Starting phenix.real_space_refine on Mon Nov 18 07:55:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8szz_40926/11_2024/8szz_40926.cif" } resolution = 2.9 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= 0.057 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 S 288 5.16 5 Na 24 4.78 5 C 31656 2.51 5 N 8064 2.21 5 O 8783 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 190 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 48815 Number of models: 1 Model: "" Number of chains: 72 Chain: "0" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "1" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "2" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "3" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "R" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "S" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "T" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "U" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "W" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "X" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "Y" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: "a" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1509 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "d" Number of atoms: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 1510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1510 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 190} 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: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "p" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "q" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "r" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "s" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "t" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "u" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "v" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "w" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "x" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "y" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "z" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 523 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 68} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2652 SG CYS I 74 122.092 64.233 34.764 1.00 35.10 S ATOM 4162 SG CYS J 74 133.241 64.199 122.132 1.00 34.89 S ATOM 5672 SG CYS K 74 103.423 133.304 121.728 1.00 36.42 S ATOM 7182 SG CYS L 74 34.889 45.979 103.692 1.00 35.71 S ATOM 8692 SG CYS M 74 122.017 133.163 64.334 1.00 35.21 S ATOM 10202 SG CYS N 74 45.960 103.640 34.826 1.00 34.11 S ATOM 11712 SG CYS O 74 45.948 133.090 103.723 1.00 34.49 S ATOM 18916 SG CYS Y 74 133.196 45.859 64.127 1.00 35.68 S ATOM 20426 SG CYS Z 74 104.008 45.793 133.201 1.00 34.84 S ATOM 21936 SG CYS a 74 122.208 103.895 133.266 1.00 34.95 S ATOM 23446 SG CYS b 74 64.079 34.691 122.107 1.00 34.38 S ATOM 24956 SG CYS c 74 133.276 103.884 45.801 1.00 34.71 S ATOM 26465 SG CYS d 74 34.641 122.170 64.099 1.00 36.22 S ATOM 27975 SG CYS e 74 34.637 103.894 122.191 1.00 34.76 S ATOM 29485 SG CYS f 74 103.978 34.790 45.861 1.00 34.48 S ATOM 30995 SG CYS g 74 122.136 34.764 103.820 1.00 35.26 S ATOM 32505 SG CYS h 74 133.206 122.123 103.829 1.00 35.74 S ATOM 34015 SG CYS i 74 45.872 64.091 133.273 1.00 34.53 S ATOM 35525 SG CYS j 74 103.882 122.080 34.829 1.00 35.52 S ATOM 37035 SG CYS k 74 64.044 133.193 45.856 1.00 36.07 S ATOM 38545 SG CYS l 74 64.215 122.153 133.316 1.00 35.51 S ATOM 40055 SG CYS m 74 45.786 34.803 64.128 1.00 34.40 S ATOM 41565 SG CYS n 74 34.761 64.278 45.895 1.00 35.90 S Time building chain proxies: 27.83, per 1000 atoms: 0.57 Number of scatterers: 48815 At special positions: 0 Unit cell: (169.68, 168.84, 169.68, 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 288 16.00 Na 24 11.00 O 8783 8.00 N 8064 7.00 C 31656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS I 163 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 163 " - pdb=" SG CYS J 201 " distance=2.01 Simple disulfide: pdb=" SG CYS K 163 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 163 " - pdb=" SG CYS L 201 " distance=2.02 Simple disulfide: pdb=" SG CYS M 163 " - pdb=" SG CYS M 201 " distance=2.04 Simple disulfide: pdb=" SG CYS N 163 " - pdb=" SG CYS N 201 " distance=2.03 Simple disulfide: pdb=" SG CYS O 163 " - pdb=" SG CYS O 201 " distance=2.03 Simple disulfide: pdb=" SG CYS U 163 " - pdb=" SG CYS U 201 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 163 " - pdb=" SG CYS Y 201 " distance=2.02 Simple disulfide: pdb=" SG CYS Z 163 " - pdb=" SG CYS Z 201 " distance=2.03 Simple disulfide: pdb=" SG CYS a 163 " - pdb=" SG CYS a 201 " distance=2.04 Simple disulfide: pdb=" SG CYS b 163 " - pdb=" SG CYS b 201 " distance=2.03 Simple disulfide: pdb=" SG CYS c 163 " - pdb=" SG CYS c 201 " distance=2.03 Simple disulfide: pdb=" SG CYS d 163 " - pdb=" SG CYS d 201 " distance=2.03 Simple disulfide: pdb=" SG CYS e 163 " - pdb=" SG CYS e 201 " distance=2.03 Simple disulfide: pdb=" SG CYS f 163 " - pdb=" SG CYS f 201 " distance=2.02 Simple disulfide: pdb=" SG CYS g 163 " - pdb=" SG CYS g 201 " distance=2.03 Simple disulfide: pdb=" SG CYS h 163 " - pdb=" SG CYS h 201 " distance=2.02 Simple disulfide: pdb=" SG CYS i 163 " - pdb=" SG CYS i 201 " distance=2.02 Simple disulfide: pdb=" SG CYS j 163 " - pdb=" SG CYS j 201 " distance=2.02 Simple disulfide: pdb=" SG CYS k 163 " - pdb=" SG CYS k 201 " distance=2.02 Simple disulfide: pdb=" SG CYS l 163 " - pdb=" SG CYS l 201 " distance=2.02 Simple disulfide: pdb=" SG CYS m 163 " - pdb=" SG CYS m 201 " distance=2.03 Simple disulfide: pdb=" SG CYS n 163 " - pdb=" SG CYS n 201 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.42 Conformation dependent library (CDL) restraints added in 6.1 seconds 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12096 Finding SS restraints... Secondary structure from input PDB file: 329 helices and 71 sheets defined 67.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain '0' and resid 1 through 35 Processing helix chain '0' and resid 37 through 70 removed outlier: 3.519A pdb=" N LEU 0 41 " --> pdb=" O SER 0 37 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU 0 64 " --> pdb=" O ARG 0 60 " (cutoff:3.500A) Processing helix chain '1' and resid 2 through 35 Processing helix chain '1' and resid 37 through 70 removed outlier: 3.518A pdb=" N LEU 1 41 " --> pdb=" O SER 1 37 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU 1 64 " --> pdb=" O ARG 1 60 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS 1 70 " --> pdb=" O LEU 1 66 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 35 Processing helix chain '2' and resid 37 through 70 removed outlier: 3.595A pdb=" N LEU 2 41 " --> pdb=" O SER 2 37 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU 2 64 " --> pdb=" O ARG 2 60 " (cutoff:3.500A) Processing helix chain '3' and resid 2 through 35 Processing helix chain '3' and resid 37 through 70 removed outlier: 3.568A pdb=" N LEU 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU 3 64 " --> pdb=" O ARG 3 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 9 Processing helix chain 'I' and resid 18 through 33 removed outlier: 3.505A pdb=" N GLY I 33 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 53 Processing helix chain 'I' and resid 53 through 60 removed outlier: 3.667A pdb=" N LYS I 57 " --> pdb=" O LEU I 53 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU I 58 " --> pdb=" O SER I 54 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS I 59 " --> pdb=" O PHE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 81 Processing helix chain 'I' and resid 91 through 100 removed outlier: 3.658A pdb=" N GLU I 100 " --> pdb=" O GLN I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 Processing helix chain 'I' and resid 130 through 135 removed outlier: 3.716A pdb=" N VAL I 134 " --> pdb=" O PRO I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 144 removed outlier: 4.033A pdb=" N VAL I 139 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLY I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 168 Processing helix chain 'I' and resid 176 through 181 removed outlier: 3.743A pdb=" N LYS I 181 " --> pdb=" O SER I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'J' and resid 2 through 9 Processing helix chain 'J' and resid 18 through 32 Processing helix chain 'J' and resid 45 through 53 Processing helix chain 'J' and resid 53 through 60 removed outlier: 3.843A pdb=" N LYS J 57 " --> pdb=" O LEU J 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU J 58 " --> pdb=" O SER J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 80 Processing helix chain 'J' and resid 91 through 102 removed outlier: 3.763A pdb=" N GLU J 100 " --> pdb=" O GLN J 96 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS J 101 " --> pdb=" O PHE J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 121 Processing helix chain 'J' and resid 130 through 135 removed outlier: 3.752A pdb=" N VAL J 134 " --> pdb=" O PRO J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 135 through 143 removed outlier: 3.945A pdb=" N VAL J 139 " --> pdb=" O GLY J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 169 Processing helix chain 'J' and resid 185 through 201 removed outlier: 3.732A pdb=" N GLU J 189 " --> pdb=" O ASP J 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 18 through 33 removed outlier: 3.583A pdb=" N ALA K 22 " --> pdb=" O ASP K 18 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 53 Processing helix chain 'K' and resid 54 through 60 removed outlier: 4.175A pdb=" N GLU K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS K 59 " --> pdb=" O PHE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 81 Processing helix chain 'K' and resid 91 through 102 Processing helix chain 'K' and resid 111 through 121 Processing helix chain 'K' and resid 130 through 135 removed outlier: 3.700A pdb=" N VAL K 134 " --> pdb=" O PRO K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 143 removed outlier: 4.109A pdb=" N VAL K 139 " --> pdb=" O GLY K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 161 through 169 Processing helix chain 'K' and resid 185 through 201 Processing helix chain 'L' and resid 2 through 9 Processing helix chain 'L' and resid 18 through 33 removed outlier: 3.526A pdb=" N ALA L 22 " --> pdb=" O ASP L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 53 Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.685A pdb=" N LYS L 59 " --> pdb=" O PHE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 80 Processing helix chain 'L' and resid 91 through 102 removed outlier: 3.740A pdb=" N GLU L 100 " --> pdb=" O GLN L 96 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS L 101 " --> pdb=" O PHE L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 121 Processing helix chain 'L' and resid 130 through 135 removed outlier: 3.653A pdb=" N VAL L 134 " --> pdb=" O PRO L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 143 removed outlier: 3.896A pdb=" N VAL L 139 " --> pdb=" O GLY L 135 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS L 143 " --> pdb=" O VAL L 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 169 Processing helix chain 'L' and resid 185 through 201 removed outlier: 3.502A pdb=" N GLU L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 9 Processing helix chain 'M' and resid 18 through 33 removed outlier: 3.589A pdb=" N ALA M 22 " --> pdb=" O ASP M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 53 Processing helix chain 'M' and resid 53 through 60 removed outlier: 3.845A pdb=" N LYS M 57 " --> pdb=" O LEU M 53 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU M 58 " --> pdb=" O SER M 54 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS M 59 " --> pdb=" O PHE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 80 Processing helix chain 'M' and resid 91 through 100 removed outlier: 3.758A pdb=" N GLU M 100 " --> pdb=" O GLN M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 121 Processing helix chain 'M' and resid 130 through 142 removed outlier: 3.700A pdb=" N VAL M 134 " --> pdb=" O PRO M 130 " (cutoff:3.500A) Proline residue: M 136 - end of helix removed outlier: 4.027A pdb=" N VAL M 139 " --> pdb=" O GLY M 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 Processing helix chain 'M' and resid 176 through 181 removed outlier: 3.587A pdb=" N LYS M 181 " --> pdb=" O SER M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 201 removed outlier: 3.511A pdb=" N ARG M 188 " --> pdb=" O PRO M 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 9 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 45 through 53 Processing helix chain 'N' and resid 70 through 80 Processing helix chain 'N' and resid 91 through 100 removed outlier: 4.025A pdb=" N GLU N 100 " --> pdb=" O GLN N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 120 Processing helix chain 'N' and resid 130 through 135 removed outlier: 3.759A pdb=" N VAL N 134 " --> pdb=" O PRO N 130 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 144 removed outlier: 4.035A pdb=" N VAL N 139 " --> pdb=" O GLY N 135 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 161 through 169 Processing helix chain 'N' and resid 176 through 181 removed outlier: 3.607A pdb=" N LYS N 181 " --> pdb=" O SER N 177 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 201 Processing helix chain 'O' and resid 2 through 9 Processing helix chain 'O' and resid 18 through 33 removed outlier: 3.626A pdb=" N ALA O 22 " --> pdb=" O ASP O 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 52 Processing helix chain 'O' and resid 53 through 60 removed outlier: 3.564A pdb=" N LYS O 59 " --> pdb=" O PHE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 80 Processing helix chain 'O' and resid 91 through 102 removed outlier: 3.772A pdb=" N GLU O 100 " --> pdb=" O GLN O 96 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS O 101 " --> pdb=" O PHE O 97 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 120 Processing helix chain 'O' and resid 130 through 135 removed outlier: 3.651A pdb=" N VAL O 134 " --> pdb=" O PRO O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 135 through 144 removed outlier: 3.946A pdb=" N VAL O 139 " --> pdb=" O GLY O 135 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLY O 144 " --> pdb=" O LYS O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 161 through 169 Processing helix chain 'O' and resid 176 through 181 removed outlier: 3.547A pdb=" N LYS O 181 " --> pdb=" O SER O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 185 through 201 Processing helix chain 'P' and resid 2 through 35 Processing helix chain 'P' and resid 37 through 70 Processing helix chain 'Q' and resid 2 through 35 removed outlier: 3.787A pdb=" N LYS Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 70 Processing helix chain 'R' and resid 2 through 35 removed outlier: 3.885A pdb=" N LYS R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 70 removed outlier: 3.530A pdb=" N LEU R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 35 Processing helix chain 'S' and resid 37 through 70 Processing helix chain 'T' and resid 2 through 35 removed outlier: 3.840A pdb=" N LYS T 34 " --> pdb=" O LYS T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 70 Processing helix chain 'U' and resid 2 through 9 Processing helix chain 'U' and resid 18 through 33 removed outlier: 3.505A pdb=" N GLY U 33 " --> pdb=" O VAL U 29 " (cutoff:3.500A) Processing helix chain 'U' and resid 45 through 53 Processing helix chain 'U' and resid 55 through 60 removed outlier: 3.832A pdb=" N LYS U 59 " --> pdb=" O PHE U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 70 through 80 Processing helix chain 'U' and resid 91 through 102 Processing helix chain 'U' and resid 111 through 121 Processing helix chain 'U' and resid 130 through 135 removed outlier: 3.731A pdb=" N VAL U 134 " --> pdb=" O PRO U 130 " (cutoff:3.500A) Processing helix chain 'U' and resid 135 through 143 removed outlier: 3.917A pdb=" N VAL U 139 " --> pdb=" O GLY U 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 158 through 169 removed outlier: 4.644A pdb=" N CYS U 163 " --> pdb=" O LEU U 159 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU U 164 " --> pdb=" O ASP U 160 " (cutoff:3.500A) Processing helix chain 'U' and resid 176 through 181 removed outlier: 3.764A pdb=" N LYS U 181 " --> pdb=" O SER U 177 " (cutoff:3.500A) Processing helix chain 'U' and resid 185 through 201 removed outlier: 3.561A pdb=" N GLU U 189 " --> pdb=" O ASP U 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 35 removed outlier: 3.882A pdb=" N LYS V 34 " --> pdb=" O LYS V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 70 Processing helix chain 'W' and resid 2 through 35 removed outlier: 3.822A pdb=" N LYS W 34 " --> pdb=" O LYS W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 70 removed outlier: 3.831A pdb=" N LYS W 70 " --> pdb=" O LEU W 66 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 35 removed outlier: 3.730A pdb=" N LYS X 34 " --> pdb=" O LYS X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 70 Processing helix chain 'Y' and resid 2 through 9 Processing helix chain 'Y' and resid 18 through 32 Processing helix chain 'Y' and resid 45 through 52 Processing helix chain 'Y' and resid 53 through 60 Processing helix chain 'Y' and resid 70 through 81 removed outlier: 3.546A pdb=" N CYS Y 74 " --> pdb=" O SER Y 70 " (cutoff:3.500A) Processing helix chain 'Y' and resid 91 through 97 Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'Y' and resid 130 through 142 removed outlier: 3.723A pdb=" N VAL Y 134 " --> pdb=" O PRO Y 130 " (cutoff:3.500A) Proline residue: Y 136 - end of helix removed outlier: 4.042A pdb=" N VAL Y 139 " --> pdb=" O GLY Y 135 " (cutoff:3.500A) Processing helix chain 'Y' and resid 161 through 169 Processing helix chain 'Y' and resid 176 through 181 removed outlier: 3.521A pdb=" N LYS Y 181 " --> pdb=" O SER Y 177 " (cutoff:3.500A) Processing helix chain 'Y' and resid 185 through 201 removed outlier: 3.610A pdb=" N GLU Y 189 " --> pdb=" O ASP Y 185 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS Y 192 " --> pdb=" O ARG Y 188 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG Y 199 " --> pdb=" O VAL Y 195 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 9 Processing helix chain 'Z' and resid 18 through 33 Processing helix chain 'Z' and resid 45 through 53 Processing helix chain 'Z' and resid 55 through 60 Processing helix chain 'Z' and resid 70 through 81 removed outlier: 3.526A pdb=" N CYS Z 74 " --> pdb=" O SER Z 70 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 102 removed outlier: 3.759A pdb=" N GLU Z 100 " --> pdb=" O GLN Z 96 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS Z 101 " --> pdb=" O PHE Z 97 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 121 Processing helix chain 'Z' and resid 130 through 135 removed outlier: 3.647A pdb=" N VAL Z 134 " --> pdb=" O PRO Z 130 " (cutoff:3.500A) Processing helix chain 'Z' and resid 135 through 142 removed outlier: 3.916A pdb=" N VAL Z 139 " --> pdb=" O GLY Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 168 removed outlier: 3.544A pdb=" N TRP Z 165 " --> pdb=" O ASN Z 161 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE Z 166 " --> pdb=" O VAL Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 183 through 201 Processing helix chain 'a' and resid 2 through 9 Processing helix chain 'a' and resid 18 through 31 Processing helix chain 'a' and resid 45 through 52 Processing helix chain 'a' and resid 53 through 59 Processing helix chain 'a' and resid 71 through 81 Processing helix chain 'a' and resid 91 through 100 removed outlier: 3.725A pdb=" N CYS a 98 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 120 Processing helix chain 'a' and resid 130 through 135 removed outlier: 3.602A pdb=" N VAL a 134 " --> pdb=" O PRO a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 136 through 141 Processing helix chain 'a' and resid 161 through 169 Processing helix chain 'a' and resid 176 through 181 removed outlier: 3.852A pdb=" N LYS a 181 " --> pdb=" O SER a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 199 removed outlier: 3.541A pdb=" N LYS a 192 " --> pdb=" O ARG a 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 9 Processing helix chain 'b' and resid 18 through 33 Processing helix chain 'b' and resid 45 through 53 Processing helix chain 'b' and resid 55 through 60 removed outlier: 3.811A pdb=" N LYS b 59 " --> pdb=" O PHE b 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 70 through 80 Processing helix chain 'b' and resid 91 through 99 Processing helix chain 'b' and resid 111 through 121 Processing helix chain 'b' and resid 130 through 135 removed outlier: 3.816A pdb=" N VAL b 134 " --> pdb=" O PRO b 130 " (cutoff:3.500A) Processing helix chain 'b' and resid 135 through 143 removed outlier: 3.935A pdb=" N VAL b 139 " --> pdb=" O GLY b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 168 Processing helix chain 'b' and resid 176 through 181 Processing helix chain 'b' and resid 183 through 201 Processing helix chain 'c' and resid 2 through 9 Processing helix chain 'c' and resid 18 through 31 Processing helix chain 'c' and resid 45 through 52 Processing helix chain 'c' and resid 53 through 60 Processing helix chain 'c' and resid 70 through 81 removed outlier: 3.532A pdb=" N CYS c 74 " --> pdb=" O SER c 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 100 removed outlier: 3.878A pdb=" N CYS c 98 " --> pdb=" O ILE c 94 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU c 100 " --> pdb=" O GLN c 96 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 120 Processing helix chain 'c' and resid 130 through 135 removed outlier: 3.739A pdb=" N VAL c 134 " --> pdb=" O PRO c 130 " (cutoff:3.500A) Processing helix chain 'c' and resid 135 through 142 removed outlier: 3.994A pdb=" N VAL c 139 " --> pdb=" O GLY c 135 " (cutoff:3.500A) Processing helix chain 'c' and resid 161 through 169 removed outlier: 3.594A pdb=" N TRP c 165 " --> pdb=" O ASN c 161 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 181 removed outlier: 3.909A pdb=" N LYS c 181 " --> pdb=" O SER c 177 " (cutoff:3.500A) Processing helix chain 'c' and resid 185 through 199 removed outlier: 3.536A pdb=" N GLU c 189 " --> pdb=" O ASP c 185 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS c 192 " --> pdb=" O ARG c 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 9 Processing helix chain 'd' and resid 18 through 33 removed outlier: 3.503A pdb=" N ALA d 22 " --> pdb=" O ASP d 18 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 52 removed outlier: 3.567A pdb=" N VAL d 49 " --> pdb=" O ASN d 45 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 60 removed outlier: 3.849A pdb=" N GLU d 58 " --> pdb=" O SER d 54 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS d 59 " --> pdb=" O PHE d 55 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 81 removed outlier: 3.580A pdb=" N CYS d 74 " --> pdb=" O SER d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 100 removed outlier: 4.119A pdb=" N CYS d 98 " --> pdb=" O ILE d 94 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU d 100 " --> pdb=" O GLN d 96 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 121 Processing helix chain 'd' and resid 130 through 135 removed outlier: 3.608A pdb=" N VAL d 134 " --> pdb=" O PRO d 130 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 141 removed outlier: 3.976A pdb=" N VAL d 139 " --> pdb=" O GLY d 135 " (cutoff:3.500A) Processing helix chain 'd' and resid 161 through 168 Processing helix chain 'd' and resid 176 through 181 Processing helix chain 'd' and resid 185 through 199 removed outlier: 3.513A pdb=" N GLU d 189 " --> pdb=" O ASP d 185 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG d 199 " --> pdb=" O VAL d 195 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 9 Processing helix chain 'e' and resid 18 through 31 Processing helix chain 'e' and resid 45 through 53 Processing helix chain 'e' and resid 53 through 58 Processing helix chain 'e' and resid 70 through 81 removed outlier: 3.566A pdb=" N CYS e 74 " --> pdb=" O SER e 70 " (cutoff:3.500A) Processing helix chain 'e' and resid 92 through 97 Processing helix chain 'e' and resid 111 through 120 Processing helix chain 'e' and resid 130 through 135 removed outlier: 3.746A pdb=" N VAL e 134 " --> pdb=" O PRO e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 135 through 143 removed outlier: 4.343A pdb=" N VAL e 139 " --> pdb=" O GLY e 135 " (cutoff:3.500A) Processing helix chain 'e' and resid 161 through 168 Processing helix chain 'e' and resid 176 through 181 removed outlier: 3.757A pdb=" N LYS e 181 " --> pdb=" O SER e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 185 through 199 removed outlier: 3.514A pdb=" N LYS e 192 " --> pdb=" O ARG e 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 9 Processing helix chain 'f' and resid 18 through 33 Processing helix chain 'f' and resid 45 through 53 Processing helix chain 'f' and resid 53 through 60 Processing helix chain 'f' and resid 70 through 81 Processing helix chain 'f' and resid 91 through 101 removed outlier: 3.849A pdb=" N GLU f 100 " --> pdb=" O GLN f 96 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS f 101 " --> pdb=" O PHE f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 111 through 122 Processing helix chain 'f' and resid 130 through 135 removed outlier: 3.761A pdb=" N VAL f 134 " --> pdb=" O PRO f 130 " (cutoff:3.500A) Processing helix chain 'f' and resid 135 through 142 removed outlier: 4.023A pdb=" N VAL f 139 " --> pdb=" O GLY f 135 " (cutoff:3.500A) Processing helix chain 'f' and resid 161 through 169 Processing helix chain 'f' and resid 176 through 181 Processing helix chain 'f' and resid 185 through 201 Processing helix chain 'g' and resid 2 through 9 Processing helix chain 'g' and resid 18 through 33 Processing helix chain 'g' and resid 45 through 52 Processing helix chain 'g' and resid 55 through 60 removed outlier: 3.737A pdb=" N LYS g 59 " --> pdb=" O PHE g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 70 through 80 Processing helix chain 'g' and resid 91 through 101 Processing helix chain 'g' and resid 111 through 120 Processing helix chain 'g' and resid 130 through 135 removed outlier: 3.674A pdb=" N VAL g 134 " --> pdb=" O PRO g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 135 through 142 removed outlier: 3.973A pdb=" N VAL g 139 " --> pdb=" O GLY g 135 " (cutoff:3.500A) Processing helix chain 'g' and resid 161 through 169 Processing helix chain 'g' and resid 185 through 201 Processing helix chain 'h' and resid 2 through 9 Processing helix chain 'h' and resid 18 through 33 Processing helix chain 'h' and resid 45 through 53 removed outlier: 3.552A pdb=" N VAL h 49 " --> pdb=" O ASN h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 53 through 60 Processing helix chain 'h' and resid 70 through 81 Processing helix chain 'h' and resid 91 through 101 removed outlier: 3.942A pdb=" N GLU h 100 " --> pdb=" O GLN h 96 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS h 101 " --> pdb=" O PHE h 97 " (cutoff:3.500A) Processing helix chain 'h' and resid 111 through 122 Processing helix chain 'h' and resid 130 through 135 removed outlier: 3.714A pdb=" N VAL h 134 " --> pdb=" O PRO h 130 " (cutoff:3.500A) Processing helix chain 'h' and resid 135 through 142 removed outlier: 3.895A pdb=" N VAL h 139 " --> pdb=" O GLY h 135 " (cutoff:3.500A) Processing helix chain 'h' and resid 161 through 169 Processing helix chain 'h' and resid 176 through 181 removed outlier: 3.523A pdb=" N LYS h 181 " --> pdb=" O SER h 177 " (cutoff:3.500A) Processing helix chain 'h' and resid 185 through 201 Processing helix chain 'i' and resid 2 through 9 Processing helix chain 'i' and resid 18 through 31 removed outlier: 3.602A pdb=" N ALA i 22 " --> pdb=" O ASP i 18 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 52 Processing helix chain 'i' and resid 70 through 81 Processing helix chain 'i' and resid 91 through 100 removed outlier: 3.592A pdb=" N CYS i 98 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU i 100 " --> pdb=" O GLN i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 120 Processing helix chain 'i' and resid 130 through 135 removed outlier: 3.733A pdb=" N VAL i 134 " --> pdb=" O PRO i 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 136 through 141 Processing helix chain 'i' and resid 161 through 169 Processing helix chain 'i' and resid 176 through 181 Processing helix chain 'i' and resid 185 through 199 removed outlier: 3.739A pdb=" N GLU i 189 " --> pdb=" O ASP i 185 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 9 Processing helix chain 'j' and resid 18 through 32 Processing helix chain 'j' and resid 45 through 53 removed outlier: 3.519A pdb=" N VAL j 49 " --> pdb=" O ASN j 45 " (cutoff:3.500A) Processing helix chain 'j' and resid 53 through 58 Processing helix chain 'j' and resid 70 through 80 Processing helix chain 'j' and resid 91 through 101 removed outlier: 3.952A pdb=" N GLU j 100 " --> pdb=" O GLN j 96 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS j 101 " --> pdb=" O PHE j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 111 through 121 Processing helix chain 'j' and resid 130 through 135 removed outlier: 3.695A pdb=" N VAL j 134 " --> pdb=" O PRO j 130 " (cutoff:3.500A) Processing helix chain 'j' and resid 135 through 144 removed outlier: 4.002A pdb=" N VAL j 139 " --> pdb=" O GLY j 135 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY j 144 " --> pdb=" O LYS j 140 " (cutoff:3.500A) Processing helix chain 'j' and resid 161 through 168 Processing helix chain 'j' and resid 176 through 181 removed outlier: 3.570A pdb=" N LYS j 181 " --> pdb=" O SER j 177 " (cutoff:3.500A) Processing helix chain 'j' and resid 185 through 201 Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'k' and resid 18 through 31 Processing helix chain 'k' and resid 45 through 53 removed outlier: 3.503A pdb=" N VAL k 49 " --> pdb=" O ASN k 45 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 60 removed outlier: 3.835A pdb=" N LYS k 57 " --> pdb=" O LEU k 53 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS k 59 " --> pdb=" O PHE k 55 " (cutoff:3.500A) Processing helix chain 'k' and resid 70 through 81 Processing helix chain 'k' and resid 91 through 100 removed outlier: 3.598A pdb=" N LYS k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU k 100 " --> pdb=" O GLN k 96 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 120 Processing helix chain 'k' and resid 130 through 135 removed outlier: 3.742A pdb=" N VAL k 134 " --> pdb=" O PRO k 130 " (cutoff:3.500A) Processing helix chain 'k' and resid 135 through 144 removed outlier: 4.145A pdb=" N VAL k 139 " --> pdb=" O GLY k 135 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLY k 144 " --> pdb=" O LYS k 140 " (cutoff:3.500A) Processing helix chain 'k' and resid 161 through 167 removed outlier: 3.600A pdb=" N TRP k 165 " --> pdb=" O ASN k 161 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE k 166 " --> pdb=" O VAL k 162 " (cutoff:3.500A) Processing helix chain 'k' and resid 176 through 181 removed outlier: 3.606A pdb=" N LYS k 181 " --> pdb=" O SER k 177 " (cutoff:3.500A) Processing helix chain 'k' and resid 185 through 199 removed outlier: 3.522A pdb=" N GLU k 189 " --> pdb=" O ASP k 185 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG k 199 " --> pdb=" O VAL k 195 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 9 Processing helix chain 'l' and resid 18 through 31 removed outlier: 3.621A pdb=" N PHE l 30 " --> pdb=" O ALA l 26 " (cutoff:3.500A) Processing helix chain 'l' and resid 45 through 52 Processing helix chain 'l' and resid 53 through 59 Processing helix chain 'l' and resid 71 through 80 Processing helix chain 'l' and resid 91 through 99 Processing helix chain 'l' and resid 111 through 121 Processing helix chain 'l' and resid 130 through 135 removed outlier: 3.785A pdb=" N VAL l 134 " --> pdb=" O PRO l 130 " (cutoff:3.500A) Processing helix chain 'l' and resid 135 through 141 removed outlier: 4.047A pdb=" N VAL l 139 " --> pdb=" O GLY l 135 " (cutoff:3.500A) Processing helix chain 'l' and resid 161 through 169 Processing helix chain 'l' and resid 176 through 181 removed outlier: 3.611A pdb=" N LYS l 181 " --> pdb=" O SER l 177 " (cutoff:3.500A) Processing helix chain 'l' and resid 185 through 199 removed outlier: 3.536A pdb=" N GLU l 189 " --> pdb=" O ASP l 185 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG l 199 " --> pdb=" O VAL l 195 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 9 Processing helix chain 'm' and resid 19 through 33 Processing helix chain 'm' and resid 45 through 53 removed outlier: 3.568A pdb=" N VAL m 49 " --> pdb=" O ASN m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 53 through 58 removed outlier: 3.580A pdb=" N LYS m 57 " --> pdb=" O LEU m 53 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU m 58 " --> pdb=" O SER m 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 53 through 58' Processing helix chain 'm' and resid 70 through 81 removed outlier: 3.583A pdb=" N CYS m 74 " --> pdb=" O SER m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 91 through 100 removed outlier: 3.701A pdb=" N CYS m 98 " --> pdb=" O ILE m 94 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU m 100 " --> pdb=" O GLN m 96 " (cutoff:3.500A) Processing helix chain 'm' and resid 111 through 120 Processing helix chain 'm' and resid 130 through 135 removed outlier: 3.609A pdb=" N VAL m 134 " --> pdb=" O PRO m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 143 Processing helix chain 'm' and resid 161 through 169 Processing helix chain 'm' and resid 176 through 181 removed outlier: 3.721A pdb=" N LYS m 181 " --> pdb=" O SER m 177 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 201 removed outlier: 3.554A pdb=" N LYS m 192 " --> pdb=" O ARG m 188 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 9 Processing helix chain 'n' and resid 18 through 33 removed outlier: 3.508A pdb=" N ALA n 22 " --> pdb=" O ASP n 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG n 23 " --> pdb=" O ALA n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 45 through 53 Processing helix chain 'n' and resid 54 through 57 Processing helix chain 'n' and resid 71 through 81 Processing helix chain 'n' and resid 92 through 100 removed outlier: 3.818A pdb=" N CYS n 98 " --> pdb=" O ILE n 94 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU n 100 " --> pdb=" O GLN n 96 " (cutoff:3.500A) Processing helix chain 'n' and resid 111 through 121 Processing helix chain 'n' and resid 130 through 135 removed outlier: 3.879A pdb=" N VAL n 134 " --> pdb=" O PRO n 130 " (cutoff:3.500A) Processing helix chain 'n' and resid 136 through 141 Processing helix chain 'n' and resid 161 through 168 Processing helix chain 'n' and resid 176 through 181 removed outlier: 3.526A pdb=" N LYS n 181 " --> pdb=" O SER n 177 " (cutoff:3.500A) Processing helix chain 'n' and resid 185 through 199 removed outlier: 3.516A pdb=" N GLU n 189 " --> pdb=" O ASP n 185 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG n 199 " --> pdb=" O VAL n 195 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 9 removed outlier: 3.506A pdb=" N LYS o 9 " --> pdb=" O LEU o 5 " (cutoff:3.500A) Processing helix chain 'o' and resid 9 through 35 Processing helix chain 'o' and resid 37 through 70 Processing helix chain 'p' and resid 2 through 9 removed outlier: 3.927A pdb=" N LEU p 7 " --> pdb=" O GLU p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 35 removed outlier: 3.709A pdb=" N GLU p 13 " --> pdb=" O LYS p 9 " (cutoff:3.500A) Processing helix chain 'p' and resid 37 through 70 removed outlier: 3.616A pdb=" N LEU p 41 " --> pdb=" O SER p 37 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 35 removed outlier: 3.924A pdb=" N ARG q 6 " --> pdb=" O ASP q 2 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU q 7 " --> pdb=" O GLU q 3 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA q 12 " --> pdb=" O ALA q 8 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU q 13 " --> pdb=" O LYS q 9 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU q 14 " --> pdb=" O GLU q 10 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 70 Processing helix chain 'r' and resid 2 through 35 removed outlier: 4.299A pdb=" N ALA r 12 " --> pdb=" O ALA r 8 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU r 13 " --> pdb=" O LYS r 9 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU r 14 " --> pdb=" O GLU r 10 " (cutoff:3.500A) Processing helix chain 'r' and resid 37 through 70 removed outlier: 3.592A pdb=" N LEU r 41 " --> pdb=" O SER r 37 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 35 Processing helix chain 's' and resid 37 through 70 removed outlier: 3.622A pdb=" N GLU s 64 " --> pdb=" O ARG s 60 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 35 removed outlier: 3.916A pdb=" N LEU t 7 " --> pdb=" O GLU t 3 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA t 12 " --> pdb=" O ALA t 8 " (cutoff:3.500A) Processing helix chain 't' and resid 37 through 70 removed outlier: 3.574A pdb=" N LEU t 41 " --> pdb=" O SER t 37 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 35 removed outlier: 3.783A pdb=" N LEU u 7 " --> pdb=" O GLU u 3 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA u 12 " --> pdb=" O ALA u 8 " (cutoff:3.500A) Processing helix chain 'u' and resid 37 through 70 removed outlier: 3.558A pdb=" N LEU u 41 " --> pdb=" O SER u 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 35 Processing helix chain 'v' and resid 37 through 70 removed outlier: 3.694A pdb=" N LEU v 41 " --> pdb=" O SER v 37 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 35 removed outlier: 4.037A pdb=" N ALA w 12 " --> pdb=" O ALA w 8 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU w 13 " --> pdb=" O LYS w 9 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU w 14 " --> pdb=" O GLU w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 37 through 70 Processing helix chain 'x' and resid 2 through 35 Processing helix chain 'x' and resid 37 through 70 removed outlier: 3.549A pdb=" N LEU x 41 " --> pdb=" O SER x 37 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU x 64 " --> pdb=" O ARG x 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 35 Processing helix chain 'y' and resid 37 through 70 removed outlier: 3.739A pdb=" N LEU y 41 " --> pdb=" O SER y 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU y 64 " --> pdb=" O ARG y 60 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS y 70 " --> pdb=" O LEU y 66 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 35 Processing helix chain 'z' and resid 37 through 70 removed outlier: 3.563A pdb=" N LEU z 41 " --> pdb=" O SER z 37 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU z 64 " --> pdb=" O ARG z 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 62 through 66 removed outlier: 4.405A pdb=" N LEU I 36 " --> pdb=" O ILE I 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 84 through 86 Processing sheet with id=AA3, first strand: chain 'I' and resid 108 through 109 Processing sheet with id=AA4, first strand: chain 'J' and resid 62 through 66 removed outlier: 6.507A pdb=" N ILE J 10 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLU J 38 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA J 12 " --> pdb=" O GLU J 38 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR J 40 " --> pdb=" O ALA J 12 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU J 14 " --> pdb=" O THR J 40 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL J 11 " --> pdb=" O VAL J 175 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'J' and resid 84 through 86 Processing sheet with id=AA6, first strand: chain 'J' and resid 108 through 109 Processing sheet with id=AA7, first strand: chain 'K' and resid 62 through 66 removed outlier: 6.693A pdb=" N ILE K 10 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLU K 38 " --> pdb=" O ILE K 10 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA K 12 " --> pdb=" O GLU K 38 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR K 40 " --> pdb=" O ALA K 12 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU K 14 " --> pdb=" O THR K 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 84 through 86 Processing sheet with id=AA9, first strand: chain 'K' and resid 108 through 109 Processing sheet with id=AB1, first strand: chain 'L' and resid 62 through 66 removed outlier: 6.674A pdb=" N ILE L 10 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N GLU L 38 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA L 12 " --> pdb=" O GLU L 38 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR L 40 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LEU L 14 " --> pdb=" O THR L 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'L' and resid 108 through 109 Processing sheet with id=AB4, first strand: chain 'M' and resid 104 through 106 removed outlier: 7.296A pdb=" N ILE M 63 " --> pdb=" O PHE M 84 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N VAL M 86 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ALA M 65 " --> pdb=" O VAL M 86 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE M 10 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLU M 38 " --> pdb=" O ILE M 10 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA M 12 " --> pdb=" O GLU M 38 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR M 40 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU M 14 " --> pdb=" O THR M 40 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 108 through 109 Processing sheet with id=AB6, first strand: chain 'N' and resid 62 through 66 removed outlier: 6.698A pdb=" N ILE N 10 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N GLU N 38 " --> pdb=" O ILE N 10 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA N 12 " --> pdb=" O GLU N 38 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR N 40 " --> pdb=" O ALA N 12 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU N 14 " --> pdb=" O THR N 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 84 through 86 Processing sheet with id=AB8, first strand: chain 'N' and resid 108 through 109 Processing sheet with id=AB9, first strand: chain 'O' and resid 62 through 66 removed outlier: 6.722A pdb=" N ILE O 10 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLU O 38 " --> pdb=" O ILE O 10 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA O 12 " --> pdb=" O GLU O 38 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N THR O 40 " --> pdb=" O ALA O 12 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU O 14 " --> pdb=" O THR O 40 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'O' and resid 84 through 86 Processing sheet with id=AC2, first strand: chain 'O' and resid 108 through 109 Processing sheet with id=AC3, first strand: chain 'U' and resid 62 through 66 removed outlier: 6.802A pdb=" N ILE U 10 " --> pdb=" O LEU U 36 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N GLU U 38 " --> pdb=" O ILE U 10 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA U 12 " --> pdb=" O GLU U 38 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR U 40 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LEU U 14 " --> pdb=" O THR U 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'U' and resid 84 through 86 Processing sheet with id=AC5, first strand: chain 'U' and resid 108 through 109 Processing sheet with id=AC6, first strand: chain 'Y' and resid 62 through 66 removed outlier: 4.245A pdb=" N LEU Y 36 " --> pdb=" O ILE Y 10 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 84 through 86 Processing sheet with id=AC8, first strand: chain 'Y' and resid 108 through 109 Processing sheet with id=AC9, first strand: chain 'Z' and resid 62 through 66 Processing sheet with id=AD1, first strand: chain 'Z' and resid 84 through 86 Processing sheet with id=AD2, first strand: chain 'Z' and resid 108 through 109 Processing sheet with id=AD3, first strand: chain 'a' and resid 62 through 66 removed outlier: 4.304A pdb=" N LEU a 36 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'a' and resid 84 through 86 Processing sheet with id=AD5, first strand: chain 'a' and resid 108 through 109 Processing sheet with id=AD6, first strand: chain 'b' and resid 62 through 66 removed outlier: 4.303A pdb=" N LEU b 36 " --> pdb=" O ILE b 10 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'b' and resid 84 through 86 Processing sheet with id=AD8, first strand: chain 'b' and resid 108 through 109 Processing sheet with id=AD9, first strand: chain 'c' and resid 62 through 66 removed outlier: 4.295A pdb=" N LEU c 36 " --> pdb=" O ILE c 10 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL c 11 " --> pdb=" O VAL c 175 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 84 through 86 Processing sheet with id=AE2, first strand: chain 'c' and resid 108 through 109 Processing sheet with id=AE3, first strand: chain 'd' and resid 62 through 66 removed outlier: 6.739A pdb=" N ILE d 10 " --> pdb=" O LEU d 36 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N GLU d 38 " --> pdb=" O ILE d 10 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA d 12 " --> pdb=" O GLU d 38 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N THR d 40 " --> pdb=" O ALA d 12 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU d 14 " --> pdb=" O THR d 40 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'd' and resid 84 through 86 Processing sheet with id=AE5, first strand: chain 'd' and resid 108 through 109 Processing sheet with id=AE6, first strand: chain 'e' and resid 62 through 66 removed outlier: 4.370A pdb=" N LEU e 36 " --> pdb=" O ILE e 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'e' and resid 84 through 86 Processing sheet with id=AE8, first strand: chain 'e' and resid 108 through 109 Processing sheet with id=AE9, first strand: chain 'f' and resid 62 through 66 removed outlier: 6.719A pdb=" N ILE f 10 " --> pdb=" O LEU f 36 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N GLU f 38 " --> pdb=" O ILE f 10 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA f 12 " --> pdb=" O GLU f 38 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N THR f 40 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU f 14 " --> pdb=" O THR f 40 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'f' and resid 84 through 86 Processing sheet with id=AF2, first strand: chain 'f' and resid 108 through 109 Processing sheet with id=AF3, first strand: chain 'g' and resid 62 through 66 removed outlier: 6.662A pdb=" N ILE g 10 " --> pdb=" O LEU g 36 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLU g 38 " --> pdb=" O ILE g 10 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA g 12 " --> pdb=" O GLU g 38 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR g 40 " --> pdb=" O ALA g 12 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU g 14 " --> pdb=" O THR g 40 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g' and resid 84 through 86 Processing sheet with id=AF5, first strand: chain 'g' and resid 108 through 109 Processing sheet with id=AF6, first strand: chain 'h' and resid 62 through 66 removed outlier: 4.224A pdb=" N LEU h 36 " --> pdb=" O ILE h 10 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 84 through 86 Processing sheet with id=AF8, first strand: chain 'h' and resid 108 through 109 Processing sheet with id=AF9, first strand: chain 'i' and resid 62 through 66 removed outlier: 4.280A pdb=" N LEU i 36 " --> pdb=" O ILE i 10 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 84 through 86 Processing sheet with id=AG2, first strand: chain 'i' and resid 108 through 109 Processing sheet with id=AG3, first strand: chain 'j' and resid 62 through 66 removed outlier: 6.586A pdb=" N ILE j 10 " --> pdb=" O LEU j 36 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLU j 38 " --> pdb=" O ILE j 10 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ALA j 12 " --> pdb=" O GLU j 38 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N THR j 40 " --> pdb=" O ALA j 12 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU j 14 " --> pdb=" O THR j 40 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'j' and resid 84 through 86 Processing sheet with id=AG5, first strand: chain 'j' and resid 108 through 109 Processing sheet with id=AG6, first strand: chain 'k' and resid 62 through 66 removed outlier: 4.257A pdb=" N LEU k 36 " --> pdb=" O ILE k 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'k' and resid 84 through 86 Processing sheet with id=AG8, first strand: chain 'k' and resid 108 through 109 Processing sheet with id=AG9, first strand: chain 'l' and resid 62 through 66 removed outlier: 6.240A pdb=" N ALA l 12 " --> pdb=" O GLU l 38 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR l 40 " --> pdb=" O ALA l 12 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU l 14 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL l 11 " --> pdb=" O VAL l 175 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'l' and resid 84 through 86 Processing sheet with id=AH2, first strand: chain 'l' and resid 108 through 109 Processing sheet with id=AH3, first strand: chain 'm' and resid 62 through 66 removed outlier: 4.274A pdb=" N LEU m 36 " --> pdb=" O ILE m 10 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'm' and resid 84 through 86 Processing sheet with id=AH5, first strand: chain 'm' and resid 108 through 109 Processing sheet with id=AH6, first strand: chain 'n' and resid 62 through 66 removed outlier: 6.676A pdb=" N ILE n 10 " --> pdb=" O LEU n 36 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLU n 38 " --> pdb=" O ILE n 10 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA n 12 " --> pdb=" O GLU n 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N THR n 40 " --> pdb=" O ALA n 12 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU n 14 " --> pdb=" O THR n 40 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'n' and resid 84 through 86 Processing sheet with id=AH8, first strand: chain 'n' and resid 108 through 109 3207 hydrogen bonds defined for protein. 9618 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.55 Time building geometry restraints manager: 14.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9418 1.33 - 1.45: 10255 1.45 - 1.58: 29334 1.58 - 1.71: 0 1.71 - 1.84: 480 Bond restraints: 49487 Sorted by residual: bond pdb=" CA VAL e 43 " pdb=" C VAL e 43 " ideal model delta sigma weight residual 1.527 1.492 0.034 8.00e-03 1.56e+04 1.84e+01 bond pdb=" CA VAL n 43 " pdb=" C VAL n 43 " ideal model delta sigma weight residual 1.527 1.493 0.033 8.00e-03 1.56e+04 1.73e+01 bond pdb=" C ILE e 39 " pdb=" O ILE e 39 " ideal model delta sigma weight residual 1.238 1.199 0.038 1.09e-02 8.42e+03 1.22e+01 bond pdb=" C ILE j 39 " pdb=" O ILE j 39 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.10e-02 8.26e+03 1.16e+01 bond pdb=" C ILE L 39 " pdb=" O ILE L 39 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.10e-02 8.26e+03 1.16e+01 ... (remaining 49482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 65906 2.47 - 4.94: 809 4.94 - 7.40: 35 7.40 - 9.87: 9 9.87 - 12.34: 8 Bond angle restraints: 66767 Sorted by residual: angle pdb=" N THR L 42 " pdb=" CA THR L 42 " pdb=" C THR L 42 " ideal model delta sigma weight residual 114.31 101.97 12.34 1.29e+00 6.01e-01 9.15e+01 angle pdb=" N THR U 42 " pdb=" CA THR U 42 " pdb=" C THR U 42 " ideal model delta sigma weight residual 114.31 102.59 11.72 1.29e+00 6.01e-01 8.25e+01 angle pdb=" N CYS k 98 " pdb=" CA CYS k 98 " pdb=" C CYS k 98 " ideal model delta sigma weight residual 114.56 103.15 11.41 1.27e+00 6.20e-01 8.07e+01 angle pdb=" N THR n 42 " pdb=" CA THR n 42 " pdb=" C THR n 42 " ideal model delta sigma weight residual 114.12 103.24 10.88 1.39e+00 5.18e-01 6.13e+01 angle pdb=" N THR e 42 " pdb=" CA THR e 42 " pdb=" C THR e 42 " ideal model delta sigma weight residual 114.12 103.29 10.83 1.39e+00 5.18e-01 6.07e+01 ... (remaining 66762 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 28269 18.00 - 36.00: 1722 36.00 - 54.00: 300 54.00 - 72.00: 130 72.00 - 90.01: 106 Dihedral angle restraints: 30527 sinusoidal: 11951 harmonic: 18576 Sorted by residual: dihedral pdb=" CA LYS o 9 " pdb=" C LYS o 9 " pdb=" N GLU o 10 " pdb=" CA GLU o 10 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA LEU Z 14 " pdb=" C LEU Z 14 " pdb=" N ARG Z 15 " pdb=" CA ARG Z 15 " ideal model delta harmonic sigma weight residual 180.00 158.33 21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LEU c 179 " pdb=" C LEU c 179 " pdb=" N VAL c 180 " pdb=" CA VAL c 180 " ideal model delta harmonic sigma weight residual -180.00 -158.80 -21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 30524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 5247 0.039 - 0.078: 2088 0.078 - 0.117: 584 0.117 - 0.155: 200 0.155 - 0.194: 17 Chirality restraints: 8136 Sorted by residual: chirality pdb=" CA VAL Y 43 " pdb=" N VAL Y 43 " pdb=" C VAL Y 43 " pdb=" CB VAL Y 43 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.44e-01 chirality pdb=" CA VAL M 43 " pdb=" N VAL M 43 " pdb=" C VAL M 43 " pdb=" CB VAL M 43 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CA VAL d 43 " pdb=" N VAL d 43 " pdb=" C VAL d 43 " pdb=" CB VAL d 43 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 8133 not shown) Planarity restraints: 8376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C PHE a 97 " 0.057 2.00e-02 2.50e+03 pdb=" O PHE a 97 " -0.022 2.00e-02 2.50e+03 pdb=" N CYS a 98 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE k 97 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C PHE k 97 " -0.055 2.00e-02 2.50e+03 pdb=" O PHE k 97 " 0.021 2.00e-02 2.50e+03 pdb=" N CYS k 98 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP o 35 " -0.047 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO o 36 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO o 36 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO o 36 " -0.039 5.00e-02 4.00e+02 ... (remaining 8373 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3560 2.74 - 3.28: 46794 3.28 - 3.82: 79189 3.82 - 4.36: 97211 4.36 - 4.90: 168895 Nonbonded interactions: 395649 Sorted by model distance: nonbonded pdb=" O ALA d 47 " pdb=" OG SER d 80 " model vdw 2.197 3.040 nonbonded pdb=" NE2 GLN V 11 " pdb=" OE1 GLN V 65 " model vdw 2.198 3.120 nonbonded pdb=" NE2 GLN 1 11 " pdb=" OE1 GLN 1 65 " model vdw 2.199 3.120 nonbonded pdb=" O ALA f 47 " pdb=" OG SER f 80 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG R 49 " pdb=" OE2 GLU R 53 " model vdw 2.215 3.120 ... (remaining 395644 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' 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 'I' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'J' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'K' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'L' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'M' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'N' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'O' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'U' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'Y' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'Z' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'a' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'b' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = chain 'c' selection = (chain 'd' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'e' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'f' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'g' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'h' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'i' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'j' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'k' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'l' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'm' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) selection = (chain 'n' and (resid 1 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 201 or resid 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 1.890 Check model and map are aligned: 0.380 Set scattering table: 0.430 Process input model: 104.310 Find NCS groups from input model: 3.320 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 49487 Z= 0.356 Angle : 0.711 12.341 66767 Z= 0.410 Chirality : 0.047 0.194 8136 Planarity : 0.007 0.072 8376 Dihedral : 14.166 90.005 18359 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.43 % Allowed : 2.48 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -1.08 (0.09), residues: 6408 helix: -0.37 (0.07), residues: 4008 sheet: -0.59 (0.15), residues: 1152 loop : -1.32 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP U 165 HIS 0.009 0.002 HIS h 89 PHE 0.039 0.002 PHE k 41 TYR 0.018 0.002 TYR f 105 ARG 0.007 0.001 ARG p 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 1162 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7791 (mtmm) REVERT: I 27 LEU cc_start: 0.7828 (tp) cc_final: 0.7577 (mt) REVERT: I 93 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7168 (mm-30) REVERT: I 97 PHE cc_start: 0.7896 (m-80) cc_final: 0.7608 (m-80) REVERT: I 119 MET cc_start: 0.8280 (mtp) cc_final: 0.8044 (mtp) REVERT: J 14 LEU cc_start: 0.8704 (tt) cc_final: 0.8493 (mt) REVERT: J 27 LEU cc_start: 0.8037 (tp) cc_final: 0.7511 (mt) REVERT: J 119 MET cc_start: 0.8269 (mtp) cc_final: 0.8007 (mtp) REVERT: J 120 LYS cc_start: 0.8060 (mttt) cc_final: 0.7700 (mptt) REVERT: K 27 LEU cc_start: 0.7756 (tp) cc_final: 0.7459 (mt) REVERT: K 119 MET cc_start: 0.8335 (mtp) cc_final: 0.8083 (mtp) REVERT: L 27 LEU cc_start: 0.7762 (tp) cc_final: 0.7528 (mt) REVERT: L 196 GLU cc_start: 0.7125 (pp20) cc_final: 0.6540 (mm-30) REVERT: M 27 LEU cc_start: 0.7879 (tp) cc_final: 0.7525 (mt) REVERT: M 91 ASP cc_start: 0.7320 (t0) cc_final: 0.7113 (t0) REVERT: M 93 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7253 (mp0) REVERT: M 110 MET cc_start: 0.8641 (ttt) cc_final: 0.8212 (ttt) REVERT: M 119 MET cc_start: 0.8276 (mtp) cc_final: 0.8003 (mtp) REVERT: N 27 LEU cc_start: 0.7904 (tp) cc_final: 0.7460 (mt) REVERT: N 97 PHE cc_start: 0.7901 (m-80) cc_final: 0.7683 (m-80) REVERT: N 163 CYS cc_start: 0.6798 (m) cc_final: 0.6583 (m) REVERT: O 7 LYS cc_start: 0.7317 (mttp) cc_final: 0.6974 (tttm) REVERT: O 23 ARG cc_start: 0.7320 (mtm180) cc_final: 0.7037 (mtm180) REVERT: O 27 LEU cc_start: 0.7792 (tp) cc_final: 0.7376 (mt) REVERT: O 57 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7328 (tttm) REVERT: O 110 MET cc_start: 0.8467 (ttt) cc_final: 0.8233 (ttt) REVERT: O 196 GLU cc_start: 0.7026 (pp20) cc_final: 0.6434 (mm-30) REVERT: P 50 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8159 (mtmm) REVERT: Q 50 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8060 (mtmm) REVERT: R 38 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.6038 (m-30) REVERT: R 50 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8355 (mtmm) REVERT: S 50 LYS cc_start: 0.8149 (mttt) cc_final: 0.7908 (mtmm) REVERT: T 50 LYS cc_start: 0.8407 (mttt) cc_final: 0.8166 (mttp) REVERT: U 119 MET cc_start: 0.8267 (mtp) cc_final: 0.7988 (mtp) REVERT: X 50 LYS cc_start: 0.8365 (mtmt) cc_final: 0.8125 (mtmm) REVERT: Y 27 LEU cc_start: 0.7949 (tp) cc_final: 0.7537 (mt) REVERT: Y 119 MET cc_start: 0.8301 (mtp) cc_final: 0.8033 (mtp) REVERT: Y 120 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7578 (mmtm) REVERT: Z 27 LEU cc_start: 0.7818 (tp) cc_final: 0.7442 (mt) REVERT: Z 119 MET cc_start: 0.8272 (mtp) cc_final: 0.8023 (mtp) REVERT: Z 120 LYS cc_start: 0.7859 (mttt) cc_final: 0.7540 (mptt) REVERT: a 27 LEU cc_start: 0.7815 (tp) cc_final: 0.7071 (mt) REVERT: a 120 LYS cc_start: 0.8080 (mttt) cc_final: 0.7778 (mmtm) REVERT: b 57 LYS cc_start: 0.7409 (ttmt) cc_final: 0.7177 (tttp) REVERT: b 119 MET cc_start: 0.8339 (mtp) cc_final: 0.7973 (mtp) REVERT: b 120 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7668 (mmtm) REVERT: c 27 LEU cc_start: 0.7807 (tp) cc_final: 0.7498 (mt) REVERT: c 119 MET cc_start: 0.8314 (mtp) cc_final: 0.8069 (mtp) REVERT: c 120 LYS cc_start: 0.8044 (mttt) cc_final: 0.7739 (mptt) REVERT: d 27 LEU cc_start: 0.7685 (tp) cc_final: 0.7481 (mt) REVERT: d 119 MET cc_start: 0.8579 (mtm) cc_final: 0.8258 (mtp) REVERT: d 120 LYS cc_start: 0.7708 (mttt) cc_final: 0.7409 (mptt) REVERT: e 27 LEU cc_start: 0.8105 (tp) cc_final: 0.7578 (mt) REVERT: e 120 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7703 (mmtm) REVERT: f 27 LEU cc_start: 0.7800 (tp) cc_final: 0.7381 (mt) REVERT: f 119 MET cc_start: 0.8309 (mtp) cc_final: 0.7983 (mtp) REVERT: g 27 LEU cc_start: 0.8029 (tp) cc_final: 0.7553 (mt) REVERT: g 93 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6971 (mp0) REVERT: g 120 LYS cc_start: 0.8061 (mttt) cc_final: 0.7717 (mptt) REVERT: h 57 LYS cc_start: 0.7803 (tmtt) cc_final: 0.7535 (tptt) REVERT: h 119 MET cc_start: 0.8318 (mtp) cc_final: 0.8010 (mtp) REVERT: h 120 LYS cc_start: 0.7727 (mttm) cc_final: 0.7483 (mptt) REVERT: i 93 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7209 (mp0) REVERT: i 97 PHE cc_start: 0.7900 (m-80) cc_final: 0.7672 (m-80) REVERT: i 119 MET cc_start: 0.8372 (mtp) cc_final: 0.8129 (mtp) REVERT: i 120 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7625 (mmtm) REVERT: i 196 GLU cc_start: 0.6870 (pp20) cc_final: 0.6543 (mm-30) REVERT: j 27 LEU cc_start: 0.7739 (tp) cc_final: 0.7520 (mt) REVERT: j 120 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7600 (mptt) REVERT: k 27 LEU cc_start: 0.8006 (tp) cc_final: 0.7507 (mt) REVERT: k 119 MET cc_start: 0.8419 (mtp) cc_final: 0.8098 (mtp) REVERT: l 27 LEU cc_start: 0.7983 (tp) cc_final: 0.7595 (mt) REVERT: l 93 GLU cc_start: 0.7372 (mp0) cc_final: 0.7113 (mm-30) REVERT: l 110 MET cc_start: 0.8533 (ttt) cc_final: 0.8286 (ttt) REVERT: m 27 LEU cc_start: 0.7800 (tp) cc_final: 0.7425 (mt) REVERT: n 120 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7486 (mmtm) REVERT: o 16 LYS cc_start: 0.8152 (mttt) cc_final: 0.7948 (mtmm) REVERT: o 50 LYS cc_start: 0.8229 (mttt) cc_final: 0.7911 (mtmm) REVERT: p 50 LYS cc_start: 0.8267 (mtmt) cc_final: 0.7952 (mtmm) REVERT: q 50 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8191 (mtmm) REVERT: t 49 ARG cc_start: 0.7665 (ttp80) cc_final: 0.7288 (ttp80) REVERT: t 50 LYS cc_start: 0.8128 (mttt) cc_final: 0.7893 (mtmm) REVERT: w 50 LYS cc_start: 0.8288 (mtmt) cc_final: 0.7964 (mtmm) REVERT: x 50 LYS cc_start: 0.8211 (mttt) cc_final: 0.7801 (mttp) REVERT: y 23 GLU cc_start: 0.7005 (tt0) cc_final: 0.6780 (mt-10) outliers start: 22 outliers final: 11 residues processed: 1184 average time/residue: 1.9677 time to fit residues: 2788.3211 Evaluate side-chains 823 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 811 time to evaluate : 5.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 ASP Chi-restraints excluded: chain Z residue 98 CYS Chi-restraints excluded: chain a residue 98 CYS Chi-restraints excluded: chain d residue 98 CYS Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain f residue 98 CYS Chi-restraints excluded: chain h residue 98 CYS Chi-restraints excluded: chain i residue 98 CYS Chi-restraints excluded: chain j residue 98 CYS Chi-restraints excluded: chain k residue 98 CYS Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 98 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 547 optimal weight: 4.9990 chunk 491 optimal weight: 0.9990 chunk 272 optimal weight: 0.6980 chunk 167 optimal weight: 4.9990 chunk 331 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 507 optimal weight: 0.2980 chunk 196 optimal weight: 20.0000 chunk 308 optimal weight: 0.1980 chunk 378 optimal weight: 1.9990 chunk 588 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 11 GLN J 8 HIS K 96 GLN K 148 ASN L 89 HIS M 45 ASN M 137 GLN N 148 ASN O 137 GLN P 33 GLN Q 11 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 11 GLN T 11 GLN Z 137 GLN b 137 GLN c 89 HIS d 20 GLN d 137 GLN e 89 HIS g 137 GLN h 89 HIS i 89 HIS j 8 HIS j 89 HIS j 137 GLN l 89 HIS m 73 GLN m 89 HIS n 137 GLN o 11 GLN q 11 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 49487 Z= 0.169 Angle : 0.485 5.203 66767 Z= 0.261 Chirality : 0.041 0.151 8136 Planarity : 0.005 0.054 8376 Dihedral : 4.606 57.224 6637 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.13 % Allowed : 12.17 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 0.75 (0.10), residues: 6408 helix: 1.30 (0.08), residues: 4032 sheet: -0.43 (0.15), residues: 1152 loop : -1.02 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP i 165 HIS 0.005 0.001 HIS L 8 PHE 0.013 0.001 PHE d 97 TYR 0.007 0.001 TYR a 105 ARG 0.005 0.001 ARG w 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 948 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 839 time to evaluate : 5.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7765 (mtmm) REVERT: 2 23 GLU cc_start: 0.7015 (tt0) cc_final: 0.6775 (mt-10) REVERT: 2 50 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8049 (mtmm) REVERT: 3 50 LYS cc_start: 0.8286 (mttt) cc_final: 0.7903 (mtmm) REVERT: I 27 LEU cc_start: 0.7989 (tp) cc_final: 0.7597 (mt) REVERT: I 93 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7177 (mm-30) REVERT: I 110 MET cc_start: 0.8532 (ttt) cc_final: 0.8178 (ttt) REVERT: I 119 MET cc_start: 0.8228 (mtp) cc_final: 0.7967 (mtp) REVERT: J 17 ASN cc_start: 0.7484 (m110) cc_final: 0.7277 (m110) REVERT: J 27 LEU cc_start: 0.8075 (tp) cc_final: 0.7553 (mt) REVERT: J 119 MET cc_start: 0.8379 (mtp) cc_final: 0.8091 (mtp) REVERT: J 120 LYS cc_start: 0.7794 (mttt) cc_final: 0.7455 (mptt) REVERT: K 27 LEU cc_start: 0.7888 (tp) cc_final: 0.7492 (mt) REVERT: K 119 MET cc_start: 0.8298 (mtp) cc_final: 0.8053 (mtp) REVERT: L 27 LEU cc_start: 0.7923 (tp) cc_final: 0.7577 (mt) REVERT: L 196 GLU cc_start: 0.6978 (pp20) cc_final: 0.6453 (mm-30) REVERT: M 27 LEU cc_start: 0.7965 (tp) cc_final: 0.7564 (mt) REVERT: M 110 MET cc_start: 0.8595 (ttt) cc_final: 0.8231 (ttt) REVERT: M 119 MET cc_start: 0.8277 (mtp) cc_final: 0.7955 (mtp) REVERT: N 2 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: N 27 LEU cc_start: 0.8008 (tp) cc_final: 0.7702 (mt) REVERT: N 163 CYS cc_start: 0.6967 (m) cc_final: 0.6690 (m) REVERT: O 7 LYS cc_start: 0.7291 (mttp) cc_final: 0.6992 (tttm) REVERT: O 27 LEU cc_start: 0.7844 (tp) cc_final: 0.7433 (mt) REVERT: O 57 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7190 (tttp) REVERT: O 196 GLU cc_start: 0.7030 (pp20) cc_final: 0.6485 (mm-30) REVERT: P 50 LYS cc_start: 0.8446 (mtmt) cc_final: 0.8081 (mtmm) REVERT: Q 50 LYS cc_start: 0.8339 (mtmt) cc_final: 0.8022 (mtmm) REVERT: R 50 LYS cc_start: 0.8547 (mtmt) cc_final: 0.8330 (mtmm) REVERT: S 50 LYS cc_start: 0.8128 (mttt) cc_final: 0.7860 (mtmm) REVERT: T 16 LYS cc_start: 0.8213 (mtmm) cc_final: 0.8004 (mtmt) REVERT: T 50 LYS cc_start: 0.8365 (mttt) cc_final: 0.7988 (mtmm) REVERT: U 54 SER cc_start: 0.8839 (p) cc_final: 0.8628 (m) REVERT: U 119 MET cc_start: 0.8283 (mtp) cc_final: 0.7990 (mtp) REVERT: U 120 LYS cc_start: 0.7779 (mttp) cc_final: 0.7395 (mptt) REVERT: X 50 LYS cc_start: 0.8396 (mtmt) cc_final: 0.8109 (mtmm) REVERT: Y 27 LEU cc_start: 0.7853 (tp) cc_final: 0.7495 (mt) REVERT: Y 119 MET cc_start: 0.8270 (mtp) cc_final: 0.7966 (mtp) REVERT: Y 120 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7512 (mmtm) REVERT: Z 27 LEU cc_start: 0.7822 (tp) cc_final: 0.7439 (mt) REVERT: Z 83 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6794 (mm-30) REVERT: Z 119 MET cc_start: 0.8219 (mtp) cc_final: 0.7968 (mtp) REVERT: Z 120 LYS cc_start: 0.7715 (mttt) cc_final: 0.7403 (mptt) REVERT: a 27 LEU cc_start: 0.7546 (tp) cc_final: 0.7265 (mt) REVERT: a 120 LYS cc_start: 0.8027 (mttt) cc_final: 0.7648 (mptt) REVERT: a 196 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6867 (mm-30) REVERT: b 57 LYS cc_start: 0.7354 (ttmt) cc_final: 0.7085 (tttp) REVERT: b 119 MET cc_start: 0.8267 (mtp) cc_final: 0.7978 (mtp) REVERT: b 120 LYS cc_start: 0.7849 (mtmt) cc_final: 0.7440 (mmtm) REVERT: c 27 LEU cc_start: 0.7741 (tp) cc_final: 0.7427 (mt) REVERT: c 119 MET cc_start: 0.8227 (mtp) cc_final: 0.8019 (mtp) REVERT: c 120 LYS cc_start: 0.8016 (mttt) cc_final: 0.7711 (mptt) REVERT: c 196 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6827 (mm-30) REVERT: d 9 LYS cc_start: 0.7917 (mttm) cc_final: 0.7557 (mtmt) REVERT: d 27 LEU cc_start: 0.7913 (tp) cc_final: 0.7582 (mt) REVERT: d 110 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8080 (ttt) REVERT: d 119 MET cc_start: 0.8461 (mtm) cc_final: 0.8176 (mtp) REVERT: d 120 LYS cc_start: 0.7716 (mttt) cc_final: 0.7391 (mptt) REVERT: e 27 LEU cc_start: 0.7995 (tp) cc_final: 0.7491 (mt) REVERT: e 101 LYS cc_start: 0.8100 (mttt) cc_final: 0.7330 (mptt) REVERT: e 120 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7697 (mmtm) REVERT: e 196 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6870 (mm-30) REVERT: f 27 LEU cc_start: 0.7775 (tp) cc_final: 0.7424 (mt) REVERT: f 62 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8152 (mm) REVERT: f 83 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: f 119 MET cc_start: 0.8324 (mtp) cc_final: 0.7989 (mtp) REVERT: f 140 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7649 (mtmt) REVERT: g 17 ASN cc_start: 0.6799 (OUTLIER) cc_final: 0.6532 (t0) REVERT: g 27 LEU cc_start: 0.8051 (tp) cc_final: 0.7584 (mt) REVERT: g 62 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (mm) REVERT: g 93 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7029 (mp0) REVERT: g 110 MET cc_start: 0.8640 (ttt) cc_final: 0.8349 (ttp) REVERT: g 120 LYS cc_start: 0.7963 (mttt) cc_final: 0.7665 (mptt) REVERT: h 119 MET cc_start: 0.8299 (mtp) cc_final: 0.7941 (mtp) REVERT: h 120 LYS cc_start: 0.7729 (mttm) cc_final: 0.7485 (mptt) REVERT: i 54 SER cc_start: 0.8747 (p) cc_final: 0.8545 (m) REVERT: i 93 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7223 (mp0) REVERT: i 119 MET cc_start: 0.8249 (mtp) cc_final: 0.8004 (mtp) REVERT: i 120 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7601 (mmtm) REVERT: j 27 LEU cc_start: 0.7940 (tp) cc_final: 0.7579 (mt) REVERT: j 120 LYS cc_start: 0.7716 (mtmt) cc_final: 0.7332 (mptt) REVERT: k 27 LEU cc_start: 0.7937 (tp) cc_final: 0.7459 (mt) REVERT: k 62 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8190 (mm) REVERT: k 93 GLU cc_start: 0.7628 (mp0) cc_final: 0.7394 (mm-30) REVERT: k 119 MET cc_start: 0.8263 (mtp) cc_final: 0.7921 (mtp) REVERT: l 27 LEU cc_start: 0.7822 (tp) cc_final: 0.7493 (mt) REVERT: l 62 ILE cc_start: 0.8494 (mm) cc_final: 0.8288 (mm) REVERT: l 95 SER cc_start: 0.8463 (t) cc_final: 0.8250 (m) REVERT: l 110 MET cc_start: 0.8591 (ttt) cc_final: 0.8248 (ttt) REVERT: m 27 LEU cc_start: 0.7828 (tp) cc_final: 0.7480 (mt) REVERT: n 120 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7405 (mmtm) REVERT: p 50 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8037 (mtmm) REVERT: q 50 LYS cc_start: 0.8451 (mtmt) cc_final: 0.8182 (mtmm) REVERT: t 50 LYS cc_start: 0.8092 (mttt) cc_final: 0.7846 (mtmm) REVERT: v 50 LYS cc_start: 0.8308 (mtmm) cc_final: 0.7949 (mtmm) REVERT: w 50 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7939 (mtmm) REVERT: x 50 LYS cc_start: 0.8187 (mttt) cc_final: 0.7952 (mttt) REVERT: y 23 GLU cc_start: 0.6919 (tt0) cc_final: 0.6656 (mt-10) outliers start: 109 outliers final: 38 residues processed: 906 average time/residue: 1.9020 time to fit residues: 2074.6686 Evaluate side-chains 795 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 745 time to evaluate : 5.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 62 MET Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain 3 residue 5 LEU Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain K residue 17 ASN Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain N residue 2 GLU Chi-restraints excluded: chain P residue 5 LEU Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain Y residue 6 LYS Chi-restraints excluded: chain Z residue 83 GLU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 98 CYS Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain a residue 196 GLU Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain d residue 98 CYS Chi-restraints excluded: chain d residue 110 MET Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 98 CYS Chi-restraints excluded: chain e residue 196 GLU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 83 GLU Chi-restraints excluded: chain f residue 140 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 17 ASN Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 99 LYS Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain k residue 98 CYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 124 THR Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 98 CYS Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain t residue 59 GLU Chi-restraints excluded: chain u residue 59 GLU Chi-restraints excluded: chain v residue 59 GLU Chi-restraints excluded: chain w residue 62 MET Chi-restraints excluded: chain x residue 30 LYS Chi-restraints excluded: chain x residue 37 SER Chi-restraints excluded: chain z residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 489 optimal weight: 5.9990 chunk 400 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 589 optimal weight: 2.9990 chunk 636 optimal weight: 0.9980 chunk 525 optimal weight: 3.9990 chunk 584 optimal weight: 10.0000 chunk 200 optimal weight: 0.8980 chunk 472 optimal weight: 0.8980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 73 GLN M 8 HIS O 89 HIS O 137 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 137 GLN c 8 HIS c 137 GLN x 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 49487 Z= 0.198 Angle : 0.477 5.649 66767 Z= 0.251 Chirality : 0.041 0.151 8136 Planarity : 0.005 0.053 8376 Dihedral : 4.221 34.561 6630 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.45 % Allowed : 14.52 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.51 (0.10), residues: 6408 helix: 1.99 (0.08), residues: 4032 sheet: -0.29 (0.15), residues: 1152 loop : -0.96 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP h 165 HIS 0.006 0.001 HIS L 8 PHE 0.021 0.001 PHE d 97 TYR 0.009 0.001 TYR f 105 ARG 0.006 0.001 ARG w 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 800 time to evaluate : 5.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7854 (mtmm) REVERT: 2 23 GLU cc_start: 0.7034 (tt0) cc_final: 0.6821 (mt-10) REVERT: 2 50 LYS cc_start: 0.8292 (ptpt) cc_final: 0.8048 (mtmm) REVERT: 3 50 LYS cc_start: 0.8311 (mttt) cc_final: 0.7909 (mtmm) REVERT: I 2 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: I 27 LEU cc_start: 0.8083 (tp) cc_final: 0.7664 (mt) REVERT: I 93 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7101 (mm-30) REVERT: I 97 PHE cc_start: 0.8071 (m-80) cc_final: 0.7799 (m-80) REVERT: I 119 MET cc_start: 0.8269 (mtp) cc_final: 0.8025 (mtp) REVERT: J 27 LEU cc_start: 0.8075 (tp) cc_final: 0.7589 (mt) REVERT: J 119 MET cc_start: 0.8384 (mtp) cc_final: 0.8078 (mtp) REVERT: J 120 LYS cc_start: 0.7805 (mttt) cc_final: 0.7484 (mptt) REVERT: K 27 LEU cc_start: 0.8018 (tp) cc_final: 0.7614 (mt) REVERT: K 54 SER cc_start: 0.8672 (p) cc_final: 0.8451 (m) REVERT: K 119 MET cc_start: 0.8318 (mtp) cc_final: 0.8043 (mtp) REVERT: L 9 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7380 (mttm) REVERT: L 27 LEU cc_start: 0.7971 (tp) cc_final: 0.7620 (mt) REVERT: L 97 PHE cc_start: 0.8013 (m-80) cc_final: 0.7800 (m-80) REVERT: L 196 GLU cc_start: 0.6971 (pp20) cc_final: 0.6461 (mm-30) REVERT: M 2 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: M 27 LEU cc_start: 0.7971 (tp) cc_final: 0.7586 (mt) REVERT: M 97 PHE cc_start: 0.8075 (m-80) cc_final: 0.7776 (m-80) REVERT: M 110 MET cc_start: 0.8629 (ttt) cc_final: 0.8220 (ttt) REVERT: M 119 MET cc_start: 0.8316 (mtp) cc_final: 0.8001 (mtp) REVERT: N 27 LEU cc_start: 0.8145 (tp) cc_final: 0.7702 (mt) REVERT: N 163 CYS cc_start: 0.6860 (m) cc_final: 0.6520 (m) REVERT: O 7 LYS cc_start: 0.7258 (mttp) cc_final: 0.7040 (tttm) REVERT: O 27 LEU cc_start: 0.7840 (tp) cc_final: 0.7482 (mt) REVERT: O 57 LYS cc_start: 0.7797 (ttmm) cc_final: 0.7236 (tttm) REVERT: O 196 GLU cc_start: 0.7052 (pp20) cc_final: 0.6488 (mm-30) REVERT: P 50 LYS cc_start: 0.8469 (mtmt) cc_final: 0.8191 (mtmm) REVERT: Q 50 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8016 (mtmm) REVERT: R 50 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8271 (mtmm) REVERT: S 50 LYS cc_start: 0.8171 (mttt) cc_final: 0.7866 (mtmm) REVERT: T 16 LYS cc_start: 0.8205 (mtmm) cc_final: 0.7996 (mtmt) REVERT: T 50 LYS cc_start: 0.8382 (mttt) cc_final: 0.8051 (mtmm) REVERT: U 119 MET cc_start: 0.8305 (mtp) cc_final: 0.8005 (mtp) REVERT: U 120 LYS cc_start: 0.7813 (mttp) cc_final: 0.7367 (mptt) REVERT: X 50 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8182 (mtmm) REVERT: Y 27 LEU cc_start: 0.7870 (tp) cc_final: 0.7508 (mt) REVERT: Y 57 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7690 (tttp) REVERT: Y 119 MET cc_start: 0.8288 (mtp) cc_final: 0.8048 (mtp) REVERT: Y 120 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7455 (mptt) REVERT: Z 27 LEU cc_start: 0.7808 (tp) cc_final: 0.7478 (mt) REVERT: Z 97 PHE cc_start: 0.8179 (m-80) cc_final: 0.7888 (m-80) REVERT: Z 119 MET cc_start: 0.8249 (mtp) cc_final: 0.8029 (mtp) REVERT: Z 120 LYS cc_start: 0.7731 (mttt) cc_final: 0.7465 (mptt) REVERT: Z 140 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7712 (mtmt) REVERT: a 27 LEU cc_start: 0.7666 (tp) cc_final: 0.7329 (mt) REVERT: a 110 MET cc_start: 0.8582 (ttp) cc_final: 0.8281 (ttt) REVERT: a 120 LYS cc_start: 0.8011 (mttt) cc_final: 0.7642 (mptt) REVERT: a 140 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: b 57 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7084 (tttp) REVERT: b 119 MET cc_start: 0.8326 (mtp) cc_final: 0.7989 (mtp) REVERT: b 120 LYS cc_start: 0.7839 (mtmt) cc_final: 0.7415 (mmtm) REVERT: c 27 LEU cc_start: 0.7804 (tp) cc_final: 0.7470 (mt) REVERT: c 119 MET cc_start: 0.8254 (mtp) cc_final: 0.8006 (mtp) REVERT: c 120 LYS cc_start: 0.8003 (mttt) cc_final: 0.7678 (mptt) REVERT: c 196 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6860 (mm-30) REVERT: d 9 LYS cc_start: 0.7893 (mttm) cc_final: 0.7528 (mtmt) REVERT: d 27 LEU cc_start: 0.7957 (tp) cc_final: 0.7579 (mt) REVERT: d 119 MET cc_start: 0.8479 (mtm) cc_final: 0.8165 (mtp) REVERT: d 120 LYS cc_start: 0.7769 (mttt) cc_final: 0.7406 (mptt) REVERT: e 27 LEU cc_start: 0.7975 (tp) cc_final: 0.7508 (mt) REVERT: e 120 LYS cc_start: 0.8081 (mtpp) cc_final: 0.7727 (mptt) REVERT: e 196 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6922 (mm-30) REVERT: f 27 LEU cc_start: 0.7825 (tp) cc_final: 0.7460 (mt) REVERT: f 62 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8181 (mm) REVERT: f 119 MET cc_start: 0.8360 (mtp) cc_final: 0.8033 (mtp) REVERT: f 140 LYS cc_start: 0.8308 (OUTLIER) cc_final: 0.7628 (mtmt) REVERT: g 27 LEU cc_start: 0.8015 (tp) cc_final: 0.7547 (mt) REVERT: g 62 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8218 (mm) REVERT: g 93 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7127 (mm-30) REVERT: g 120 LYS cc_start: 0.7951 (mttt) cc_final: 0.7633 (mptt) REVERT: h 62 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8134 (mm) REVERT: h 119 MET cc_start: 0.8333 (mtp) cc_final: 0.7966 (mtp) REVERT: h 120 LYS cc_start: 0.7743 (mttm) cc_final: 0.7463 (mptt) REVERT: i 62 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8176 (mm) REVERT: i 93 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7225 (mm-30) REVERT: i 119 MET cc_start: 0.8264 (mtp) cc_final: 0.8013 (mtp) REVERT: i 120 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7661 (mmtm) REVERT: j 27 LEU cc_start: 0.8050 (tp) cc_final: 0.7551 (mt) REVERT: j 31 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6975 (mt-10) REVERT: j 97 PHE cc_start: 0.8101 (m-80) cc_final: 0.7822 (m-80) REVERT: j 120 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7360 (mptt) REVERT: k 27 LEU cc_start: 0.7950 (tp) cc_final: 0.7511 (mt) REVERT: k 62 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8180 (mm) REVERT: k 93 GLU cc_start: 0.7535 (mp0) cc_final: 0.7309 (mm-30) REVERT: k 119 MET cc_start: 0.8269 (mtp) cc_final: 0.7937 (mtp) REVERT: l 27 LEU cc_start: 0.7848 (tp) cc_final: 0.7466 (mt) REVERT: l 62 ILE cc_start: 0.8519 (mm) cc_final: 0.8273 (mm) REVERT: l 110 MET cc_start: 0.8547 (ttt) cc_final: 0.8179 (ttt) REVERT: m 27 LEU cc_start: 0.7843 (tp) cc_final: 0.7502 (mt) REVERT: n 27 LEU cc_start: 0.8061 (tp) cc_final: 0.7511 (mt) REVERT: n 99 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7800 (ttmm) REVERT: n 120 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7459 (mmtm) REVERT: o 50 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7925 (mtmm) REVERT: o 59 GLU cc_start: 0.7885 (tt0) cc_final: 0.7627 (pt0) REVERT: p 50 LYS cc_start: 0.8347 (mtmt) cc_final: 0.8051 (mtmm) REVERT: q 50 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8255 (mtmm) REVERT: s 50 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7800 (mtmm) REVERT: t 50 LYS cc_start: 0.8109 (mttt) cc_final: 0.7857 (mtmm) REVERT: v 5 LEU cc_start: 0.6597 (OUTLIER) cc_final: 0.6336 (mt) REVERT: v 50 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7953 (mtmm) REVERT: w 50 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7989 (mtmm) REVERT: y 23 GLU cc_start: 0.6985 (tt0) cc_final: 0.6719 (mt-10) outliers start: 125 outliers final: 38 residues processed: 880 average time/residue: 1.8809 time to fit residues: 1996.6885 Evaluate side-chains 796 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 741 time to evaluate : 5.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 5 LEU Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain L residue 9 LYS Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain W residue 62 MET Chi-restraints excluded: chain Y residue 6 LYS Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 98 CYS Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 140 LYS Chi-restraints excluded: chain a residue 167 LYS Chi-restraints excluded: chain b residue 10 ILE Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 143 LYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 196 GLU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 140 LYS Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 62 ILE Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 167 LYS Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 99 LYS Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 582 optimal weight: 0.9990 chunk 443 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 281 optimal weight: 5.9990 chunk 395 optimal weight: 0.0170 chunk 591 optimal weight: 7.9990 chunk 626 optimal weight: 8.9990 chunk 309 optimal weight: 0.0970 chunk 560 optimal weight: 4.9990 chunk 168 optimal weight: 20.0000 overall best weight: 1.2820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 137 GLN V 11 GLN a 137 GLN y 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 49487 Z= 0.183 Angle : 0.449 5.039 66767 Z= 0.237 Chirality : 0.041 0.148 8136 Planarity : 0.005 0.053 8376 Dihedral : 4.008 34.384 6625 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.48 % Allowed : 15.69 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.89 (0.10), residues: 6408 helix: 2.34 (0.08), residues: 4032 sheet: -0.22 (0.15), residues: 1152 loop : -0.97 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP h 165 HIS 0.005 0.001 HIS L 8 PHE 0.019 0.001 PHE c 97 TYR 0.007 0.001 TYR a 105 ARG 0.006 0.000 ARG y 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 784 time to evaluate : 5.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8306 (mtpp) cc_final: 0.7855 (mtmm) REVERT: 2 23 GLU cc_start: 0.7052 (tt0) cc_final: 0.6823 (mt-10) REVERT: 3 50 LYS cc_start: 0.8356 (mttt) cc_final: 0.7944 (mtmm) REVERT: I 27 LEU cc_start: 0.8060 (tp) cc_final: 0.7638 (mt) REVERT: I 93 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7094 (mm-30) REVERT: I 97 PHE cc_start: 0.8123 (m-80) cc_final: 0.7849 (m-80) REVERT: I 101 LYS cc_start: 0.8065 (mptt) cc_final: 0.7821 (mttt) REVERT: I 110 MET cc_start: 0.8428 (ttt) cc_final: 0.8047 (ttt) REVERT: I 119 MET cc_start: 0.8286 (mtp) cc_final: 0.8045 (mtp) REVERT: J 27 LEU cc_start: 0.8050 (tp) cc_final: 0.7584 (mt) REVERT: J 119 MET cc_start: 0.8376 (mtp) cc_final: 0.8067 (mtp) REVERT: J 120 LYS cc_start: 0.7833 (mttt) cc_final: 0.7510 (mptt) REVERT: K 27 LEU cc_start: 0.7988 (tp) cc_final: 0.7609 (mt) REVERT: K 54 SER cc_start: 0.8656 (p) cc_final: 0.8435 (m) REVERT: K 101 LYS cc_start: 0.7261 (mmtt) cc_final: 0.7005 (mptt) REVERT: K 119 MET cc_start: 0.8322 (mtp) cc_final: 0.8049 (mtp) REVERT: K 177 SER cc_start: 0.9015 (p) cc_final: 0.8561 (m) REVERT: L 27 LEU cc_start: 0.7968 (tp) cc_final: 0.7609 (mt) REVERT: L 196 GLU cc_start: 0.6978 (pp20) cc_final: 0.6487 (mm-30) REVERT: M 27 LEU cc_start: 0.7994 (tp) cc_final: 0.7592 (mt) REVERT: M 110 MET cc_start: 0.8601 (ttt) cc_final: 0.8151 (ttp) REVERT: M 119 MET cc_start: 0.8294 (mtp) cc_final: 0.8017 (mtp) REVERT: N 27 LEU cc_start: 0.8163 (tp) cc_final: 0.7718 (mt) REVERT: N 163 CYS cc_start: 0.6787 (m) cc_final: 0.6542 (m) REVERT: O 27 LEU cc_start: 0.7833 (tp) cc_final: 0.7463 (mt) REVERT: O 57 LYS cc_start: 0.7770 (ttmm) cc_final: 0.7194 (tttm) REVERT: O 196 GLU cc_start: 0.7058 (pp20) cc_final: 0.6490 (mm-30) REVERT: P 50 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8210 (mtmm) REVERT: Q 50 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8023 (mtmm) REVERT: S 50 LYS cc_start: 0.8168 (mttt) cc_final: 0.7850 (mtmm) REVERT: S 65 GLN cc_start: 0.6896 (OUTLIER) cc_final: 0.5636 (tp40) REVERT: T 16 LYS cc_start: 0.8233 (mtmm) cc_final: 0.8022 (mtmt) REVERT: T 50 LYS cc_start: 0.8356 (mttt) cc_final: 0.8004 (mtmm) REVERT: U 119 MET cc_start: 0.8284 (mtp) cc_final: 0.7976 (mtp) REVERT: U 120 LYS cc_start: 0.7877 (mttp) cc_final: 0.7436 (mptt) REVERT: X 50 LYS cc_start: 0.8389 (mtmt) cc_final: 0.8103 (mtmm) REVERT: Y 27 LEU cc_start: 0.7838 (tp) cc_final: 0.7475 (mt) REVERT: Y 57 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7639 (tttp) REVERT: Y 119 MET cc_start: 0.8302 (mtp) cc_final: 0.8048 (mtp) REVERT: Y 120 LYS cc_start: 0.7880 (mtpt) cc_final: 0.7451 (mptt) REVERT: Z 27 LEU cc_start: 0.7783 (tp) cc_final: 0.7457 (mt) REVERT: Z 97 PHE cc_start: 0.8219 (m-80) cc_final: 0.7927 (m-80) REVERT: Z 120 LYS cc_start: 0.7795 (mttt) cc_final: 0.7474 (mptt) REVERT: Z 140 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7667 (mtmt) REVERT: a 27 LEU cc_start: 0.7651 (tp) cc_final: 0.7344 (mt) REVERT: a 93 GLU cc_start: 0.7480 (mp0) cc_final: 0.7139 (mm-30) REVERT: a 120 LYS cc_start: 0.7978 (mttt) cc_final: 0.7620 (mptt) REVERT: a 196 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: b 7 LYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7712 (tttm) REVERT: b 57 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7094 (tttp) REVERT: b 119 MET cc_start: 0.8323 (mtp) cc_final: 0.8016 (mtp) REVERT: b 120 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7428 (mmtm) REVERT: c 27 LEU cc_start: 0.7864 (tp) cc_final: 0.7521 (mt) REVERT: c 119 MET cc_start: 0.8241 (mtp) cc_final: 0.7994 (mtp) REVERT: c 120 LYS cc_start: 0.8006 (mttt) cc_final: 0.7678 (mptt) REVERT: c 196 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6866 (mm-30) REVERT: d 9 LYS cc_start: 0.7892 (mttm) cc_final: 0.7543 (mtmt) REVERT: d 17 ASN cc_start: 0.7420 (p0) cc_final: 0.7194 (p0) REVERT: d 27 LEU cc_start: 0.7948 (tp) cc_final: 0.7614 (mt) REVERT: d 110 MET cc_start: 0.8501 (ttt) cc_final: 0.8274 (ttt) REVERT: d 119 MET cc_start: 0.8461 (mtm) cc_final: 0.8126 (mtp) REVERT: d 120 LYS cc_start: 0.7760 (mttt) cc_final: 0.7379 (mptt) REVERT: e 27 LEU cc_start: 0.8063 (tp) cc_final: 0.7592 (mt) REVERT: e 120 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7716 (mptt) REVERT: e 196 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6964 (mm-30) REVERT: f 27 LEU cc_start: 0.7860 (tp) cc_final: 0.7501 (mt) REVERT: f 62 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8169 (mm) REVERT: f 119 MET cc_start: 0.8355 (mtp) cc_final: 0.8052 (mtp) REVERT: f 140 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7574 (mtmt) REVERT: g 2 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7103 (tt0) REVERT: g 27 LEU cc_start: 0.8042 (tp) cc_final: 0.7568 (mt) REVERT: g 62 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8225 (mm) REVERT: g 93 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7106 (mm-30) REVERT: g 120 LYS cc_start: 0.7940 (mttt) cc_final: 0.7603 (mptt) REVERT: h 62 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8158 (mm) REVERT: h 96 GLN cc_start: 0.7572 (tt0) cc_final: 0.7334 (tt0) REVERT: h 119 MET cc_start: 0.8288 (mtp) cc_final: 0.7924 (mtp) REVERT: h 120 LYS cc_start: 0.7802 (mttm) cc_final: 0.7526 (mptt) REVERT: i 62 ILE cc_start: 0.8474 (OUTLIER) cc_final: 0.8144 (mm) REVERT: i 93 GLU cc_start: 0.7505 (mt-10) cc_final: 0.7254 (mm-30) REVERT: i 119 MET cc_start: 0.8251 (mtp) cc_final: 0.8006 (mtp) REVERT: i 120 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7571 (mptt) REVERT: j 27 LEU cc_start: 0.8021 (tp) cc_final: 0.7522 (mt) REVERT: j 31 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7010 (mt-10) REVERT: j 120 LYS cc_start: 0.7767 (mtmt) cc_final: 0.7352 (mptt) REVERT: k 27 LEU cc_start: 0.7915 (tp) cc_final: 0.7526 (mt) REVERT: k 62 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8171 (mm) REVERT: k 97 PHE cc_start: 0.7726 (m-80) cc_final: 0.7499 (m-80) REVERT: k 119 MET cc_start: 0.8262 (mtp) cc_final: 0.7919 (mtp) REVERT: l 27 LEU cc_start: 0.7822 (tp) cc_final: 0.7453 (mt) REVERT: l 62 ILE cc_start: 0.8504 (mm) cc_final: 0.8256 (mm) REVERT: l 110 MET cc_start: 0.8563 (ttt) cc_final: 0.8123 (ttt) REVERT: m 27 LEU cc_start: 0.7816 (tp) cc_final: 0.7490 (mt) REVERT: n 27 LEU cc_start: 0.8073 (tp) cc_final: 0.7614 (mt) REVERT: n 99 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7847 (ttmm) REVERT: n 120 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7493 (mmtm) REVERT: o 50 LYS cc_start: 0.8375 (mtpp) cc_final: 0.7923 (mtmm) REVERT: p 50 LYS cc_start: 0.8345 (mtmt) cc_final: 0.8039 (mtmm) REVERT: q 50 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8211 (mtmm) REVERT: s 50 LYS cc_start: 0.8398 (mtpp) cc_final: 0.7896 (mtmm) REVERT: t 50 LYS cc_start: 0.8153 (mttt) cc_final: 0.7873 (mtmm) REVERT: v 5 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6316 (mt) REVERT: v 50 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7970 (mtmm) REVERT: w 50 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8018 (mtmm) REVERT: y 23 GLU cc_start: 0.6945 (tt0) cc_final: 0.6698 (mt-10) outliers start: 127 outliers final: 45 residues processed: 883 average time/residue: 1.8478 time to fit residues: 1972.0142 Evaluate side-chains 804 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 742 time to evaluate : 5.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 62 MET Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 15 LEU Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 98 CYS Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 196 GLU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 98 CYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 196 GLU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 140 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 6 LYS Chi-restraints excluded: chain g residue 62 ILE Chi-restraints excluded: chain g residue 98 CYS Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 62 ILE Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 99 LYS Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain k residue 98 CYS Chi-restraints excluded: chain m residue 6 LYS Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 99 LYS Chi-restraints excluded: chain p residue 59 GLU Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain x residue 59 GLU Chi-restraints excluded: chain y residue 59 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 521 optimal weight: 0.9980 chunk 355 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 466 optimal weight: 0.9980 chunk 258 optimal weight: 0.0370 chunk 534 optimal weight: 0.4980 chunk 432 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 319 optimal weight: 4.9990 chunk 562 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN 3 11 GLN a 96 GLN p 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 49487 Z= 0.135 Angle : 0.414 6.521 66767 Z= 0.218 Chirality : 0.040 0.148 8136 Planarity : 0.004 0.052 8376 Dihedral : 3.816 32.896 6625 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.02 % Allowed : 16.38 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.20 (0.10), residues: 6408 helix: 2.62 (0.08), residues: 4032 sheet: -0.17 (0.15), residues: 1152 loop : -0.90 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP h 165 HIS 0.004 0.001 HIS L 8 PHE 0.024 0.001 PHE d 97 TYR 0.005 0.001 TYR a 105 ARG 0.006 0.000 ARG p 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 781 time to evaluate : 5.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7926 (mtmm) REVERT: 2 23 GLU cc_start: 0.6997 (tt0) cc_final: 0.6771 (mt-10) REVERT: 2 50 LYS cc_start: 0.8444 (mtpt) cc_final: 0.8056 (mtmm) REVERT: 3 50 LYS cc_start: 0.8339 (mttt) cc_final: 0.7912 (mtmm) REVERT: I 27 LEU cc_start: 0.7999 (tp) cc_final: 0.7597 (mt) REVERT: I 93 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7077 (mm-30) REVERT: I 119 MET cc_start: 0.8254 (mtp) cc_final: 0.7989 (mtp) REVERT: J 27 LEU cc_start: 0.8038 (tp) cc_final: 0.7584 (mt) REVERT: J 119 MET cc_start: 0.8321 (mtp) cc_final: 0.8024 (mtp) REVERT: J 120 LYS cc_start: 0.7825 (mttt) cc_final: 0.7503 (mptt) REVERT: K 27 LEU cc_start: 0.7970 (tp) cc_final: 0.7573 (mt) REVERT: K 101 LYS cc_start: 0.7197 (mmtt) cc_final: 0.6986 (mptt) REVERT: K 110 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8146 (ttt) REVERT: K 119 MET cc_start: 0.8307 (mtp) cc_final: 0.8030 (mtp) REVERT: K 177 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8552 (m) REVERT: L 27 LEU cc_start: 0.7989 (tp) cc_final: 0.7544 (mt) REVERT: L 196 GLU cc_start: 0.6986 (pp20) cc_final: 0.6531 (mm-30) REVERT: M 2 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7224 (tt0) REVERT: M 14 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8623 (mt) REVERT: M 27 LEU cc_start: 0.8050 (tp) cc_final: 0.7517 (mt) REVERT: M 110 MET cc_start: 0.8584 (ttt) cc_final: 0.8126 (ttp) REVERT: M 119 MET cc_start: 0.8358 (mtp) cc_final: 0.8024 (mtp) REVERT: N 2 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: N 9 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7502 (mttt) REVERT: N 27 LEU cc_start: 0.8154 (tp) cc_final: 0.7717 (mt) REVERT: N 54 SER cc_start: 0.8699 (OUTLIER) cc_final: 0.8401 (m) REVERT: N 59 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7281 (mtmt) REVERT: N 163 CYS cc_start: 0.6769 (m) cc_final: 0.6476 (m) REVERT: O 27 LEU cc_start: 0.7788 (tp) cc_final: 0.7428 (mt) REVERT: O 57 LYS cc_start: 0.7746 (ttmm) cc_final: 0.7159 (tttm) REVERT: O 196 GLU cc_start: 0.7050 (pp20) cc_final: 0.6591 (mm-30) REVERT: P 50 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8154 (mtmm) REVERT: Q 50 LYS cc_start: 0.8336 (mtmt) cc_final: 0.8036 (mtmm) REVERT: S 50 LYS cc_start: 0.8182 (mttt) cc_final: 0.7854 (mtmm) REVERT: S 65 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.5560 (tp40) REVERT: T 16 LYS cc_start: 0.8216 (mtmm) cc_final: 0.8000 (mtmt) REVERT: T 50 LYS cc_start: 0.8311 (mttt) cc_final: 0.8041 (mttp) REVERT: U 14 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8519 (mt) REVERT: U 119 MET cc_start: 0.8225 (mtp) cc_final: 0.7893 (mtp) REVERT: U 120 LYS cc_start: 0.7835 (mttp) cc_final: 0.7401 (mptt) REVERT: X 50 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8144 (mtmm) REVERT: X 57 ASP cc_start: 0.7326 (m-30) cc_final: 0.7099 (m-30) REVERT: Y 27 LEU cc_start: 0.7845 (tp) cc_final: 0.7493 (mt) REVERT: Y 57 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7658 (tttp) REVERT: Y 93 GLU cc_start: 0.7450 (mp0) cc_final: 0.7207 (mm-30) REVERT: Y 119 MET cc_start: 0.8268 (mtp) cc_final: 0.8013 (mtp) REVERT: Y 120 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7439 (mptt) REVERT: Z 27 LEU cc_start: 0.7753 (tp) cc_final: 0.7426 (mt) REVERT: Z 97 PHE cc_start: 0.8207 (m-80) cc_final: 0.7947 (m-80) REVERT: Z 120 LYS cc_start: 0.7751 (mttt) cc_final: 0.7441 (mptt) REVERT: Z 140 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7644 (mtmt) REVERT: a 27 LEU cc_start: 0.7635 (tp) cc_final: 0.7335 (mt) REVERT: a 93 GLU cc_start: 0.7379 (mp0) cc_final: 0.7164 (mm-30) REVERT: a 110 MET cc_start: 0.8529 (ttp) cc_final: 0.8302 (ttt) REVERT: a 120 LYS cc_start: 0.8004 (mttt) cc_final: 0.7653 (mptt) REVERT: a 196 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6817 (mm-30) REVERT: b 17 ASN cc_start: 0.7407 (OUTLIER) cc_final: 0.7143 (t0) REVERT: b 57 LYS cc_start: 0.7347 (ttmt) cc_final: 0.7031 (tttp) REVERT: b 119 MET cc_start: 0.8244 (mtp) cc_final: 0.7956 (mtp) REVERT: b 120 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7415 (mmtm) REVERT: c 27 LEU cc_start: 0.7858 (tp) cc_final: 0.7511 (mt) REVERT: c 119 MET cc_start: 0.8222 (mtp) cc_final: 0.7967 (mtp) REVERT: c 120 LYS cc_start: 0.7987 (mttt) cc_final: 0.7670 (mptt) REVERT: c 196 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: d 17 ASN cc_start: 0.7420 (p0) cc_final: 0.7214 (p0) REVERT: d 27 LEU cc_start: 0.7908 (tp) cc_final: 0.7518 (mt) REVERT: d 110 MET cc_start: 0.8488 (ttt) cc_final: 0.8144 (ttt) REVERT: d 119 MET cc_start: 0.8430 (mtm) cc_final: 0.8099 (mtp) REVERT: d 120 LYS cc_start: 0.7739 (mttt) cc_final: 0.7392 (mptt) REVERT: e 27 LEU cc_start: 0.8100 (tp) cc_final: 0.7631 (mt) REVERT: e 120 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7732 (mptt) REVERT: e 196 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: f 27 LEU cc_start: 0.7837 (tp) cc_final: 0.7476 (mt) REVERT: f 119 MET cc_start: 0.8271 (mtp) cc_final: 0.7970 (mtp) REVERT: f 140 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8056 (mtmm) REVERT: g 2 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7111 (tt0) REVERT: g 17 ASN cc_start: 0.6943 (OUTLIER) cc_final: 0.6722 (t0) REVERT: g 27 LEU cc_start: 0.8037 (tp) cc_final: 0.7554 (mt) REVERT: g 93 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7084 (mm-30) REVERT: g 120 LYS cc_start: 0.7913 (mttt) cc_final: 0.7593 (mptt) REVERT: h 96 GLN cc_start: 0.7588 (tt0) cc_final: 0.7373 (tt0) REVERT: h 119 MET cc_start: 0.8250 (mtp) cc_final: 0.7907 (mtp) REVERT: h 120 LYS cc_start: 0.7764 (mttm) cc_final: 0.7487 (mptt) REVERT: i 93 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7185 (mm-30) REVERT: i 119 MET cc_start: 0.8210 (mtp) cc_final: 0.7957 (mtp) REVERT: i 120 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7631 (mptt) REVERT: j 27 LEU cc_start: 0.8015 (tp) cc_final: 0.7494 (mt) REVERT: j 31 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7034 (mt-10) REVERT: j 120 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7348 (mptt) REVERT: k 27 LEU cc_start: 0.7913 (tp) cc_final: 0.7528 (mt) REVERT: k 62 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8152 (mm) REVERT: k 119 MET cc_start: 0.8219 (mtp) cc_final: 0.7857 (mtp) REVERT: l 27 LEU cc_start: 0.7797 (tp) cc_final: 0.7426 (mt) REVERT: l 110 MET cc_start: 0.8521 (ttt) cc_final: 0.8113 (ttt) REVERT: m 27 LEU cc_start: 0.7799 (tp) cc_final: 0.7482 (mt) REVERT: m 93 GLU cc_start: 0.7427 (mp0) cc_final: 0.7210 (mt-10) REVERT: n 27 LEU cc_start: 0.8040 (tp) cc_final: 0.7548 (mt) REVERT: n 101 LYS cc_start: 0.7900 (mptt) cc_final: 0.7656 (mptt) REVERT: n 120 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7509 (mmtm) REVERT: o 50 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7950 (mtmm) REVERT: p 50 LYS cc_start: 0.8332 (mtmt) cc_final: 0.8018 (mtmm) REVERT: s 50 LYS cc_start: 0.8392 (mtpp) cc_final: 0.7886 (mtmm) REVERT: t 49 ARG cc_start: 0.7585 (ttp80) cc_final: 0.7323 (ttp80) REVERT: t 50 LYS cc_start: 0.8132 (mttt) cc_final: 0.7851 (mtmm) REVERT: v 50 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8001 (mtmm) REVERT: w 50 LYS cc_start: 0.8373 (mtmt) cc_final: 0.7976 (mtmm) REVERT: y 23 GLU cc_start: 0.6952 (tt0) cc_final: 0.6704 (mt-10) REVERT: y 50 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7998 (mtmm) outliers start: 103 outliers final: 37 residues processed: 854 average time/residue: 1.8581 time to fit residues: 1916.6853 Evaluate side-chains 801 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 743 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 62 MET Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain M residue 2 GLU Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain N residue 2 GLU Chi-restraints excluded: chain N residue 9 LYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 62 MET Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 196 GLU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 17 ASN Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain e residue 196 GLU Chi-restraints excluded: chain f residue 140 LYS Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 17 ASN Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain p residue 62 MET Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain s residue 62 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 210 optimal weight: 0.9980 chunk 564 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 chunk 367 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 626 optimal weight: 8.9990 chunk 520 optimal weight: 4.9990 chunk 290 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 329 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN I 8 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49487 Z= 0.172 Angle : 0.436 5.891 66767 Z= 0.229 Chirality : 0.041 0.148 8136 Planarity : 0.004 0.053 8376 Dihedral : 3.831 33.668 6625 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.33 % Allowed : 16.40 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.25 (0.10), residues: 6408 helix: 2.68 (0.08), residues: 3984 sheet: -0.17 (0.15), residues: 1152 loop : -0.84 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 165 HIS 0.005 0.001 HIS L 8 PHE 0.027 0.001 PHE d 97 TYR 0.006 0.001 TYR a 105 ARG 0.007 0.000 ARG s 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 768 time to evaluate : 5.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7940 (mtmm) REVERT: 2 23 GLU cc_start: 0.7017 (tt0) cc_final: 0.6784 (mt-10) REVERT: 3 50 LYS cc_start: 0.8361 (mttt) cc_final: 0.7938 (mtmm) REVERT: I 27 LEU cc_start: 0.7989 (tp) cc_final: 0.7591 (mt) REVERT: I 101 LYS cc_start: 0.8059 (mptt) cc_final: 0.7852 (mttt) REVERT: I 119 MET cc_start: 0.8274 (mtp) cc_final: 0.8022 (mtp) REVERT: J 27 LEU cc_start: 0.8023 (tp) cc_final: 0.7583 (mt) REVERT: J 119 MET cc_start: 0.8324 (mtp) cc_final: 0.8039 (mtp) REVERT: J 120 LYS cc_start: 0.7846 (mttt) cc_final: 0.7517 (mptt) REVERT: K 27 LEU cc_start: 0.7966 (tp) cc_final: 0.7536 (mt) REVERT: K 101 LYS cc_start: 0.7231 (mmtt) cc_final: 0.7011 (mptt) REVERT: K 110 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8088 (ttt) REVERT: K 119 MET cc_start: 0.8316 (mtp) cc_final: 0.8053 (mtp) REVERT: K 177 SER cc_start: 0.9002 (OUTLIER) cc_final: 0.8573 (m) REVERT: L 27 LEU cc_start: 0.7962 (tp) cc_final: 0.7444 (mt) REVERT: L 31 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7096 (mt-10) REVERT: L 196 GLU cc_start: 0.6965 (pp20) cc_final: 0.6513 (mm-30) REVERT: M 14 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8600 (mt) REVERT: M 27 LEU cc_start: 0.8051 (tp) cc_final: 0.7579 (mt) REVERT: M 110 MET cc_start: 0.8569 (ttt) cc_final: 0.8166 (ttt) REVERT: M 119 MET cc_start: 0.8372 (mtp) cc_final: 0.8043 (mtp) REVERT: N 14 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8559 (mt) REVERT: N 27 LEU cc_start: 0.8206 (tp) cc_final: 0.7740 (mt) REVERT: N 54 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8412 (m) REVERT: O 27 LEU cc_start: 0.7798 (tp) cc_final: 0.7438 (mt) REVERT: O 57 LYS cc_start: 0.7721 (ttmm) cc_final: 0.7223 (tttm) REVERT: O 196 GLU cc_start: 0.7057 (pp20) cc_final: 0.6592 (mm-30) REVERT: P 50 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8133 (mtmm) REVERT: Q 50 LYS cc_start: 0.8331 (mtmt) cc_final: 0.8027 (mtmm) REVERT: S 50 LYS cc_start: 0.8177 (mttt) cc_final: 0.7841 (mtmm) REVERT: S 65 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5574 (tp40) REVERT: T 16 LYS cc_start: 0.8227 (mtmm) cc_final: 0.8010 (mtmt) REVERT: T 50 LYS cc_start: 0.8328 (mttt) cc_final: 0.7964 (mtmm) REVERT: U 14 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8554 (mt) REVERT: U 119 MET cc_start: 0.8238 (mtp) cc_final: 0.7933 (mtp) REVERT: U 120 LYS cc_start: 0.7858 (mttp) cc_final: 0.7403 (mptt) REVERT: X 50 LYS cc_start: 0.8436 (mtmt) cc_final: 0.8145 (mtmm) REVERT: Y 27 LEU cc_start: 0.7849 (tp) cc_final: 0.7490 (mt) REVERT: Y 57 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7645 (tttp) REVERT: Y 93 GLU cc_start: 0.7406 (mp0) cc_final: 0.7168 (mm-30) REVERT: Y 119 MET cc_start: 0.8283 (mtp) cc_final: 0.8042 (mtp) REVERT: Y 120 LYS cc_start: 0.7881 (mtpt) cc_final: 0.7458 (mptt) REVERT: Z 27 LEU cc_start: 0.7757 (tp) cc_final: 0.7441 (mt) REVERT: Z 97 PHE cc_start: 0.8173 (m-80) cc_final: 0.7938 (m-80) REVERT: Z 120 LYS cc_start: 0.7742 (mttt) cc_final: 0.7427 (mptt) REVERT: Z 140 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7610 (mtmt) REVERT: a 27 LEU cc_start: 0.7650 (tp) cc_final: 0.7401 (mt) REVERT: a 93 GLU cc_start: 0.7363 (mp0) cc_final: 0.7159 (mm-30) REVERT: a 110 MET cc_start: 0.8526 (ttp) cc_final: 0.8306 (ttt) REVERT: a 120 LYS cc_start: 0.8005 (mttt) cc_final: 0.7648 (mptt) REVERT: a 196 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6823 (mm-30) REVERT: b 17 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7165 (t0) REVERT: b 57 LYS cc_start: 0.7338 (ttmt) cc_final: 0.7007 (tttp) REVERT: b 119 MET cc_start: 0.8268 (mtp) cc_final: 0.7981 (mtp) REVERT: b 120 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7418 (mmtm) REVERT: c 27 LEU cc_start: 0.7868 (tp) cc_final: 0.7531 (mt) REVERT: c 119 MET cc_start: 0.8234 (mtp) cc_final: 0.7989 (mtp) REVERT: c 120 LYS cc_start: 0.7992 (mttt) cc_final: 0.7660 (mptt) REVERT: c 196 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.7102 (mm-30) REVERT: d 27 LEU cc_start: 0.7947 (tp) cc_final: 0.7548 (mt) REVERT: d 119 MET cc_start: 0.8485 (mtm) cc_final: 0.8178 (mtp) REVERT: d 120 LYS cc_start: 0.7765 (mttt) cc_final: 0.7410 (mptt) REVERT: e 27 LEU cc_start: 0.8117 (tp) cc_final: 0.7653 (mt) REVERT: e 120 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7732 (mptt) REVERT: e 196 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6983 (mm-30) REVERT: f 27 LEU cc_start: 0.7841 (tp) cc_final: 0.7487 (mt) REVERT: f 62 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8161 (mm) REVERT: f 119 MET cc_start: 0.8316 (mtp) cc_final: 0.8028 (mtp) REVERT: g 2 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7128 (tt0) REVERT: g 27 LEU cc_start: 0.8028 (tp) cc_final: 0.7561 (mt) REVERT: g 93 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7122 (mm-30) REVERT: g 120 LYS cc_start: 0.7943 (mttt) cc_final: 0.7637 (mptt) REVERT: h 27 LEU cc_start: 0.8173 (tp) cc_final: 0.7566 (mt) REVERT: h 119 MET cc_start: 0.8260 (mtp) cc_final: 0.7929 (mtp) REVERT: h 120 LYS cc_start: 0.7772 (mttm) cc_final: 0.7478 (mptt) REVERT: i 62 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8119 (mm) REVERT: i 93 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7131 (mm-30) REVERT: i 119 MET cc_start: 0.8227 (mtp) cc_final: 0.7965 (mtp) REVERT: i 120 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7618 (mptt) REVERT: j 27 LEU cc_start: 0.7993 (tp) cc_final: 0.7480 (mt) REVERT: j 31 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7092 (mt-10) REVERT: j 120 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7376 (mptt) REVERT: k 27 LEU cc_start: 0.7948 (tp) cc_final: 0.7546 (mt) REVERT: k 62 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8165 (mm) REVERT: k 119 MET cc_start: 0.8219 (mtp) cc_final: 0.7897 (mtp) REVERT: l 27 LEU cc_start: 0.7832 (tp) cc_final: 0.7466 (mt) REVERT: l 110 MET cc_start: 0.8530 (ttt) cc_final: 0.8124 (ttt) REVERT: l 196 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: m 27 LEU cc_start: 0.7813 (tp) cc_final: 0.7494 (mt) REVERT: n 27 LEU cc_start: 0.8079 (tp) cc_final: 0.7622 (mt) REVERT: n 101 LYS cc_start: 0.7846 (mptt) cc_final: 0.7611 (mptt) REVERT: n 120 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7463 (mptt) REVERT: o 50 LYS cc_start: 0.8418 (mtpp) cc_final: 0.7964 (mtmm) REVERT: p 50 LYS cc_start: 0.8319 (mtmt) cc_final: 0.7984 (mtmm) REVERT: q 35 ASP cc_start: 0.6479 (m-30) cc_final: 0.6278 (m-30) REVERT: s 50 LYS cc_start: 0.8396 (mtpp) cc_final: 0.7881 (mtmm) REVERT: t 50 LYS cc_start: 0.8152 (mttt) cc_final: 0.7861 (mtmm) REVERT: v 5 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6308 (mt) REVERT: v 50 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8014 (mtmm) REVERT: w 50 LYS cc_start: 0.8393 (mtmt) cc_final: 0.8089 (mtmm) REVERT: y 23 GLU cc_start: 0.6963 (tt0) cc_final: 0.6698 (mt-10) REVERT: y 50 LYS cc_start: 0.8438 (mtpt) cc_final: 0.7991 (mtmm) outliers start: 119 outliers final: 51 residues processed: 854 average time/residue: 1.9101 time to fit residues: 1969.7981 Evaluate side-chains 809 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 737 time to evaluate : 5.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 31 GLU Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 14 LEU Chi-restraints excluded: chain N residue 14 LEU Chi-restraints excluded: chain N residue 17 ASN Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain S residue 30 LYS Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 17 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 57 LYS Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain a residue 196 GLU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 17 ASN Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 98 CYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 83 GLU Chi-restraints excluded: chain e residue 196 GLU Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 98 CYS Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain i residue 62 ILE Chi-restraints excluded: chain i residue 167 LYS Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 62 ILE Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain l residue 196 GLU Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 14 LEU Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain p residue 62 MET Chi-restraints excluded: chain r residue 62 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain t residue 62 MET Chi-restraints excluded: chain v residue 5 LEU Chi-restraints excluded: chain y residue 62 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 604 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 357 optimal weight: 1.9990 chunk 457 optimal weight: 0.0770 chunk 354 optimal weight: 0.0010 chunk 527 optimal weight: 0.9980 chunk 350 optimal weight: 6.9990 chunk 624 optimal weight: 0.9980 chunk 390 optimal weight: 7.9990 chunk 380 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 overall best weight: 0.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN 2 11 GLN y 11 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 49487 Z= 0.125 Angle : 0.406 6.192 66767 Z= 0.214 Chirality : 0.040 0.147 8136 Planarity : 0.004 0.051 8376 Dihedral : 3.686 32.236 6625 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.78 % Allowed : 17.10 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.45 (0.10), residues: 6408 helix: 2.86 (0.08), residues: 4008 sheet: -0.12 (0.15), residues: 1152 loop : -0.87 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP h 165 HIS 0.004 0.001 HIS L 8 PHE 0.026 0.001 PHE d 97 TYR 0.004 0.001 TYR f 105 ARG 0.005 0.000 ARG z 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 857 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 766 time to evaluate : 5.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8326 (mtpp) cc_final: 0.7954 (mtmm) REVERT: 2 23 GLU cc_start: 0.6985 (tt0) cc_final: 0.6781 (mt-10) REVERT: 2 50 LYS cc_start: 0.8467 (mtpt) cc_final: 0.8109 (mtmm) REVERT: 3 50 LYS cc_start: 0.8352 (mttt) cc_final: 0.7927 (mtmm) REVERT: I 27 LEU cc_start: 0.7999 (tp) cc_final: 0.7587 (mt) REVERT: I 119 MET cc_start: 0.8248 (mtp) cc_final: 0.7975 (mtp) REVERT: J 27 LEU cc_start: 0.8012 (tp) cc_final: 0.7580 (mt) REVERT: J 119 MET cc_start: 0.8284 (mtp) cc_final: 0.8016 (mtp) REVERT: J 120 LYS cc_start: 0.7814 (mttt) cc_final: 0.7489 (mptt) REVERT: K 27 LEU cc_start: 0.8040 (tp) cc_final: 0.7571 (mt) REVERT: K 101 LYS cc_start: 0.7210 (mmtt) cc_final: 0.6944 (mptt) REVERT: K 110 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8139 (ttt) REVERT: K 119 MET cc_start: 0.8291 (mtp) cc_final: 0.8013 (mtp) REVERT: K 177 SER cc_start: 0.8999 (OUTLIER) cc_final: 0.8573 (m) REVERT: L 27 LEU cc_start: 0.7961 (tp) cc_final: 0.7582 (mt) REVERT: M 27 LEU cc_start: 0.8024 (tp) cc_final: 0.7555 (mt) REVERT: M 110 MET cc_start: 0.8540 (ttt) cc_final: 0.8088 (ttp) REVERT: M 119 MET cc_start: 0.8349 (mtp) cc_final: 0.8034 (mtp) REVERT: N 27 LEU cc_start: 0.8160 (tp) cc_final: 0.7656 (mt) REVERT: N 54 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8386 (m) REVERT: N 59 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7247 (mtmt) REVERT: O 27 LEU cc_start: 0.7769 (tp) cc_final: 0.7428 (mt) REVERT: O 57 LYS cc_start: 0.7705 (ttmm) cc_final: 0.7206 (tttm) REVERT: O 140 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7440 (mtmt) REVERT: O 196 GLU cc_start: 0.7050 (pp20) cc_final: 0.6605 (mm-30) REVERT: P 50 LYS cc_start: 0.8419 (mtmt) cc_final: 0.8122 (mtmm) REVERT: Q 50 LYS cc_start: 0.8321 (mtmt) cc_final: 0.8026 (mtmm) REVERT: S 50 LYS cc_start: 0.8187 (mttt) cc_final: 0.7852 (mtmm) REVERT: S 65 GLN cc_start: 0.6750 (OUTLIER) cc_final: 0.5498 (tp40) REVERT: T 16 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7974 (mtmt) REVERT: T 50 LYS cc_start: 0.8307 (mttt) cc_final: 0.8031 (mttp) REVERT: U 119 MET cc_start: 0.8211 (mtp) cc_final: 0.7884 (mtp) REVERT: U 120 LYS cc_start: 0.7820 (mttp) cc_final: 0.7394 (mptt) REVERT: X 50 LYS cc_start: 0.8428 (mtmt) cc_final: 0.8142 (mtmm) REVERT: Y 27 LEU cc_start: 0.7836 (tp) cc_final: 0.7467 (mt) REVERT: Y 93 GLU cc_start: 0.7435 (mp0) cc_final: 0.7170 (mm-30) REVERT: Y 119 MET cc_start: 0.8245 (mtp) cc_final: 0.7992 (mtp) REVERT: Y 120 LYS cc_start: 0.7883 (mtpt) cc_final: 0.7467 (mptt) REVERT: Y 167 LYS cc_start: 0.7940 (mtmm) cc_final: 0.7696 (mtmt) REVERT: Z 27 LEU cc_start: 0.7724 (tp) cc_final: 0.7404 (mt) REVERT: Z 120 LYS cc_start: 0.7719 (mttt) cc_final: 0.7402 (mptt) REVERT: Z 140 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7602 (mtmt) REVERT: a 27 LEU cc_start: 0.7627 (tp) cc_final: 0.7380 (mt) REVERT: a 120 LYS cc_start: 0.8000 (mttt) cc_final: 0.7643 (mptt) REVERT: a 196 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6813 (mm-30) REVERT: b 57 LYS cc_start: 0.7273 (ttmt) cc_final: 0.6951 (tttp) REVERT: b 119 MET cc_start: 0.8205 (mtp) cc_final: 0.7929 (mtp) REVERT: b 120 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7419 (mmtm) REVERT: c 27 LEU cc_start: 0.7864 (tp) cc_final: 0.7516 (mt) REVERT: c 119 MET cc_start: 0.8204 (mtp) cc_final: 0.7940 (mtp) REVERT: c 120 LYS cc_start: 0.7990 (mttt) cc_final: 0.7678 (mptt) REVERT: c 196 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: d 27 LEU cc_start: 0.7939 (tp) cc_final: 0.7585 (mt) REVERT: d 119 MET cc_start: 0.8440 (mtm) cc_final: 0.8111 (mtp) REVERT: d 120 LYS cc_start: 0.7787 (mttt) cc_final: 0.7436 (mptt) REVERT: e 27 LEU cc_start: 0.8096 (tp) cc_final: 0.7618 (mt) REVERT: e 120 LYS cc_start: 0.8022 (mtpp) cc_final: 0.7733 (mptt) REVERT: f 27 LEU cc_start: 0.7823 (tp) cc_final: 0.7466 (mt) REVERT: f 119 MET cc_start: 0.8237 (mtp) cc_final: 0.7939 (mtp) REVERT: g 2 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: g 27 LEU cc_start: 0.8011 (tp) cc_final: 0.7543 (mt) REVERT: g 93 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7121 (mm-30) REVERT: g 120 LYS cc_start: 0.7916 (mttt) cc_final: 0.7609 (mptt) REVERT: h 119 MET cc_start: 0.8226 (mtp) cc_final: 0.7891 (mtp) REVERT: h 120 LYS cc_start: 0.7763 (mttm) cc_final: 0.7469 (mptt) REVERT: i 93 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7129 (mm-30) REVERT: i 119 MET cc_start: 0.8179 (mtp) cc_final: 0.7917 (mtp) REVERT: i 120 LYS cc_start: 0.7990 (mtmt) cc_final: 0.7646 (mptt) REVERT: j 27 LEU cc_start: 0.7985 (tp) cc_final: 0.7578 (mt) REVERT: j 120 LYS cc_start: 0.7807 (mtmt) cc_final: 0.7366 (mptt) REVERT: k 27 LEU cc_start: 0.7943 (tp) cc_final: 0.7546 (mt) REVERT: k 119 MET cc_start: 0.8178 (mtp) cc_final: 0.7845 (mtp) REVERT: l 27 LEU cc_start: 0.7809 (tp) cc_final: 0.7437 (mt) REVERT: l 196 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6875 (mm-30) REVERT: m 27 LEU cc_start: 0.7798 (tp) cc_final: 0.7490 (mt) REVERT: n 27 LEU cc_start: 0.8058 (tp) cc_final: 0.7582 (mt) REVERT: n 120 LYS cc_start: 0.7809 (mtmt) cc_final: 0.7447 (mptt) REVERT: o 50 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7936 (mtmm) REVERT: p 50 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7997 (mtmm) REVERT: s 50 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7898 (mtmm) REVERT: t 49 ARG cc_start: 0.7598 (ttp80) cc_final: 0.7384 (ttp80) REVERT: t 50 LYS cc_start: 0.8146 (mttt) cc_final: 0.7878 (mtmm) REVERT: v 5 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6292 (mt) REVERT: v 50 LYS cc_start: 0.8318 (mtmm) cc_final: 0.7991 (mtmm) REVERT: w 50 LYS cc_start: 0.8329 (mtmt) cc_final: 0.8038 (mtmm) REVERT: y 23 GLU cc_start: 0.6860 (tt0) cc_final: 0.6629 (mt-10) outliers start: 91 outliers final: 38 residues processed: 824 average time/residue: 1.9366 time to fit residues: 1922.2314 Evaluate side-chains 776 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 726 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 17 ASN Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 37 ILE Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain a residue 196 GLU Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 17 ASN Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain c residue 196 GLU Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain l residue 196 GLU Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain p residue 62 MET Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain v residue 5 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 386 optimal weight: 2.9990 chunk 249 optimal weight: 1.9990 chunk 373 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 121 optimal weight: 0.0980 chunk 397 optimal weight: 0.9990 chunk 425 optimal weight: 0.9990 chunk 308 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 490 optimal weight: 6.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN 2 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 49487 Z= 0.161 Angle : 0.431 6.283 66767 Z= 0.225 Chirality : 0.041 0.146 8136 Planarity : 0.004 0.091 8376 Dihedral : 3.741 32.798 6625 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.64 % Allowed : 17.39 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.42 (0.10), residues: 6408 helix: 2.85 (0.08), residues: 3984 sheet: -0.16 (0.15), residues: 1152 loop : -0.80 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP a 165 HIS 0.004 0.001 HIS L 8 PHE 0.031 0.001 PHE i 97 TYR 0.005 0.001 TYR a 105 ARG 0.008 0.000 ARG u 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 750 time to evaluate : 5.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7936 (mtmm) REVERT: 2 23 GLU cc_start: 0.7013 (tt0) cc_final: 0.6785 (mt-10) REVERT: 2 50 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8104 (mtmm) REVERT: 3 50 LYS cc_start: 0.8371 (mttt) cc_final: 0.7940 (mtmm) REVERT: I 2 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: I 27 LEU cc_start: 0.8008 (tp) cc_final: 0.7582 (mt) REVERT: I 41 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.7335 (m-80) REVERT: I 93 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7141 (mp0) REVERT: I 119 MET cc_start: 0.8275 (mtp) cc_final: 0.8016 (mtp) REVERT: J 27 LEU cc_start: 0.7962 (tp) cc_final: 0.7541 (mt) REVERT: J 119 MET cc_start: 0.8302 (mtp) cc_final: 0.8048 (mtp) REVERT: J 120 LYS cc_start: 0.7833 (mttt) cc_final: 0.7505 (mptt) REVERT: K 27 LEU cc_start: 0.8009 (tp) cc_final: 0.7554 (mt) REVERT: K 101 LYS cc_start: 0.7190 (mmtt) cc_final: 0.6929 (mptt) REVERT: K 110 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8106 (ttt) REVERT: K 119 MET cc_start: 0.8317 (mtp) cc_final: 0.8058 (mtp) REVERT: K 177 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8572 (m) REVERT: L 27 LEU cc_start: 0.8003 (tp) cc_final: 0.7623 (mt) REVERT: M 27 LEU cc_start: 0.8008 (tp) cc_final: 0.7635 (mt) REVERT: M 119 MET cc_start: 0.8373 (mtp) cc_final: 0.8052 (mtp) REVERT: N 27 LEU cc_start: 0.8085 (tp) cc_final: 0.7703 (mt) REVERT: N 54 SER cc_start: 0.8654 (OUTLIER) cc_final: 0.8369 (m) REVERT: N 59 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7245 (mtmt) REVERT: O 27 LEU cc_start: 0.7780 (tp) cc_final: 0.7439 (mt) REVERT: O 57 LYS cc_start: 0.7730 (ttmm) cc_final: 0.7226 (tttm) REVERT: O 140 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7477 (mtmt) REVERT: O 196 GLU cc_start: 0.7054 (pp20) cc_final: 0.6608 (mm-30) REVERT: P 50 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8128 (mtmm) REVERT: Q 50 LYS cc_start: 0.8333 (mtmt) cc_final: 0.8061 (mtmm) REVERT: S 50 LYS cc_start: 0.8210 (mttt) cc_final: 0.7879 (mtmm) REVERT: S 65 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5484 (tp40) REVERT: T 16 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7995 (mtmt) REVERT: T 50 LYS cc_start: 0.8325 (mttt) cc_final: 0.7963 (mtmm) REVERT: U 119 MET cc_start: 0.8246 (mtp) cc_final: 0.7918 (mtp) REVERT: U 120 LYS cc_start: 0.7844 (mttp) cc_final: 0.7381 (mptt) REVERT: X 50 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8164 (mtmm) REVERT: Y 27 LEU cc_start: 0.7857 (tp) cc_final: 0.7481 (mt) REVERT: Y 93 GLU cc_start: 0.7426 (mp0) cc_final: 0.7175 (mm-30) REVERT: Y 119 MET cc_start: 0.8278 (mtp) cc_final: 0.8034 (mtp) REVERT: Y 120 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7460 (mptt) REVERT: Y 167 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7682 (mtmt) REVERT: Z 27 LEU cc_start: 0.7744 (tp) cc_final: 0.7439 (mt) REVERT: Z 120 LYS cc_start: 0.7740 (mttt) cc_final: 0.7406 (mptt) REVERT: Z 140 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7625 (mtmt) REVERT: a 27 LEU cc_start: 0.7658 (tp) cc_final: 0.7405 (mt) REVERT: a 120 LYS cc_start: 0.8005 (mttt) cc_final: 0.7649 (mptt) REVERT: b 17 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.7179 (t0) REVERT: b 57 LYS cc_start: 0.7289 (ttmt) cc_final: 0.6957 (tttp) REVERT: b 119 MET cc_start: 0.8252 (mtp) cc_final: 0.7971 (mtp) REVERT: b 120 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7419 (mmtm) REVERT: c 27 LEU cc_start: 0.7882 (tp) cc_final: 0.7543 (mt) REVERT: c 119 MET cc_start: 0.8224 (mtp) cc_final: 0.7977 (mtp) REVERT: c 120 LYS cc_start: 0.8019 (mttt) cc_final: 0.7687 (mptt) REVERT: d 27 LEU cc_start: 0.7947 (tp) cc_final: 0.7589 (mt) REVERT: d 119 MET cc_start: 0.8477 (mtm) cc_final: 0.8127 (mtp) REVERT: d 120 LYS cc_start: 0.7833 (mttt) cc_final: 0.7452 (mptt) REVERT: e 27 LEU cc_start: 0.8071 (tp) cc_final: 0.7588 (mt) REVERT: e 120 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7740 (mptt) REVERT: f 27 LEU cc_start: 0.7832 (tp) cc_final: 0.7480 (mt) REVERT: f 62 ILE cc_start: 0.8418 (OUTLIER) cc_final: 0.8154 (mm) REVERT: f 119 MET cc_start: 0.8298 (mtp) cc_final: 0.8009 (mtp) REVERT: g 2 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: g 27 LEU cc_start: 0.8006 (tp) cc_final: 0.7553 (mt) REVERT: g 93 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7140 (mm-30) REVERT: g 120 LYS cc_start: 0.7943 (mttt) cc_final: 0.7626 (mptt) REVERT: h 27 LEU cc_start: 0.8109 (tp) cc_final: 0.7575 (mt) REVERT: h 119 MET cc_start: 0.8244 (mtp) cc_final: 0.7924 (mtp) REVERT: h 120 LYS cc_start: 0.7774 (mttm) cc_final: 0.7474 (mptt) REVERT: i 93 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7140 (mm-30) REVERT: i 119 MET cc_start: 0.8208 (mtp) cc_final: 0.7959 (mtp) REVERT: i 120 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7624 (mptt) REVERT: j 27 LEU cc_start: 0.7961 (tp) cc_final: 0.7529 (mt) REVERT: j 120 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7377 (mptt) REVERT: k 27 LEU cc_start: 0.7963 (tp) cc_final: 0.7551 (mt) REVERT: k 119 MET cc_start: 0.8205 (mtp) cc_final: 0.7871 (mtp) REVERT: l 27 LEU cc_start: 0.7832 (tp) cc_final: 0.7456 (mt) REVERT: l 196 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: m 27 LEU cc_start: 0.7804 (tp) cc_final: 0.7495 (mt) REVERT: n 27 LEU cc_start: 0.8080 (tp) cc_final: 0.7640 (mt) REVERT: n 97 PHE cc_start: 0.8096 (m-80) cc_final: 0.7867 (m-80) REVERT: n 120 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7470 (mptt) REVERT: o 50 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7971 (mtmm) REVERT: p 50 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7996 (mtmm) REVERT: s 50 LYS cc_start: 0.8436 (mtpp) cc_final: 0.7911 (mtmm) REVERT: t 50 LYS cc_start: 0.8161 (mttt) cc_final: 0.7860 (mtmm) REVERT: v 5 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6305 (mt) REVERT: v 50 LYS cc_start: 0.8357 (mtmm) cc_final: 0.8024 (mtmm) REVERT: w 50 LYS cc_start: 0.8395 (mtmt) cc_final: 0.8099 (mtmm) REVERT: y 23 GLU cc_start: 0.6921 (tt0) cc_final: 0.6681 (mt-10) outliers start: 84 outliers final: 44 residues processed: 810 average time/residue: 1.9031 time to fit residues: 1860.8263 Evaluate side-chains 791 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 733 time to evaluate : 5.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 17 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 4 LEU Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 98 CYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 177 SER Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain l residue 196 GLU Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 177 SER Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain u residue 62 MET Chi-restraints excluded: chain v residue 5 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 568 optimal weight: 0.8980 chunk 598 optimal weight: 5.9990 chunk 545 optimal weight: 4.9990 chunk 582 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 457 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 chunk 525 optimal weight: 2.9990 chunk 550 optimal weight: 0.0570 chunk 579 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 49487 Z= 0.194 Angle : 0.455 5.922 66767 Z= 0.238 Chirality : 0.041 0.146 8136 Planarity : 0.004 0.082 8376 Dihedral : 3.845 35.045 6625 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.53 % Allowed : 17.55 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.33 (0.10), residues: 6408 helix: 2.79 (0.08), residues: 4008 sheet: -0.17 (0.15), residues: 1152 loop : -0.97 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP i 165 HIS 0.005 0.001 HIS L 8 PHE 0.032 0.001 PHE i 97 TYR 0.006 0.001 TYR a 105 ARG 0.005 0.000 ARG t 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 755 time to evaluate : 5.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8324 (mtpp) cc_final: 0.7962 (mtmm) REVERT: 2 23 GLU cc_start: 0.7019 (tt0) cc_final: 0.6810 (mt-10) REVERT: 2 50 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8110 (mtmm) REVERT: 3 50 LYS cc_start: 0.8397 (mttt) cc_final: 0.7955 (mtmm) REVERT: I 2 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: I 27 LEU cc_start: 0.8052 (tp) cc_final: 0.7627 (mt) REVERT: I 41 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7473 (m-80) REVERT: I 93 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7182 (mp0) REVERT: I 119 MET cc_start: 0.8289 (mtp) cc_final: 0.8016 (mtp) REVERT: J 27 LEU cc_start: 0.7958 (tp) cc_final: 0.7564 (mt) REVERT: J 119 MET cc_start: 0.8315 (mtp) cc_final: 0.8053 (mtp) REVERT: J 120 LYS cc_start: 0.7846 (mttt) cc_final: 0.7502 (mptt) REVERT: K 27 LEU cc_start: 0.8003 (tp) cc_final: 0.7561 (mt) REVERT: K 101 LYS cc_start: 0.7208 (mmtt) cc_final: 0.6947 (mptt) REVERT: K 110 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8113 (ttt) REVERT: K 119 MET cc_start: 0.8324 (mtp) cc_final: 0.8071 (mtp) REVERT: K 177 SER cc_start: 0.9008 (OUTLIER) cc_final: 0.8594 (m) REVERT: L 27 LEU cc_start: 0.7973 (tp) cc_final: 0.7603 (mt) REVERT: M 27 LEU cc_start: 0.8030 (tp) cc_final: 0.7621 (mt) REVERT: M 119 MET cc_start: 0.8374 (mtp) cc_final: 0.8049 (mtp) REVERT: N 27 LEU cc_start: 0.8093 (tp) cc_final: 0.7705 (mt) REVERT: N 54 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.8415 (m) REVERT: N 59 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7261 (mtmt) REVERT: O 27 LEU cc_start: 0.7787 (tp) cc_final: 0.7448 (mt) REVERT: O 57 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7256 (tttm) REVERT: O 140 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7503 (mtmt) REVERT: O 196 GLU cc_start: 0.7055 (pp20) cc_final: 0.6595 (mm-30) REVERT: P 50 LYS cc_start: 0.8490 (mtmt) cc_final: 0.8190 (mtmm) REVERT: Q 50 LYS cc_start: 0.8414 (mtmt) cc_final: 0.8109 (mtmm) REVERT: R 50 LYS cc_start: 0.8406 (mtmm) cc_final: 0.8036 (mttt) REVERT: S 50 LYS cc_start: 0.8219 (mttt) cc_final: 0.7913 (mtmm) REVERT: S 65 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.5521 (tp40) REVERT: T 16 LYS cc_start: 0.8218 (mtmm) cc_final: 0.7999 (mtmt) REVERT: T 50 LYS cc_start: 0.8356 (mttt) cc_final: 0.7993 (mtmm) REVERT: U 119 MET cc_start: 0.8248 (mtp) cc_final: 0.7920 (mtp) REVERT: U 120 LYS cc_start: 0.7836 (mttp) cc_final: 0.7382 (mptt) REVERT: X 50 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8117 (mtmm) REVERT: Y 27 LEU cc_start: 0.7866 (tp) cc_final: 0.7490 (mt) REVERT: Y 93 GLU cc_start: 0.7382 (mp0) cc_final: 0.7152 (mm-30) REVERT: Y 119 MET cc_start: 0.8290 (mtp) cc_final: 0.8038 (mtp) REVERT: Y 120 LYS cc_start: 0.7902 (mtpt) cc_final: 0.7459 (mptt) REVERT: Y 167 LYS cc_start: 0.7934 (mtmm) cc_final: 0.7666 (mtmt) REVERT: Z 27 LEU cc_start: 0.7735 (tp) cc_final: 0.7439 (mt) REVERT: Z 120 LYS cc_start: 0.7769 (mttt) cc_final: 0.7413 (mptt) REVERT: Z 140 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7668 (mtmt) REVERT: a 27 LEU cc_start: 0.7675 (tp) cc_final: 0.7415 (mt) REVERT: a 120 LYS cc_start: 0.8035 (mttt) cc_final: 0.7701 (mptt) REVERT: b 17 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.7212 (t0) REVERT: b 57 LYS cc_start: 0.7355 (ttmt) cc_final: 0.6966 (tttp) REVERT: b 119 MET cc_start: 0.8279 (mtp) cc_final: 0.7994 (mtp) REVERT: b 120 LYS cc_start: 0.7804 (mtmt) cc_final: 0.7370 (mptt) REVERT: c 27 LEU cc_start: 0.7889 (tp) cc_final: 0.7550 (mt) REVERT: c 119 MET cc_start: 0.8238 (mtp) cc_final: 0.7980 (mtp) REVERT: c 120 LYS cc_start: 0.8033 (mttt) cc_final: 0.7694 (mptt) REVERT: d 27 LEU cc_start: 0.8001 (tp) cc_final: 0.7643 (mt) REVERT: d 119 MET cc_start: 0.8496 (mtm) cc_final: 0.8146 (mtp) REVERT: d 120 LYS cc_start: 0.7825 (mttt) cc_final: 0.7437 (mptt) REVERT: e 6 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7795 (ttmt) REVERT: e 27 LEU cc_start: 0.8079 (tp) cc_final: 0.7592 (mt) REVERT: e 120 LYS cc_start: 0.8033 (mtpp) cc_final: 0.7742 (mptt) REVERT: f 27 LEU cc_start: 0.7837 (tp) cc_final: 0.7486 (mt) REVERT: f 62 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8179 (mm) REVERT: f 119 MET cc_start: 0.8321 (mtp) cc_final: 0.8024 (mtp) REVERT: g 27 LEU cc_start: 0.7984 (tp) cc_final: 0.7549 (mt) REVERT: g 93 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7101 (mm-30) REVERT: g 120 LYS cc_start: 0.7963 (mttt) cc_final: 0.7642 (mptt) REVERT: h 27 LEU cc_start: 0.8102 (tp) cc_final: 0.7578 (mt) REVERT: h 119 MET cc_start: 0.8268 (mtp) cc_final: 0.7924 (mtp) REVERT: h 120 LYS cc_start: 0.7756 (mttm) cc_final: 0.7461 (mptt) REVERT: i 93 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7121 (mm-30) REVERT: i 119 MET cc_start: 0.8230 (mtp) cc_final: 0.7976 (mtp) REVERT: i 120 LYS cc_start: 0.7940 (mtmt) cc_final: 0.7619 (mptt) REVERT: j 27 LEU cc_start: 0.7988 (tp) cc_final: 0.7515 (mt) REVERT: j 120 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7383 (mptt) REVERT: k 27 LEU cc_start: 0.7997 (tp) cc_final: 0.7588 (mt) REVERT: k 119 MET cc_start: 0.8226 (mtp) cc_final: 0.7897 (mtp) REVERT: l 27 LEU cc_start: 0.7835 (tp) cc_final: 0.7461 (mt) REVERT: l 196 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: m 27 LEU cc_start: 0.7817 (tp) cc_final: 0.7502 (mt) REVERT: n 27 LEU cc_start: 0.8064 (tp) cc_final: 0.7653 (mt) REVERT: n 120 LYS cc_start: 0.7836 (mtmt) cc_final: 0.7488 (mptt) REVERT: o 50 LYS cc_start: 0.8425 (mtpp) cc_final: 0.7992 (mtmm) REVERT: p 50 LYS cc_start: 0.8356 (mtmt) cc_final: 0.8015 (mtmm) REVERT: s 50 LYS cc_start: 0.8449 (mtpp) cc_final: 0.7927 (mtmm) REVERT: t 50 LYS cc_start: 0.8180 (mttt) cc_final: 0.7889 (mtmm) REVERT: v 5 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.6328 (mt) REVERT: v 50 LYS cc_start: 0.8365 (mtmm) cc_final: 0.8034 (mtmm) REVERT: w 50 LYS cc_start: 0.8387 (mtmt) cc_final: 0.8077 (mtmm) REVERT: y 23 GLU cc_start: 0.6969 (tt0) cc_final: 0.6715 (mt-10) outliers start: 78 outliers final: 47 residues processed: 816 average time/residue: 1.9251 time to fit residues: 1899.8833 Evaluate side-chains 793 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 732 time to evaluate : 5.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 103 VAL Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 17 ASN Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 98 CYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 62 ILE Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 98 CYS Chi-restraints excluded: chain k residue 177 SER Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain l residue 196 GLU Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 177 SER Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain t residue 62 MET Chi-restraints excluded: chain u residue 62 MET Chi-restraints excluded: chain v residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 382 optimal weight: 2.9990 chunk 615 optimal weight: 1.9990 chunk 375 optimal weight: 0.7980 chunk 291 optimal weight: 3.9990 chunk 427 optimal weight: 6.9990 chunk 645 optimal weight: 0.7980 chunk 594 optimal weight: 2.9990 chunk 514 optimal weight: 5.9990 chunk 53 optimal weight: 0.4980 chunk 397 optimal weight: 1.9990 chunk 315 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN I 89 HIS y 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 49487 Z= 0.158 Angle : 0.440 6.668 66767 Z= 0.231 Chirality : 0.041 0.146 8136 Planarity : 0.004 0.075 8376 Dihedral : 3.793 34.829 6625 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.31 % Allowed : 17.90 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.41 (0.10), residues: 6408 helix: 2.86 (0.08), residues: 4008 sheet: -0.17 (0.15), residues: 1152 loop : -0.96 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP h 165 HIS 0.004 0.001 HIS L 8 PHE 0.033 0.001 PHE i 97 TYR 0.005 0.001 TYR a 105 ARG 0.005 0.000 ARG t 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12816 Ramachandran restraints generated. 6408 Oldfield, 0 Emsley, 6408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 749 time to evaluate : 5.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 50 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7964 (mtmm) REVERT: 2 50 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8097 (mtmm) REVERT: 3 50 LYS cc_start: 0.8389 (mttt) cc_final: 0.7946 (mtmm) REVERT: I 2 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7258 (tt0) REVERT: I 27 LEU cc_start: 0.8079 (tp) cc_final: 0.7644 (mt) REVERT: I 41 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: I 93 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7164 (mp0) REVERT: I 119 MET cc_start: 0.8276 (mtp) cc_final: 0.7993 (mtp) REVERT: J 27 LEU cc_start: 0.7939 (tp) cc_final: 0.7553 (mt) REVERT: J 119 MET cc_start: 0.8303 (mtp) cc_final: 0.8026 (mtp) REVERT: J 120 LYS cc_start: 0.7822 (mttt) cc_final: 0.7489 (mptt) REVERT: K 27 LEU cc_start: 0.7987 (tp) cc_final: 0.7550 (mt) REVERT: K 101 LYS cc_start: 0.7207 (mmtt) cc_final: 0.6942 (mptt) REVERT: K 110 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8111 (ttt) REVERT: K 119 MET cc_start: 0.8313 (mtp) cc_final: 0.8050 (mtp) REVERT: K 177 SER cc_start: 0.9012 (OUTLIER) cc_final: 0.8601 (m) REVERT: L 27 LEU cc_start: 0.8003 (tp) cc_final: 0.7640 (mt) REVERT: M 27 LEU cc_start: 0.8017 (tp) cc_final: 0.7637 (mt) REVERT: M 119 MET cc_start: 0.8369 (mtp) cc_final: 0.8053 (mtp) REVERT: N 2 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: N 27 LEU cc_start: 0.8092 (tp) cc_final: 0.7696 (mt) REVERT: N 54 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8397 (m) REVERT: N 59 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7239 (mtmt) REVERT: N 143 LYS cc_start: 0.7964 (tppt) cc_final: 0.7683 (mttm) REVERT: O 27 LEU cc_start: 0.7759 (tp) cc_final: 0.7450 (mt) REVERT: O 57 LYS cc_start: 0.7761 (ttmm) cc_final: 0.7243 (tttm) REVERT: O 140 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7479 (mtmt) REVERT: O 196 GLU cc_start: 0.7024 (pp20) cc_final: 0.6567 (mm-30) REVERT: P 50 LYS cc_start: 0.8457 (mtmt) cc_final: 0.8156 (mtmm) REVERT: Q 50 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8107 (mtmm) REVERT: R 50 LYS cc_start: 0.8379 (mtmm) cc_final: 0.8007 (mttt) REVERT: S 50 LYS cc_start: 0.8297 (mttt) cc_final: 0.7941 (mtmm) REVERT: S 65 GLN cc_start: 0.6753 (OUTLIER) cc_final: 0.5509 (tp40) REVERT: T 16 LYS cc_start: 0.8225 (mtmm) cc_final: 0.8011 (mtmt) REVERT: T 50 LYS cc_start: 0.8353 (mttt) cc_final: 0.8076 (mttp) REVERT: U 119 MET cc_start: 0.8245 (mtp) cc_final: 0.7931 (mtp) REVERT: U 120 LYS cc_start: 0.7822 (mttp) cc_final: 0.7380 (mptt) REVERT: X 50 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8186 (mtmm) REVERT: Y 27 LEU cc_start: 0.7847 (tp) cc_final: 0.7456 (mt) REVERT: Y 93 GLU cc_start: 0.7395 (mp0) cc_final: 0.7137 (mm-30) REVERT: Y 119 MET cc_start: 0.8270 (mtp) cc_final: 0.8027 (mtp) REVERT: Y 120 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7457 (mptt) REVERT: Y 167 LYS cc_start: 0.7933 (mtmm) cc_final: 0.7659 (mtmt) REVERT: Z 27 LEU cc_start: 0.7702 (tp) cc_final: 0.7409 (mt) REVERT: Z 120 LYS cc_start: 0.7741 (mttt) cc_final: 0.7393 (mptt) REVERT: Z 140 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7647 (mtmt) REVERT: a 27 LEU cc_start: 0.7664 (tp) cc_final: 0.7402 (mt) REVERT: a 120 LYS cc_start: 0.8018 (mttt) cc_final: 0.7656 (mptt) REVERT: b 57 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6921 (tttp) REVERT: b 119 MET cc_start: 0.8259 (mtp) cc_final: 0.7982 (mtp) REVERT: b 120 LYS cc_start: 0.7786 (mtmt) cc_final: 0.7359 (mptt) REVERT: c 27 LEU cc_start: 0.7875 (tp) cc_final: 0.7545 (mt) REVERT: c 119 MET cc_start: 0.8224 (mtp) cc_final: 0.7952 (mtp) REVERT: c 120 LYS cc_start: 0.8020 (mttt) cc_final: 0.7682 (mptt) REVERT: d 27 LEU cc_start: 0.7976 (tp) cc_final: 0.7615 (mt) REVERT: d 119 MET cc_start: 0.8484 (mtm) cc_final: 0.8164 (mtp) REVERT: d 120 LYS cc_start: 0.7815 (mttt) cc_final: 0.7434 (mptt) REVERT: e 6 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7818 (ttmt) REVERT: e 27 LEU cc_start: 0.8073 (tp) cc_final: 0.7580 (mt) REVERT: e 120 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7738 (mptt) REVERT: f 27 LEU cc_start: 0.7804 (tp) cc_final: 0.7447 (mt) REVERT: f 119 MET cc_start: 0.8298 (mtp) cc_final: 0.8009 (mtp) REVERT: g 2 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: g 27 LEU cc_start: 0.7975 (tp) cc_final: 0.7544 (mt) REVERT: g 93 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7102 (mm-30) REVERT: g 120 LYS cc_start: 0.7948 (mttt) cc_final: 0.7638 (mptt) REVERT: h 27 LEU cc_start: 0.8140 (tp) cc_final: 0.7612 (mt) REVERT: h 119 MET cc_start: 0.8246 (mtp) cc_final: 0.7891 (mtp) REVERT: h 120 LYS cc_start: 0.7744 (mttm) cc_final: 0.7447 (mptt) REVERT: i 93 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7152 (mm-30) REVERT: i 119 MET cc_start: 0.8208 (mtp) cc_final: 0.7943 (mtp) REVERT: i 120 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7623 (mptt) REVERT: j 27 LEU cc_start: 0.8058 (tp) cc_final: 0.7466 (mt) REVERT: j 31 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: j 120 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7373 (mptt) REVERT: k 27 LEU cc_start: 0.7989 (tp) cc_final: 0.7570 (mt) REVERT: k 119 MET cc_start: 0.8205 (mtp) cc_final: 0.7877 (mtp) REVERT: l 27 LEU cc_start: 0.7794 (tp) cc_final: 0.7418 (mt) REVERT: l 196 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: m 27 LEU cc_start: 0.7811 (tp) cc_final: 0.7504 (mt) REVERT: n 27 LEU cc_start: 0.8059 (tp) cc_final: 0.7643 (mt) REVERT: n 120 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7480 (mptt) REVERT: o 50 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7995 (mtmm) REVERT: p 50 LYS cc_start: 0.8350 (mtmt) cc_final: 0.8020 (mtmm) REVERT: s 50 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7926 (mtmm) REVERT: t 50 LYS cc_start: 0.8189 (mttt) cc_final: 0.7921 (mtmm) REVERT: v 5 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6293 (mt) REVERT: v 50 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8035 (mtmm) REVERT: w 50 LYS cc_start: 0.8383 (mtmt) cc_final: 0.8080 (mtmm) REVERT: y 23 GLU cc_start: 0.6933 (tt0) cc_final: 0.6704 (mt-10) REVERT: y 50 LYS cc_start: 0.8462 (mtpt) cc_final: 0.8199 (mttt) outliers start: 67 outliers final: 43 residues processed: 800 average time/residue: 1.9848 time to fit residues: 1944.0272 Evaluate side-chains 785 residues out of total 5400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 727 time to evaluate : 6.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 2 GLU Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 41 PHE Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 98 CYS Chi-restraints excluded: chain J residue 177 SER Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 110 MET Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain L residue 98 CYS Chi-restraints excluded: chain N residue 2 GLU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 SER Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain N residue 177 SER Chi-restraints excluded: chain O residue 140 LYS Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain S residue 65 GLN Chi-restraints excluded: chain T residue 62 MET Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 62 MET Chi-restraints excluded: chain W residue 1 THR Chi-restraints excluded: chain Y residue 29 VAL Chi-restraints excluded: chain Y residue 98 CYS Chi-restraints excluded: chain Z residue 1 MET Chi-restraints excluded: chain Z residue 29 VAL Chi-restraints excluded: chain Z residue 140 LYS Chi-restraints excluded: chain Z residue 164 GLU Chi-restraints excluded: chain Z residue 177 SER Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 177 SER Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 29 VAL Chi-restraints excluded: chain b residue 98 CYS Chi-restraints excluded: chain c residue 29 VAL Chi-restraints excluded: chain c residue 98 CYS Chi-restraints excluded: chain c residue 177 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain f residue 143 LYS Chi-restraints excluded: chain f residue 177 SER Chi-restraints excluded: chain g residue 2 GLU Chi-restraints excluded: chain g residue 177 SER Chi-restraints excluded: chain h residue 177 SER Chi-restraints excluded: chain j residue 31 GLU Chi-restraints excluded: chain j residue 177 SER Chi-restraints excluded: chain k residue 29 VAL Chi-restraints excluded: chain k residue 177 SER Chi-restraints excluded: chain l residue 17 ASN Chi-restraints excluded: chain l residue 196 GLU Chi-restraints excluded: chain m residue 177 SER Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 177 SER Chi-restraints excluded: chain s residue 59 GLU Chi-restraints excluded: chain v residue 5 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 648 random chunks: chunk 408 optimal weight: 0.6980 chunk 547 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 474 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 514 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 528 optimal weight: 0.0980 chunk 65 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 11 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.132973 restraints weight = 51009.868| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.50 r_work: 0.3297 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 49487 Z= 0.138 Angle : 0.426 6.452 66767 Z= 0.224 Chirality : 0.040 0.146 8136 Planarity : 0.004 0.070 8376 Dihedral : 3.725 33.403 6625 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.29 % Allowed : 18.06 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 2.50 (0.10), residues: 6408 helix: 2.94 (0.08), residues: 4008 sheet: -0.16 (0.15), residues: 1152 loop : -0.94 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP h 165 HIS 0.004 0.001 HIS L 8 PHE 0.031 0.001 PHE i 97 TYR 0.004 0.001 TYR f 105 ARG 0.005 0.000 ARG Q 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26005.96 seconds wall clock time: 452 minutes 24.47 seconds (27144.47 seconds total)