0.8416 (tpp) REVERT: l 58 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8489 (t0) REVERT: m 35 MET cc_start: 0.8783 (mtp) cc_final: 0.8525 (mtp) REVERT: m 77 TYR cc_start: 0.8827 (t80) cc_final: 0.8523 (t80) REVERT: n 15 THR cc_start: 0.9227 (m) cc_final: 0.9003 (p) REVERT: n 110 MET cc_start: 0.8344 (mmt) cc_final: 0.8113 (mmt) REVERT: n 129 ILE cc_start: 0.9139 (mt) cc_final: 0.8864 (mt) REVERT: o 83 THR cc_start: 0.8923 (t) cc_final: 0.8683 (t) REVERT: p 8 ILE cc_start: 0.9256 (tt) cc_final: 0.8915 (mt) REVERT: p 46 TYR cc_start: 0.8773 (m-80) cc_final: 0.8546 (m-80) REVERT: p 101 TYR cc_start: 0.9035 (m-80) cc_final: 0.8729 (m-80) REVERT: p 129 ILE cc_start: 0.9182 (mt) cc_final: 0.8932 (mt) REVERT: q 8 ILE cc_start: 0.8958 (tt) cc_final: 0.8613 (mt) REVERT: r 58 ASN cc_start: 0.8901 (t0) cc_final: 0.8284 (t0) REVERT: r 129 ILE cc_start: 0.9062 (mt) cc_final: 0.8853 (mt) REVERT: s 46 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.6907 (t80) REVERT: t 101 TYR cc_start: 0.8948 (m-80) cc_final: 0.8706 (m-80) REVERT: t 115 MET cc_start: 0.8719 (mmm) cc_final: 0.8493 (mmm) REVERT: v 8 ILE cc_start: 0.9024 (tt) cc_final: 0.8706 (mt) REVERT: v 35 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8183 (mtm) REVERT: w 93 LEU cc_start: 0.9233 (mt) cc_final: 0.9027 (mp) REVERT: x 58 ASN cc_start: 0.9029 (t0) cc_final: 0.8497 (t0) REVERT: x 115 MET cc_start: 0.8943 (mmm) cc_final: 0.8397 (mmm) REVERT: y 113 GLU cc_start: 0.8084 (tp30) cc_final: 0.7721 (tp30) REVERT: z 69 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8075 (tt) outliers start: 230 outliers final: 146 residues processed: 1626 average time/residue: 0.7070 time to fit residues: 2001.6060 Evaluate side-chains 1562 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1390 time to evaluate : 6.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 27 ASP Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain J residue 68 SER Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 191 GLU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain M residue 187 LYS Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 133 SER Chi-restraints excluded: chain P residue 174 THR Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 71 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 191 GLU Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 149 GLU Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 163 SER Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 174 THR Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 191 GLU Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 14 MET Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain Z residue 174 THR Chi-restraints excluded: chain a residue 65 ASN Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain d residue 65 ASN Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain k residue 132 ASN Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 46 TYR Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 97 LEU Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 132 ASN Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 62 VAL Chi-restraints excluded: chain y residue 82 ASN Chi-restraints excluded: chain y residue 123 SER Chi-restraints excluded: chain z residue 69 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 535 optimal weight: 3.9990 chunk 345 optimal weight: 0.9990 chunk 516 optimal weight: 0.9990 chunk 260 optimal weight: 0.9990 chunk 170 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 550 optimal weight: 2.9990 chunk 589 optimal weight: 0.9980 chunk 427 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 680 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN D 103 ASN F 60 ASN J 42 ASN L 60 ASN N 60 ASN ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN R 60 ASN V 42 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 65 ASN f 25 GLN g 25 GLN i 25 GLN j 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN k 25 GLN l 25 GLN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN ** m 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 132 ASN n 50 ASN o 25 GLN ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 HIS ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 132 ASN ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 82872 Z= 0.185 Angle : 0.599 13.145 115264 Z= 0.335 Chirality : 0.039 0.224 13114 Planarity : 0.003 0.045 12372 Dihedral : 16.854 75.149 17200 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.94 % Allowed : 19.34 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 8346 helix: 0.71 (0.07), residues: 5590 sheet: -0.11 (0.30), residues: 312 loop : -2.13 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 142 HIS 0.003 0.001 HIS S 48 PHE 0.020 0.002 PHE S 54 TYR 0.023 0.001 TYR g 117 ARG 0.005 0.000 ARG d 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1689 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1481 time to evaluate : 5.962 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8803 (mt) REVERT: A 115 MET cc_start: 0.8452 (mmm) cc_final: 0.8121 (tpt) REVERT: A 120 ASN cc_start: 0.7943 (p0) cc_final: 0.7635 (p0) REVERT: A 152 GLU cc_start: 0.6962 (tm-30) cc_final: 0.6492 (tm-30) REVERT: A 168 VAL cc_start: 0.9224 (t) cc_final: 0.8901 (p) REVERT: B 120 ASN cc_start: 0.8227 (p0) cc_final: 0.7493 (p0) REVERT: B 152 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6485 (tm-30) REVERT: C 75 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8285 (pp) REVERT: C 95 TYR cc_start: 0.8725 (m-80) cc_final: 0.8427 (m-80) REVERT: C 152 GLU cc_start: 0.6991 (tm-30) cc_final: 0.6572 (tm-30) REVERT: D 66 ILE cc_start: 0.8997 (mm) cc_final: 0.8764 (mt) REVERT: D 75 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8721 (pp) REVERT: D 88 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9024 (mt) REVERT: D 120 ASN cc_start: 0.8228 (p0) cc_final: 0.7479 (p0) REVERT: E 25 MET cc_start: 0.8958 (mmm) cc_final: 0.8594 (mmm) REVERT: E 95 TYR cc_start: 0.8937 (m-80) cc_final: 0.8612 (m-80) REVERT: E 152 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6307 (tm-30) REVERT: F 75 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8896 (pp) REVERT: F 88 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8868 (mt) REVERT: F 120 ASN cc_start: 0.8768 (p0) cc_final: 0.8157 (p0) REVERT: F 168 VAL cc_start: 0.9261 (t) cc_final: 0.8877 (p) REVERT: G 120 ASN cc_start: 0.8019 (p0) cc_final: 0.7494 (p0) REVERT: G 152 GLU cc_start: 0.6734 (tm-30) cc_final: 0.6136 (tm-30) REVERT: H 75 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8589 (pp) REVERT: H 88 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.8973 (mt) REVERT: H 104 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7763 (mp0) REVERT: H 120 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.7894 (p0) REVERT: H 152 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6534 (tm-30) REVERT: H 154 GLU cc_start: 0.6659 (mp0) cc_final: 0.6358 (mp0) REVERT: I 88 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8444 (mt) REVERT: I 152 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6707 (tm-30) REVERT: I 168 VAL cc_start: 0.9416 (t) cc_final: 0.9136 (p) REVERT: J 77 TYR cc_start: 0.8619 (m-80) cc_final: 0.8383 (m-80) REVERT: J 95 TYR cc_start: 0.8904 (m-80) cc_final: 0.8413 (m-10) REVERT: J 151 GLU cc_start: 0.7606 (pt0) cc_final: 0.7298 (pm20) REVERT: J 163 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.9020 (m) REVERT: K 75 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8571 (pp) REVERT: K 88 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8515 (mt) REVERT: K 152 GLU cc_start: 0.6175 (tm-30) cc_final: 0.5699 (tm-30) REVERT: K 168 VAL cc_start: 0.9315 (t) cc_final: 0.9053 (p) REVERT: L 88 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8879 (mt) REVERT: L 120 ASN cc_start: 0.7805 (p0) cc_final: 0.7092 (p0) REVERT: L 152 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6092 (tm-30) REVERT: M 75 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8642 (pp) REVERT: M 152 GLU cc_start: 0.6612 (tm-30) cc_final: 0.6271 (tm-30) REVERT: N 95 TYR cc_start: 0.8858 (m-80) cc_final: 0.8451 (m-80) REVERT: N 97 ASN cc_start: 0.8031 (t0) cc_final: 0.7753 (t0) REVERT: P 75 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8662 (pp) REVERT: Q 152 GLU cc_start: 0.6845 (tm-30) cc_final: 0.6303 (tm-30) REVERT: R 66 ILE cc_start: 0.9096 (mm) cc_final: 0.8777 (mt) REVERT: R 97 ASN cc_start: 0.8129 (t0) cc_final: 0.7621 (t0) REVERT: R 120 ASN cc_start: 0.8441 (p0) cc_final: 0.8028 (p0) REVERT: S 88 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8369 (mt) REVERT: T 75 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8877 (pp) REVERT: T 152 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6241 (tm-30) REVERT: T 168 VAL cc_start: 0.9184 (t) cc_final: 0.8881 (p) REVERT: U 16 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8610 (mm) REVERT: U 151 GLU cc_start: 0.7689 (pt0) cc_final: 0.7384 (pm20) REVERT: U 162 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7938 (mtp180) REVERT: V 20 ARG cc_start: 0.8900 (ttp-170) cc_final: 0.8466 (ttp-170) REVERT: V 31 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7105 (mt-10) REVERT: V 88 ILE cc_start: 0.9003 (OUTLIER) cc_final: 0.8514 (mt) REVERT: V 119 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7761 (mt-10) REVERT: V 120 ASN cc_start: 0.8182 (p0) cc_final: 0.7885 (p0) REVERT: W 115 MET cc_start: 0.8822 (tpp) cc_final: 0.8586 (tpt) REVERT: X 88 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8622 (mt) REVERT: Y 120 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.7602 (p0) REVERT: Z 25 MET cc_start: 0.9008 (mtp) cc_final: 0.8771 (mtm) REVERT: Z 97 ASN cc_start: 0.7909 (t0) cc_final: 0.7633 (t0) REVERT: Z 114 THR cc_start: 0.8867 (t) cc_final: 0.8656 (t) REVERT: a 83 THR cc_start: 0.8831 (t) cc_final: 0.8559 (t) REVERT: a 122 LYS cc_start: 0.6239 (ptmt) cc_final: 0.5580 (mttt) REVERT: b 35 MET cc_start: 0.8566 (mtp) cc_final: 0.7826 (mpp) REVERT: c 82 ASN cc_start: 0.8430 (p0) cc_final: 0.8101 (p0) REVERT: c 122 LYS cc_start: 0.7018 (ptmt) cc_final: 0.5525 (mttt) REVERT: d 122 LYS cc_start: 0.6405 (ptmt) cc_final: 0.5389 (mtpt) REVERT: e 8 ILE cc_start: 0.8937 (tt) cc_final: 0.8592 (mt) REVERT: f 82 ASN cc_start: 0.8478 (p0) cc_final: 0.8033 (p0) REVERT: f 110 MET cc_start: 0.8281 (mmt) cc_final: 0.7904 (mmt) REVERT: f 117 TYR cc_start: 0.8708 (t80) cc_final: 0.8294 (t80) REVERT: g 8 ILE cc_start: 0.9081 (tt) cc_final: 0.8741 (mt) REVERT: g 35 MET cc_start: 0.8386 (mtp) cc_final: 0.8047 (mtp) REVERT: h 81 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8670 (mp) REVERT: h 110 MET cc_start: 0.8185 (mmt) cc_final: 0.7956 (mmt) REVERT: h 122 LYS cc_start: 0.7273 (ptmt) cc_final: 0.6909 (ptmt) REVERT: h 129 ILE cc_start: 0.9127 (mt) cc_final: 0.8814 (mt) REVERT: j 110 MET cc_start: 0.8661 (mmt) cc_final: 0.8457 (tpp) REVERT: l 58 ASN cc_start: 0.8936 (OUTLIER) cc_final: 0.8481 (t0) REVERT: m 77 TYR cc_start: 0.8817 (t80) cc_final: 0.8533 (t80) REVERT: n 129 ILE cc_start: 0.9090 (mt) cc_final: 0.8869 (mt) REVERT: o 58 ASN cc_start: 0.8666 (t0) cc_final: 0.8399 (t0) REVERT: o 83 THR cc_start: 0.8916 (t) cc_final: 0.8659 (t) REVERT: o 110 MET cc_start: 0.8476 (mmt) cc_final: 0.8052 (mmt) REVERT: p 8 ILE cc_start: 0.9256 (tt) cc_final: 0.8916 (mt) REVERT: p 115 MET cc_start: 0.8791 (mmm) cc_final: 0.8536 (mmm) REVERT: q 8 ILE cc_start: 0.9020 (tt) cc_final: 0.8611 (mt) REVERT: q 101 TYR cc_start: 0.8935 (m-80) cc_final: 0.8704 (m-80) REVERT: r 101 TYR cc_start: 0.8951 (m-80) cc_final: 0.8685 (m-80) REVERT: r 115 MET cc_start: 0.8615 (mmm) cc_final: 0.8408 (mmm) REVERT: r 129 ILE cc_start: 0.8992 (mt) cc_final: 0.8761 (mt) REVERT: s 133 MET cc_start: 0.8580 (tpp) cc_final: 0.8334 (tpt) REVERT: t 15 THR cc_start: 0.9356 (m) cc_final: 0.9134 (p) REVERT: t 101 TYR cc_start: 0.8952 (m-80) cc_final: 0.8688 (m-80) REVERT: u 35 MET cc_start: 0.8574 (mtp) cc_final: 0.7949 (mpp) REVERT: v 8 ILE cc_start: 0.8966 (tt) cc_final: 0.8665 (mt) REVERT: v 35 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8251 (mtm) REVERT: x 33 LYS cc_start: 0.8659 (mtmm) cc_final: 0.7415 (mmtt) REVERT: x 58 ASN cc_start: 0.9021 (t0) cc_final: 0.8461 (t0) REVERT: x 115 MET cc_start: 0.8957 (mmm) cc_final: 0.8553 (mmm) REVERT: y 35 MET cc_start: 0.8700 (mtp) cc_final: 0.7816 (mpp) REVERT: y 113 GLU cc_start: 0.8134 (tp30) cc_final: 0.7753 (tp30) REVERT: z 69 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8271 (tt) outliers start: 208 outliers final: 141 residues processed: 1624 average time/residue: 0.7570 time to fit residues: 2149.4690 Evaluate side-chains 1586 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1418 time to evaluate : 5.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 103 ASN Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 88 ILE Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain K residue 75 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain N residue 190 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 174 THR Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 16 LEU Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 125 ARG Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 75 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 174 THR Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 174 THR Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain Z residue 174 THR Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 69 LEU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 124 THR Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain k residue 14 ILE Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain k residue 122 LYS Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain m residue 132 ASN Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 40 GLN Chi-restraints excluded: chain v residue 43 MET Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 126 THR Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain z residue 69 LEU Chi-restraints excluded: chain z residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 787 optimal weight: 10.0000 chunk 829 optimal weight: 5.9990 chunk 756 optimal weight: 0.9990 chunk 806 optimal weight: 10.0000 chunk 828 optimal weight: 2.9990 chunk 485 optimal weight: 3.9990 chunk 351 optimal weight: 8.9990 chunk 633 optimal weight: 0.9990 chunk 247 optimal weight: 30.0000 chunk 728 optimal weight: 3.9990 chunk 762 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN ** D 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 60 ASN L 60 ASN N 60 ASN ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 ASN R 60 ASN S 108 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN a 25 GLN a 65 ASN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 ASN e 25 GLN e 65 ASN f 25 GLN h 25 GLN i 25 GLN j 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 25 GLN o 65 ASN ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN r 82 ASN ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 60 HIS t 82 ASN ** v 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 132 ASN ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 82872 Z= 0.255 Angle : 0.636 13.320 115264 Z= 0.354 Chirality : 0.042 0.235 13114 Planarity : 0.003 0.048 12372 Dihedral : 16.887 75.929 17200 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.42 % Favored : 92.56 % Rotamer: Outliers : 3.04 % Allowed : 19.82 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8346 helix: 0.67 (0.07), residues: 5668 sheet: -0.10 (0.30), residues: 312 loop : -2.31 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 142 HIS 0.005 0.002 HIS L 48 PHE 0.018 0.002 PHE C 89 TYR 0.024 0.001 TYR q 117 ARG 0.005 0.000 ARG W 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1655 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 1440 time to evaluate : 7.086 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.8841 (mt) REVERT: A 115 MET cc_start: 0.8454 (mmm) cc_final: 0.8122 (tpt) REVERT: A 120 ASN cc_start: 0.8147 (p0) cc_final: 0.7875 (p0) REVERT: A 152 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6647 (tm-30) REVERT: A 168 VAL cc_start: 0.9276 (t) cc_final: 0.8946 (p) REVERT: B 120 ASN cc_start: 0.8305 (p0) cc_final: 0.7608 (p0) REVERT: C 75 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 88 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8857 (mt) REVERT: C 95 TYR cc_start: 0.8785 (m-80) cc_final: 0.8370 (m-80) REVERT: C 103 ASN cc_start: 0.8679 (p0) cc_final: 0.8456 (p0) REVERT: C 104 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7968 (mp0) REVERT: C 152 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6490 (tm-30) REVERT: C 154 GLU cc_start: 0.6834 (mp0) cc_final: 0.6497 (mp0) REVERT: D 66 ILE cc_start: 0.9077 (mm) cc_final: 0.8848 (mt) REVERT: D 75 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8659 (pp) REVERT: D 88 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9029 (mt) REVERT: E 152 GLU cc_start: 0.7390 (tm-30) cc_final: 0.6399 (tm-30) REVERT: F 75 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8917 (pp) REVERT: F 88 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8914 (mt) REVERT: F 120 ASN cc_start: 0.8788 (p0) cc_final: 0.8229 (p0) REVERT: G 120 ASN cc_start: 0.8156 (p0) cc_final: 0.7703 (p0) REVERT: G 152 GLU cc_start: 0.6847 (tm-30) cc_final: 0.6277 (tm-30) REVERT: H 75 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8628 (pp) REVERT: H 104 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7840 (mp0) REVERT: H 120 ASN cc_start: 0.8622 (OUTLIER) cc_final: 0.8031 (p0) REVERT: H 152 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6621 (tm-30) REVERT: I 88 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8564 (mt) REVERT: I 152 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6670 (tm-30) REVERT: I 168 VAL cc_start: 0.9435 (t) cc_final: 0.9170 (p) REVERT: I 182 GLU cc_start: 0.8473 (tp30) cc_final: 0.8237 (tp30) REVERT: J 77 TYR cc_start: 0.8688 (m-80) cc_final: 0.8441 (m-80) REVERT: J 95 TYR cc_start: 0.8957 (m-80) cc_final: 0.8546 (m-80) REVERT: J 151 GLU cc_start: 0.7504 (pt0) cc_final: 0.7240 (pm20) REVERT: J 152 GLU cc_start: 0.6818 (tm-30) cc_final: 0.6461 (tm-30) REVERT: J 154 GLU cc_start: 0.6474 (mp0) cc_final: 0.6125 (mp0) REVERT: J 163 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.9042 (m) REVERT: K 88 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8497 (mt) REVERT: K 120 ASN cc_start: 0.8197 (p0) cc_final: 0.7942 (p0) REVERT: K 152 GLU cc_start: 0.6500 (tm-30) cc_final: 0.6001 (tm-30) REVERT: K 168 VAL cc_start: 0.9330 (t) cc_final: 0.9057 (p) REVERT: L 88 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.8983 (mt) REVERT: L 104 GLU cc_start: 0.7651 (mp0) cc_final: 0.7357 (mp0) REVERT: L 120 ASN cc_start: 0.7931 (p0) cc_final: 0.7088 (p0) REVERT: L 152 GLU cc_start: 0.6808 (tm-30) cc_final: 0.6438 (tm-30) REVERT: M 75 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8653 (pp) REVERT: M 152 GLU cc_start: 0.6794 (tm-30) cc_final: 0.6398 (tm-30) REVERT: N 95 TYR cc_start: 0.8981 (m-80) cc_final: 0.8502 (m-80) REVERT: N 97 ASN cc_start: 0.8099 (t0) cc_final: 0.7721 (t0) REVERT: N 108 ASN cc_start: 0.8725 (m-40) cc_final: 0.8003 (m110) REVERT: O 152 GLU cc_start: 0.6633 (tm-30) cc_final: 0.6297 (tm-30) REVERT: P 57 TYR cc_start: 0.9129 (m-10) cc_final: 0.8654 (m-80) REVERT: P 75 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8730 (pp) REVERT: P 120 ASN cc_start: 0.8636 (p0) cc_final: 0.8376 (p0) REVERT: Q 152 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6344 (tm-30) REVERT: R 66 ILE cc_start: 0.9105 (mm) cc_final: 0.8806 (mt) REVERT: R 97 ASN cc_start: 0.8196 (t0) cc_final: 0.7652 (t0) REVERT: R 120 ASN cc_start: 0.8531 (p0) cc_final: 0.8201 (p0) REVERT: S 88 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8455 (mt) REVERT: T 75 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8876 (pp) REVERT: T 152 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: T 168 VAL cc_start: 0.9164 (t) cc_final: 0.8881 (p) REVERT: U 88 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8325 (mt) REVERT: U 151 GLU cc_start: 0.7704 (pt0) cc_final: 0.7349 (pm20) REVERT: V 31 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7265 (mt-10) REVERT: V 88 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8648 (mt) REVERT: V 119 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7787 (mt-10) REVERT: W 115 MET cc_start: 0.8885 (tpp) cc_final: 0.8625 (tpt) REVERT: X 88 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8653 (mt) REVERT: Y 120 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.7777 (p0) REVERT: Z 25 MET cc_start: 0.9086 (mtp) cc_final: 0.8864 (mtm) REVERT: Z 97 ASN cc_start: 0.7992 (t0) cc_final: 0.7662 (t0) REVERT: Z 114 THR cc_start: 0.8903 (t) cc_final: 0.8677 (t) REVERT: a 122 LYS cc_start: 0.6336 (ptmt) cc_final: 0.5684 (mtpt) REVERT: b 35 MET cc_start: 0.8657 (mtp) cc_final: 0.7915 (mpp) REVERT: c 35 MET cc_start: 0.8515 (mtp) cc_final: 0.7875 (mpp) REVERT: c 122 LYS cc_start: 0.7000 (ptmt) cc_final: 0.5489 (mttt) REVERT: d 122 LYS cc_start: 0.6455 (ptmt) cc_final: 0.5428 (mtpt) REVERT: e 8 ILE cc_start: 0.9044 (tt) cc_final: 0.8751 (mt) REVERT: f 110 MET cc_start: 0.8302 (mmt) cc_final: 0.7936 (mmt) REVERT: f 117 TYR cc_start: 0.8761 (t80) cc_final: 0.8342 (t80) REVERT: g 8 ILE cc_start: 0.9151 (tt) cc_final: 0.8821 (mt) REVERT: g 35 MET cc_start: 0.8445 (mtp) cc_final: 0.8189 (mtp) REVERT: h 81 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8685 (mp) REVERT: h 110 MET cc_start: 0.8188 (mmt) cc_final: 0.7928 (mmt) REVERT: h 122 LYS cc_start: 0.7350 (ptmt) cc_final: 0.6963 (ptmt) REVERT: h 129 ILE cc_start: 0.9173 (mt) cc_final: 0.8850 (mt) REVERT: j 110 MET cc_start: 0.8706 (mmt) cc_final: 0.8456 (mmt) REVERT: l 58 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8558 (t0) REVERT: m 35 MET cc_start: 0.8799 (mtp) cc_final: 0.8040 (mpp) REVERT: m 77 TYR cc_start: 0.8924 (t80) cc_final: 0.8662 (t80) REVERT: n 110 MET cc_start: 0.8718 (mmt) cc_final: 0.8433 (tpp) REVERT: n 129 ILE cc_start: 0.9128 (mt) cc_final: 0.8912 (mt) REVERT: p 8 ILE cc_start: 0.9294 (tt) cc_final: 0.8964 (mt) REVERT: p 46 TYR cc_start: 0.8839 (m-80) cc_final: 0.8607 (m-80) REVERT: p 115 MET cc_start: 0.8771 (mmm) cc_final: 0.8533 (mmm) REVERT: q 8 ILE cc_start: 0.9006 (tt) cc_final: 0.8683 (mt) REVERT: r 115 MET cc_start: 0.8595 (mmm) cc_final: 0.8372 (mmm) REVERT: r 129 ILE cc_start: 0.9040 (mt) cc_final: 0.8811 (mt) REVERT: s 133 MET cc_start: 0.8602 (tpp) cc_final: 0.8361 (tpt) REVERT: u 35 MET cc_start: 0.8659 (mtp) cc_final: 0.7996 (mpp) REVERT: v 8 ILE cc_start: 0.8983 (tt) cc_final: 0.8660 (mt) REVERT: v 35 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8241 (mtm) REVERT: v 110 MET cc_start: 0.8644 (mmt) cc_final: 0.8064 (mmt) REVERT: w 93 LEU cc_start: 0.9253 (mt) cc_final: 0.9046 (mp) REVERT: x 33 LYS cc_start: 0.8987 (mtmm) cc_final: 0.7579 (mmtt) REVERT: x 58 ASN cc_start: 0.9050 (t0) cc_final: 0.8438 (t0) REVERT: x 115 MET cc_start: 0.8914 (mmm) cc_final: 0.8572 (mmm) REVERT: y 8 ILE cc_start: 0.8778 (tt) cc_final: 0.8455 (mt) REVERT: y 35 MET cc_start: 0.8794 (mtp) cc_final: 0.7922 (mpp) REVERT: y 113 GLU cc_start: 0.8137 (tp30) cc_final: 0.7748 (tp30) REVERT: z 69 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8300 (tt) outliers start: 215 outliers final: 158 residues processed: 1582 average time/residue: 0.6983 time to fit residues: 1925.5615 Evaluate side-chains 1603 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1419 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain K residue 68 SER Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 129 GLU Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 68 SER Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 174 THR Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 125 ARG Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 174 THR Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain Z residue 174 THR Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain d residue 65 ASN Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 124 THR Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 40 GLN Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 126 THR Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 62 VAL Chi-restraints excluded: chain y residue 125 THR Chi-restraints excluded: chain z residue 69 LEU Chi-restraints excluded: chain z residue 81 LEU Chi-restraints excluded: chain z residue 122 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 803 optimal weight: 6.9990 chunk 529 optimal weight: 0.9990 chunk 852 optimal weight: 7.9990 chunk 520 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 592 optimal weight: 4.9990 chunk 894 optimal weight: 7.9990 chunk 823 optimal weight: 6.9990 chunk 712 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 550 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 120 ASN B 136 ASN D 103 ASN H 60 ASN J 42 ASN L 60 ASN N 60 ASN ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 136 ASN X 60 ASN ** X 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN a 25 GLN a 65 ASN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 ASN ** e 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 65 ASN ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 ASN ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 132 ASN ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 65 ASN ** w 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 82872 Z= 0.274 Angle : 0.687 59.200 115264 Z= 0.387 Chirality : 0.042 0.233 13114 Planarity : 0.003 0.063 12372 Dihedral : 16.886 75.919 17200 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 2.83 % Allowed : 20.08 % Favored : 77.09 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8346 helix: 0.67 (0.07), residues: 5668 sheet: -0.09 (0.30), residues: 312 loop : -2.30 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 142 HIS 0.005 0.002 HIS L 48 PHE 0.020 0.002 PHE D 54 TYR 0.022 0.001 TYR X 18 ARG 0.017 0.000 ARG N 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16692 Ramachandran restraints generated. 8346 Oldfield, 0 Emsley, 8346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1632 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 1432 time to evaluate : 5.925 Fit side-chains TARDY: cannot create tardy model for: "MET A 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET E 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET F 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET G 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET H 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET I 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET J 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET K 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET L 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET M 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET N 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET O 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET P 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Q 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET R 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET S 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET U 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET V 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET W 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET X 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET Y 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET Z 1 " (corrupted residue). Skipping it. REVERT: A 88 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8842 (mt) REVERT: A 115 MET cc_start: 0.8450 (mmm) cc_final: 0.8117 (tpt) REVERT: A 120 ASN cc_start: 0.8153 (p0) cc_final: 0.7866 (p0) REVERT: A 152 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 168 VAL cc_start: 0.9275 (t) cc_final: 0.8945 (p) REVERT: C 75 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8348 (pp) REVERT: C 88 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8855 (mt) REVERT: C 95 TYR cc_start: 0.8784 (m-80) cc_final: 0.8378 (m-80) REVERT: C 103 ASN cc_start: 0.8662 (p0) cc_final: 0.8450 (p0) REVERT: C 104 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7972 (mp0) REVERT: C 152 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6486 (tm-30) REVERT: C 154 GLU cc_start: 0.6870 (mp0) cc_final: 0.6547 (mp0) REVERT: D 66 ILE cc_start: 0.9073 (mm) cc_final: 0.8847 (mt) REVERT: D 75 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8662 (pp) REVERT: D 86 MET cc_start: 0.8398 (tpp) cc_final: 0.8197 (tpp) REVERT: D 88 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9027 (mt) REVERT: E 152 GLU cc_start: 0.7393 (tm-30) cc_final: 0.6402 (tm-30) REVERT: F 75 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8927 (pp) REVERT: F 88 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8916 (mt) REVERT: F 120 ASN cc_start: 0.8738 (p0) cc_final: 0.8174 (p0) REVERT: G 120 ASN cc_start: 0.8133 (p0) cc_final: 0.7711 (p0) REVERT: G 152 GLU cc_start: 0.6874 (tm-30) cc_final: 0.6277 (tm-30) REVERT: H 75 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8613 (pp) REVERT: H 104 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7846 (mp0) REVERT: H 120 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8027 (p0) REVERT: H 152 GLU cc_start: 0.7300 (tm-30) cc_final: 0.6613 (tm-30) REVERT: H 154 GLU cc_start: 0.6789 (mp0) cc_final: 0.6494 (mp0) REVERT: I 88 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8564 (mt) REVERT: I 152 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6668 (tm-30) REVERT: I 168 VAL cc_start: 0.9435 (t) cc_final: 0.9169 (p) REVERT: I 182 GLU cc_start: 0.8475 (tp30) cc_final: 0.8221 (tp30) REVERT: J 77 TYR cc_start: 0.8682 (m-80) cc_final: 0.8436 (m-80) REVERT: J 95 TYR cc_start: 0.8956 (m-80) cc_final: 0.8545 (m-80) REVERT: J 151 GLU cc_start: 0.7499 (pt0) cc_final: 0.7241 (pm20) REVERT: J 152 GLU cc_start: 0.6830 (tm-30) cc_final: 0.6463 (tm-30) REVERT: J 154 GLU cc_start: 0.6461 (mp0) cc_final: 0.6125 (mp0) REVERT: J 163 SER cc_start: 0.9322 (OUTLIER) cc_final: 0.9041 (m) REVERT: K 88 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8498 (mt) REVERT: K 120 ASN cc_start: 0.8161 (p0) cc_final: 0.7937 (p0) REVERT: K 152 GLU cc_start: 0.6506 (tm-30) cc_final: 0.5995 (tm-30) REVERT: K 168 VAL cc_start: 0.9326 (t) cc_final: 0.9058 (p) REVERT: L 88 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.8982 (mt) REVERT: L 104 GLU cc_start: 0.7674 (mp0) cc_final: 0.7379 (mp0) REVERT: L 120 ASN cc_start: 0.7933 (p0) cc_final: 0.7088 (p0) REVERT: L 152 GLU cc_start: 0.6804 (tm-30) cc_final: 0.6437 (tm-30) REVERT: M 75 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8654 (pp) REVERT: M 152 GLU cc_start: 0.6747 (tm-30) cc_final: 0.6398 (tm-30) REVERT: N 95 TYR cc_start: 0.8972 (m-80) cc_final: 0.8502 (m-80) REVERT: N 97 ASN cc_start: 0.8101 (t0) cc_final: 0.7719 (t0) REVERT: N 108 ASN cc_start: 0.8734 (m-40) cc_final: 0.8002 (m110) REVERT: O 152 GLU cc_start: 0.6641 (tm-30) cc_final: 0.6290 (tm-30) REVERT: P 57 TYR cc_start: 0.9127 (m-10) cc_final: 0.8662 (m-80) REVERT: P 75 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8730 (pp) REVERT: P 120 ASN cc_start: 0.8636 (p0) cc_final: 0.8376 (p0) REVERT: Q 152 GLU cc_start: 0.6843 (tm-30) cc_final: 0.6346 (tm-30) REVERT: R 66 ILE cc_start: 0.9097 (mm) cc_final: 0.8804 (mt) REVERT: R 97 ASN cc_start: 0.8209 (t0) cc_final: 0.7649 (t0) REVERT: R 120 ASN cc_start: 0.8534 (p0) cc_final: 0.8200 (p0) REVERT: S 88 ILE cc_start: 0.8964 (OUTLIER) cc_final: 0.8448 (mt) REVERT: T 75 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8875 (pp) REVERT: T 152 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6370 (tm-30) REVERT: T 168 VAL cc_start: 0.9164 (t) cc_final: 0.8882 (p) REVERT: U 88 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8320 (mt) REVERT: U 151 GLU cc_start: 0.7706 (pt0) cc_final: 0.7348 (pm20) REVERT: V 31 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7264 (mt-10) REVERT: V 88 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8646 (mt) REVERT: V 119 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7785 (mt-10) REVERT: W 115 MET cc_start: 0.8888 (tpp) cc_final: 0.8624 (tpt) REVERT: X 88 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8648 (mt) REVERT: Y 120 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.7775 (p0) REVERT: Y 168 VAL cc_start: 0.9245 (t) cc_final: 0.8949 (p) REVERT: Z 25 MET cc_start: 0.9093 (mtp) cc_final: 0.8862 (mtm) REVERT: Z 97 ASN cc_start: 0.7988 (t0) cc_final: 0.7658 (t0) REVERT: Z 114 THR cc_start: 0.8898 (t) cc_final: 0.8677 (t) REVERT: a 122 LYS cc_start: 0.6340 (ptmt) cc_final: 0.5685 (mtpt) REVERT: c 35 MET cc_start: 0.8519 (mtp) cc_final: 0.7876 (mpp) REVERT: c 122 LYS cc_start: 0.6991 (ptmt) cc_final: 0.5490 (mttt) REVERT: d 122 LYS cc_start: 0.6450 (ptmt) cc_final: 0.5421 (mtpt) REVERT: e 8 ILE cc_start: 0.9045 (tt) cc_final: 0.8755 (mt) REVERT: f 110 MET cc_start: 0.8308 (mmt) cc_final: 0.7931 (mmt) REVERT: f 117 TYR cc_start: 0.8759 (t80) cc_final: 0.8343 (t80) REVERT: g 8 ILE cc_start: 0.9146 (tt) cc_final: 0.8821 (mt) REVERT: g 35 MET cc_start: 0.8447 (mtp) cc_final: 0.8186 (mtp) REVERT: h 81 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8696 (mp) REVERT: h 101 TYR cc_start: 0.8868 (m-80) cc_final: 0.8225 (m-80) REVERT: h 110 MET cc_start: 0.8176 (mmt) cc_final: 0.7931 (mmt) REVERT: h 122 LYS cc_start: 0.7370 (ptmt) cc_final: 0.6965 (ptmt) REVERT: h 129 ILE cc_start: 0.9174 (mt) cc_final: 0.8849 (mt) REVERT: j 110 MET cc_start: 0.8704 (mmt) cc_final: 0.8449 (mmt) REVERT: k 115 MET cc_start: 0.8957 (mmm) cc_final: 0.8659 (mmm) REVERT: l 58 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8510 (t0) REVERT: m 35 MET cc_start: 0.8799 (mtp) cc_final: 0.8059 (mpp) REVERT: m 77 TYR cc_start: 0.8928 (t80) cc_final: 0.8663 (t80) REVERT: n 110 MET cc_start: 0.8711 (mmt) cc_final: 0.8423 (tpp) REVERT: n 129 ILE cc_start: 0.9155 (mt) cc_final: 0.8916 (mt) REVERT: p 8 ILE cc_start: 0.9293 (tt) cc_final: 0.8962 (mt) REVERT: p 115 MET cc_start: 0.8772 (mmm) cc_final: 0.8531 (mmm) REVERT: q 8 ILE cc_start: 0.8996 (tt) cc_final: 0.8686 (mt) REVERT: r 115 MET cc_start: 0.8578 (mmm) cc_final: 0.8378 (mmm) REVERT: r 129 ILE cc_start: 0.9033 (mt) cc_final: 0.8810 (mt) REVERT: s 133 MET cc_start: 0.8600 (tpp) cc_final: 0.8368 (tpt) REVERT: u 35 MET cc_start: 0.8657 (mtp) cc_final: 0.7998 (mpp) REVERT: v 8 ILE cc_start: 0.8984 (tt) cc_final: 0.8662 (mt) REVERT: v 35 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: v 110 MET cc_start: 0.8631 (mmt) cc_final: 0.8058 (mmt) REVERT: w 93 LEU cc_start: 0.9253 (mt) cc_final: 0.9043 (mp) REVERT: x 33 LYS cc_start: 0.8974 (mtmm) cc_final: 0.7577 (mmtt) REVERT: x 58 ASN cc_start: 0.9054 (t0) cc_final: 0.8436 (t0) REVERT: x 115 MET cc_start: 0.8906 (mmm) cc_final: 0.8573 (mmm) REVERT: y 8 ILE cc_start: 0.8774 (tt) cc_final: 0.8454 (mt) REVERT: y 35 MET cc_start: 0.8789 (mtp) cc_final: 0.7915 (mpp) REVERT: y 113 GLU cc_start: 0.8135 (tp30) cc_final: 0.7748 (tp30) REVERT: z 69 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8298 (tt) outliers start: 200 outliers final: 168 residues processed: 1564 average time/residue: 0.6976 time to fit residues: 1901.4262 Evaluate side-chains 1619 residues out of total 7306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1425 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 120 ASN Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 163 SER Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 163 SER Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 133 SER Chi-restraints excluded: chain F residue 174 THR Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 68 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 88 ILE Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 174 THR Chi-restraints excluded: chain G residue 193 ILE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 120 ASN Chi-restraints excluded: chain H residue 191 GLU Chi-restraints excluded: chain I residue 68 SER Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 133 SER Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 163 SER Chi-restraints excluded: chain J residue 190 GLU Chi-restraints excluded: chain K residue 81 ILE Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 163 SER Chi-restraints excluded: chain K residue 174 THR Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain L residue 64 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain L residue 114 THR Chi-restraints excluded: chain L residue 116 THR Chi-restraints excluded: chain L residue 133 SER Chi-restraints excluded: chain L residue 174 THR Chi-restraints excluded: chain L residue 193 ILE Chi-restraints excluded: chain M residue 75 LEU Chi-restraints excluded: chain M residue 174 THR Chi-restraints excluded: chain N residue 68 SER Chi-restraints excluded: chain N residue 151 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 133 SER Chi-restraints excluded: chain O residue 163 SER Chi-restraints excluded: chain O residue 174 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain P residue 74 ASP Chi-restraints excluded: chain P residue 75 LEU Chi-restraints excluded: chain P residue 129 GLU Chi-restraints excluded: chain P residue 174 THR Chi-restraints excluded: chain P residue 192 ILE Chi-restraints excluded: chain P residue 193 ILE Chi-restraints excluded: chain Q residue 75 LEU Chi-restraints excluded: chain Q residue 174 THR Chi-restraints excluded: chain R residue 68 SER Chi-restraints excluded: chain R residue 88 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain S residue 75 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 133 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain S residue 192 ILE Chi-restraints excluded: chain T residue 75 LEU Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 152 GLU Chi-restraints excluded: chain T residue 174 THR Chi-restraints excluded: chain T residue 192 ILE Chi-restraints excluded: chain T residue 193 ILE Chi-restraints excluded: chain U residue 75 LEU Chi-restraints excluded: chain U residue 88 ILE Chi-restraints excluded: chain U residue 125 ARG Chi-restraints excluded: chain U residue 174 THR Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain V residue 71 SER Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 172 SER Chi-restraints excluded: chain V residue 174 THR Chi-restraints excluded: chain V residue 191 GLU Chi-restraints excluded: chain W residue 174 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 31 GLU Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 88 ILE Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 129 GLU Chi-restraints excluded: chain X residue 149 GLU Chi-restraints excluded: chain X residue 193 ILE Chi-restraints excluded: chain Y residue 75 LEU Chi-restraints excluded: chain Y residue 88 ILE Chi-restraints excluded: chain Y residue 120 ASN Chi-restraints excluded: chain Y residue 174 THR Chi-restraints excluded: chain Z residue 75 LEU Chi-restraints excluded: chain Z residue 96 SER Chi-restraints excluded: chain Z residue 172 SER Chi-restraints excluded: chain Z residue 174 THR Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 69 LEU Chi-restraints excluded: chain b residue 123 SER Chi-restraints excluded: chain b residue 124 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain c residue 62 VAL Chi-restraints excluded: chain c residue 123 SER Chi-restraints excluded: chain c residue 124 THR Chi-restraints excluded: chain d residue 65 ASN Chi-restraints excluded: chain d residue 125 THR Chi-restraints excluded: chain e residue 36 VAL Chi-restraints excluded: chain e residue 62 VAL Chi-restraints excluded: chain e residue 69 LEU Chi-restraints excluded: chain f residue 123 SER Chi-restraints excluded: chain g residue 69 LEU Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 124 THR Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 43 MET Chi-restraints excluded: chain j residue 82 ASN Chi-restraints excluded: chain j residue 125 THR Chi-restraints excluded: chain j residue 126 THR Chi-restraints excluded: chain k residue 43 MET Chi-restraints excluded: chain l residue 19 VAL Chi-restraints excluded: chain l residue 35 MET Chi-restraints excluded: chain l residue 36 VAL Chi-restraints excluded: chain l residue 43 MET Chi-restraints excluded: chain l residue 51 GLN Chi-restraints excluded: chain l residue 58 ASN Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain l residue 123 SER Chi-restraints excluded: chain l residue 125 THR Chi-restraints excluded: chain m residue 69 LEU Chi-restraints excluded: chain n residue 69 LEU Chi-restraints excluded: chain n residue 123 SER Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 123 SER Chi-restraints excluded: chain p residue 19 VAL Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain q residue 43 MET Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 36 VAL Chi-restraints excluded: chain s residue 123 SER Chi-restraints excluded: chain s residue 125 THR Chi-restraints excluded: chain s residue 130 ILE Chi-restraints excluded: chain t residue 51 GLN Chi-restraints excluded: chain u residue 69 LEU Chi-restraints excluded: chain u residue 88 GLU Chi-restraints excluded: chain v residue 14 ILE Chi-restraints excluded: chain v residue 35 MET Chi-restraints excluded: chain v residue 36 VAL Chi-restraints excluded: chain v residue 40 GLN Chi-restraints excluded: chain v residue 124 THR Chi-restraints excluded: chain v residue 126 THR Chi-restraints excluded: chain w residue 123 SER Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 126 THR Chi-restraints excluded: chain y residue 26 THR Chi-restraints excluded: chain y residue 62 VAL Chi-restraints excluded: chain y residue 125 THR Chi-restraints excluded: chain z residue 37 VAL Chi-restraints excluded: chain z residue 69 LEU Chi-restraints excluded: chain z residue 122 LYS Chi-restraints excluded: chain z residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 898 random chunks: chunk 436 optimal weight: 5.9990 chunk 565 optimal weight: 7.9990 chunk 758 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 656 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 713 optimal weight: 0.9980 chunk 298 optimal weight: 1.9990 chunk 732 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 136 ASN F 60 ASN H 60 ASN J 42 ASN L 60 ASN N 60 ASN ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 60 ASN ** X 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 ASN a 25 GLN ** b 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 65 ASN ** e 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 25 GLN ** j 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 25 GLN ** s 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.105782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.094287 restraints weight = 123640.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096361 restraints weight = 69914.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.097693 restraints weight = 47235.348| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.167 82872 Z= 0.274 Angle : 0.685 55.156 115264 Z= 0.388 Chirality : 0.042 0.233 13114 Planarity : 0.003 0.063 12372 Dihedral : 16.886 75.919 17200 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.54 % Favored : 92.44 % Rotamer: Outliers : 2.74 % Allowed : 20.16 % Favored : 77.09 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.09), residues: 8346 helix: 0.67 (0.07), residues: 5668 sheet: -0.09 (0.30), residues: 312 loop : -2.30 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 142 HIS 0.005 0.002 HIS L 48 PHE 0.020 0.002 PHE D 54 TYR 0.022 0.001 TYR X 18 ARG 0.017 0.000 ARG N 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26127.58 seconds wall clock time: 454 minutes 25.03 seconds (27265.03 seconds total)