Starting phenix.real_space_refine on Tue Apr 16 19:26:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/04_2024/6pee_20315_neut_updated.pdb" } resolution = 3.42 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= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 25620 2.51 5 N 7050 2.21 5 O 7680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ARG 397": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A ASP 525": "OD1" <-> "OD2" Residue "A ASP 555": "OD1" <-> "OD2" Residue "A ARG 556": "NH1" <-> "NH2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B GLU 429": "OE1" <-> "OE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B ASP 445": "OD1" <-> "OD2" Residue "B ASP 525": "OD1" <-> "OD2" Residue "B ASP 555": "OD1" <-> "OD2" Residue "B ARG 556": "NH1" <-> "NH2" Residue "C PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C ASP 274": "OD1" <-> "OD2" Residue "C ASP 312": "OD1" <-> "OD2" Residue "C GLU 319": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ARG 397": "NH1" <-> "NH2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C ASP 433": "OD1" <-> "OD2" Residue "C ASP 439": "OD1" <-> "OD2" Residue "C ASP 445": "OD1" <-> "OD2" Residue "C ASP 525": "OD1" <-> "OD2" Residue "C ASP 555": "OD1" <-> "OD2" Residue "C ARG 556": "NH1" <-> "NH2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ASP 274": "OD1" <-> "OD2" Residue "D ASP 312": "OD1" <-> "OD2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D ASP 333": "OD1" <-> "OD2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ARG 397": "NH1" <-> "NH2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D ASP 433": "OD1" <-> "OD2" Residue "D ASP 439": "OD1" <-> "OD2" Residue "D ASP 445": "OD1" <-> "OD2" Residue "D ASP 525": "OD1" <-> "OD2" Residue "D ASP 555": "OD1" <-> "OD2" Residue "D ARG 556": "NH1" <-> "NH2" Residue "F PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 212": "OE1" <-> "OE2" Residue "F ASP 274": "OD1" <-> "OD2" Residue "F ASP 312": "OD1" <-> "OD2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F ASP 333": "OD1" <-> "OD2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ARG 397": "NH1" <-> "NH2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F ASP 433": "OD1" <-> "OD2" Residue "F ASP 439": "OD1" <-> "OD2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F ASP 525": "OD1" <-> "OD2" Residue "F ASP 555": "OD1" <-> "OD2" Residue "F ARG 556": "NH1" <-> "NH2" Residue "G PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 212": "OE1" <-> "OE2" Residue "G ASP 274": "OD1" <-> "OD2" Residue "G ASP 312": "OD1" <-> "OD2" Residue "G GLU 319": "OE1" <-> "OE2" Residue "G ASP 333": "OD1" <-> "OD2" Residue "G ASP 348": "OD1" <-> "OD2" Residue "G GLU 361": "OE1" <-> "OE2" Residue "G ARG 397": "NH1" <-> "NH2" Residue "G GLU 429": "OE1" <-> "OE2" Residue "G ASP 433": "OD1" <-> "OD2" Residue "G ASP 439": "OD1" <-> "OD2" Residue "G ASP 445": "OD1" <-> "OD2" Residue "G ASP 525": "OD1" <-> "OD2" Residue "G ASP 555": "OD1" <-> "OD2" Residue "G ARG 556": "NH1" <-> "NH2" Residue "H PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H ASP 274": "OD1" <-> "OD2" Residue "H ASP 312": "OD1" <-> "OD2" Residue "H GLU 319": "OE1" <-> "OE2" Residue "H ASP 333": "OD1" <-> "OD2" Residue "H ASP 348": "OD1" <-> "OD2" Residue "H GLU 361": "OE1" <-> "OE2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H GLU 429": "OE1" <-> "OE2" Residue "H ASP 433": "OD1" <-> "OD2" Residue "H ASP 439": "OD1" <-> "OD2" Residue "H ASP 445": "OD1" <-> "OD2" Residue "H ASP 525": "OD1" <-> "OD2" Residue "H ASP 555": "OD1" <-> "OD2" Residue "H ARG 556": "NH1" <-> "NH2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I ASP 274": "OD1" <-> "OD2" Residue "I ASP 312": "OD1" <-> "OD2" Residue "I GLU 319": "OE1" <-> "OE2" Residue "I ASP 333": "OD1" <-> "OD2" Residue "I ASP 348": "OD1" <-> "OD2" Residue "I GLU 361": "OE1" <-> "OE2" Residue "I ARG 397": "NH1" <-> "NH2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "I ASP 433": "OD1" <-> "OD2" Residue "I ASP 439": "OD1" <-> "OD2" Residue "I ASP 445": "OD1" <-> "OD2" Residue "I ASP 525": "OD1" <-> "OD2" Residue "I ASP 555": "OD1" <-> "OD2" Residue "I ARG 556": "NH1" <-> "NH2" Residue "J PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 212": "OE1" <-> "OE2" Residue "J ASP 274": "OD1" <-> "OD2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J GLU 319": "OE1" <-> "OE2" Residue "J ASP 333": "OD1" <-> "OD2" Residue "J ASP 348": "OD1" <-> "OD2" Residue "J GLU 361": "OE1" <-> "OE2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J ASP 433": "OD1" <-> "OD2" Residue "J ASP 439": "OD1" <-> "OD2" Residue "J ASP 445": "OD1" <-> "OD2" Residue "J ASP 525": "OD1" <-> "OD2" Residue "J ASP 555": "OD1" <-> "OD2" Residue "J ARG 556": "NH1" <-> "NH2" Residue "K PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 212": "OE1" <-> "OE2" Residue "K ASP 274": "OD1" <-> "OD2" Residue "K ASP 312": "OD1" <-> "OD2" Residue "K GLU 319": "OE1" <-> "OE2" Residue "K ASP 333": "OD1" <-> "OD2" Residue "K ASP 348": "OD1" <-> "OD2" Residue "K GLU 361": "OE1" <-> "OE2" Residue "K ARG 397": "NH1" <-> "NH2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K ASP 433": "OD1" <-> "OD2" Residue "K ASP 439": "OD1" <-> "OD2" Residue "K ASP 445": "OD1" <-> "OD2" Residue "K ASP 525": "OD1" <-> "OD2" Residue "K ASP 555": "OD1" <-> "OD2" Residue "K ARG 556": "NH1" <-> "NH2" Residue "L PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 212": "OE1" <-> "OE2" Residue "L ASP 274": "OD1" <-> "OD2" Residue "L ASP 312": "OD1" <-> "OD2" Residue "L GLU 319": "OE1" <-> "OE2" Residue "L ASP 333": "OD1" <-> "OD2" Residue "L ASP 348": "OD1" <-> "OD2" Residue "L GLU 361": "OE1" <-> "OE2" Residue "L ARG 397": "NH1" <-> "NH2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L ASP 433": "OD1" <-> "OD2" Residue "L ASP 439": "OD1" <-> "OD2" Residue "L ASP 445": "OD1" <-> "OD2" Residue "L ASP 525": "OD1" <-> "OD2" Residue "L ASP 555": "OD1" <-> "OD2" Residue "L ARG 556": "NH1" <-> "NH2" Residue "M PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 212": "OE1" <-> "OE2" Residue "M ASP 274": "OD1" <-> "OD2" Residue "M ASP 312": "OD1" <-> "OD2" Residue "M GLU 319": "OE1" <-> "OE2" Residue "M ASP 333": "OD1" <-> "OD2" Residue "M ASP 348": "OD1" <-> "OD2" Residue "M GLU 361": "OE1" <-> "OE2" Residue "M ARG 397": "NH1" <-> "NH2" Residue "M GLU 429": "OE1" <-> "OE2" Residue "M ASP 433": "OD1" <-> "OD2" Residue "M ASP 439": "OD1" <-> "OD2" Residue "M ASP 445": "OD1" <-> "OD2" Residue "M ASP 525": "OD1" <-> "OD2" Residue "M ASP 555": "OD1" <-> "OD2" Residue "M ARG 556": "NH1" <-> "NH2" Residue "N PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 212": "OE1" <-> "OE2" Residue "N ASP 274": "OD1" <-> "OD2" Residue "N ASP 312": "OD1" <-> "OD2" Residue "N GLU 319": "OE1" <-> "OE2" Residue "N ASP 333": "OD1" <-> "OD2" Residue "N ASP 348": "OD1" <-> "OD2" Residue "N GLU 361": "OE1" <-> "OE2" Residue "N ARG 397": "NH1" <-> "NH2" Residue "N GLU 429": "OE1" <-> "OE2" Residue "N ASP 433": "OD1" <-> "OD2" Residue "N ASP 439": "OD1" <-> "OD2" Residue "N ASP 445": "OD1" <-> "OD2" Residue "N ASP 525": "OD1" <-> "OD2" Residue "N ASP 555": "OD1" <-> "OD2" Residue "N ARG 556": "NH1" <-> "NH2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 212": "OE1" <-> "OE2" Residue "O ASP 274": "OD1" <-> "OD2" Residue "O ASP 312": "OD1" <-> "OD2" Residue "O GLU 319": "OE1" <-> "OE2" Residue "O ASP 333": "OD1" <-> "OD2" Residue "O ASP 348": "OD1" <-> "OD2" Residue "O GLU 361": "OE1" <-> "OE2" Residue "O ARG 397": "NH1" <-> "NH2" Residue "O GLU 429": "OE1" <-> "OE2" Residue "O ASP 433": "OD1" <-> "OD2" Residue "O ASP 439": "OD1" <-> "OD2" Residue "O ASP 445": "OD1" <-> "OD2" Residue "O ASP 525": "OD1" <-> "OD2" Residue "O ASP 555": "OD1" <-> "OD2" Residue "O ARG 556": "NH1" <-> "NH2" Residue "P PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 212": "OE1" <-> "OE2" Residue "P ASP 274": "OD1" <-> "OD2" Residue "P ASP 312": "OD1" <-> "OD2" Residue "P GLU 319": "OE1" <-> "OE2" Residue "P ASP 333": "OD1" <-> "OD2" Residue "P ASP 348": "OD1" <-> "OD2" Residue "P GLU 361": "OE1" <-> "OE2" Residue "P ARG 397": "NH1" <-> "NH2" Residue "P GLU 429": "OE1" <-> "OE2" Residue "P ASP 433": "OD1" <-> "OD2" Residue "P ASP 439": "OD1" <-> "OD2" Residue "P ASP 445": "OD1" <-> "OD2" Residue "P ASP 525": "OD1" <-> "OD2" Residue "P ASP 555": "OD1" <-> "OD2" Residue "P ARG 556": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40440 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 2656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2656 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 330} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "I" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "J" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "K" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "L" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "O" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "P" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {'LDA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 19.51, per 1000 atoms: 0.48 Number of scatterers: 40440 At special positions: 0 Unit cell: (160.74, 167.58, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 7680 8.00 N 7050 7.00 C 25620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.29 Conformation dependent library (CDL) restraints added in 7.3 seconds 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9570 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 75 sheets defined 14.2% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.67 Creating SS restraints... Processing helix chain 'A' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE A 211 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.973A pdb=" N HIS A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 293 " --> pdb=" O PHE A 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA A 296 " --> pdb=" O MET A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL A 530 " --> pdb=" O ALA A 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN A 531 " --> pdb=" O SER A 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 535 " --> pdb=" O ASN A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 551 through 554 No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'B' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE B 211 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 296 " --> pdb=" O MET B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 443 No H-bonds generated for 'chain 'B' and resid 441 through 443' Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 526 through 537 removed outlier: 3.582A pdb=" N VAL B 530 " --> pdb=" O ALA B 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN B 532 " --> pdb=" O GLU B 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS B 535 " --> pdb=" O ASN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 549 No H-bonds generated for 'chain 'B' and resid 547 through 549' Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.516A pdb=" N ILE C 211 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 293 " --> pdb=" O PHE C 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 443 No H-bonds generated for 'chain 'C' and resid 441 through 443' Processing helix chain 'C' and resid 487 through 489 No H-bonds generated for 'chain 'C' and resid 487 through 489' Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL C 530 " --> pdb=" O ALA C 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN C 531 " --> pdb=" O SER C 527 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 535 " --> pdb=" O ASN C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 551 through 554 No H-bonds generated for 'chain 'C' and resid 551 through 554' Processing helix chain 'D' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE D 211 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU D 293 " --> pdb=" O PHE D 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 487 through 489 No H-bonds generated for 'chain 'D' and resid 487 through 489' Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL D 530 " --> pdb=" O ALA D 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 532 " --> pdb=" O GLU D 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS D 535 " --> pdb=" O ASN D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 549 No H-bonds generated for 'chain 'D' and resid 547 through 549' Processing helix chain 'D' and resid 551 through 554 No H-bonds generated for 'chain 'D' and resid 551 through 554' Processing helix chain 'F' and resid 207 through 214 removed outlier: 3.518A pdb=" N ILE F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 296 removed outlier: 3.973A pdb=" N HIS F 288 " --> pdb=" O ALA F 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU F 293 " --> pdb=" O PHE F 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS F 295 " --> pdb=" O GLU F 291 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA F 296 " --> pdb=" O MET F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 443 No H-bonds generated for 'chain 'F' and resid 441 through 443' Processing helix chain 'F' and resid 487 through 489 No H-bonds generated for 'chain 'F' and resid 487 through 489' Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'F' and resid 526 through 537 removed outlier: 3.582A pdb=" N VAL F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN F 531 " --> pdb=" O SER F 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN F 532 " --> pdb=" O GLU F 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS F 535 " --> pdb=" O ASN F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 549 No H-bonds generated for 'chain 'F' and resid 547 through 549' Processing helix chain 'F' and resid 551 through 554 No H-bonds generated for 'chain 'F' and resid 551 through 554' Processing helix chain 'G' and resid 207 through 214 removed outlier: 3.519A pdb=" N ILE G 211 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU G 212 " --> pdb=" O ALA G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS G 288 " --> pdb=" O ALA G 284 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 293 " --> pdb=" O PHE G 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 296 " --> pdb=" O MET G 292 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 443 No H-bonds generated for 'chain 'G' and resid 441 through 443' Processing helix chain 'G' and resid 487 through 489 No H-bonds generated for 'chain 'G' and resid 487 through 489' Processing helix chain 'G' and resid 494 through 496 No H-bonds generated for 'chain 'G' and resid 494 through 496' Processing helix chain 'G' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL G 530 " --> pdb=" O ALA G 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN G 531 " --> pdb=" O SER G 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 532 " --> pdb=" O GLU G 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS G 535 " --> pdb=" O ASN G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 549 No H-bonds generated for 'chain 'G' and resid 547 through 549' Processing helix chain 'G' and resid 551 through 554 No H-bonds generated for 'chain 'G' and resid 551 through 554' Processing helix chain 'H' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE H 211 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU H 212 " --> pdb=" O ALA H 208 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 296 removed outlier: 3.973A pdb=" N HIS H 288 " --> pdb=" O ALA H 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU H 293 " --> pdb=" O PHE H 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS H 295 " --> pdb=" O GLU H 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA H 296 " --> pdb=" O MET H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 443 No H-bonds generated for 'chain 'H' and resid 441 through 443' Processing helix chain 'H' and resid 487 through 489 No H-bonds generated for 'chain 'H' and resid 487 through 489' Processing helix chain 'H' and resid 494 through 496 No H-bonds generated for 'chain 'H' and resid 494 through 496' Processing helix chain 'H' and resid 526 through 537 removed outlier: 3.582A pdb=" N VAL H 530 " --> pdb=" O ALA H 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN H 531 " --> pdb=" O SER H 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN H 532 " --> pdb=" O GLU H 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS H 535 " --> pdb=" O ASN H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 549 No H-bonds generated for 'chain 'H' and resid 547 through 549' Processing helix chain 'H' and resid 551 through 554 No H-bonds generated for 'chain 'H' and resid 551 through 554' Processing helix chain 'I' and resid 207 through 214 removed outlier: 3.518A pdb=" N ILE I 211 " --> pdb=" O ILE I 207 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU I 212 " --> pdb=" O ALA I 208 " (cutoff:3.500A) Processing helix chain 'I' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS I 288 " --> pdb=" O ALA I 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU I 293 " --> pdb=" O PHE I 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 295 " --> pdb=" O GLU I 291 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 296 " --> pdb=" O MET I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 443 No H-bonds generated for 'chain 'I' and resid 441 through 443' Processing helix chain 'I' and resid 487 through 489 No H-bonds generated for 'chain 'I' and resid 487 through 489' Processing helix chain 'I' and resid 494 through 496 No H-bonds generated for 'chain 'I' and resid 494 through 496' Processing helix chain 'I' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL I 530 " --> pdb=" O ALA I 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN I 531 " --> pdb=" O SER I 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN I 532 " --> pdb=" O GLU I 528 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS I 535 " --> pdb=" O ASN I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 549 No H-bonds generated for 'chain 'I' and resid 547 through 549' Processing helix chain 'I' and resid 551 through 554 No H-bonds generated for 'chain 'I' and resid 551 through 554' Processing helix chain 'J' and resid 207 through 214 removed outlier: 3.518A pdb=" N ILE J 211 " --> pdb=" O ILE J 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU J 212 " --> pdb=" O ALA J 208 " (cutoff:3.500A) Processing helix chain 'J' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS J 288 " --> pdb=" O ALA J 284 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU J 293 " --> pdb=" O PHE J 289 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS J 295 " --> pdb=" O GLU J 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA J 296 " --> pdb=" O MET J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 443 No H-bonds generated for 'chain 'J' and resid 441 through 443' Processing helix chain 'J' and resid 487 through 489 No H-bonds generated for 'chain 'J' and resid 487 through 489' Processing helix chain 'J' and resid 494 through 496 No H-bonds generated for 'chain 'J' and resid 494 through 496' Processing helix chain 'J' and resid 526 through 537 removed outlier: 3.582A pdb=" N VAL J 530 " --> pdb=" O ALA J 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN J 531 " --> pdb=" O SER J 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN J 532 " --> pdb=" O GLU J 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS J 535 " --> pdb=" O ASN J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 549 No H-bonds generated for 'chain 'J' and resid 547 through 549' Processing helix chain 'J' and resid 551 through 554 No H-bonds generated for 'chain 'J' and resid 551 through 554' Processing helix chain 'K' and resid 207 through 214 removed outlier: 3.518A pdb=" N ILE K 211 " --> pdb=" O ILE K 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU K 212 " --> pdb=" O ALA K 208 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS K 288 " --> pdb=" O ALA K 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU K 293 " --> pdb=" O PHE K 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS K 295 " --> pdb=" O GLU K 291 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA K 296 " --> pdb=" O MET K 292 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 443 No H-bonds generated for 'chain 'K' and resid 441 through 443' Processing helix chain 'K' and resid 487 through 489 No H-bonds generated for 'chain 'K' and resid 487 through 489' Processing helix chain 'K' and resid 494 through 496 No H-bonds generated for 'chain 'K' and resid 494 through 496' Processing helix chain 'K' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL K 530 " --> pdb=" O ALA K 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN K 531 " --> pdb=" O SER K 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN K 532 " --> pdb=" O GLU K 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS K 535 " --> pdb=" O ASN K 531 " (cutoff:3.500A) Processing helix chain 'K' and resid 547 through 549 No H-bonds generated for 'chain 'K' and resid 547 through 549' Processing helix chain 'K' and resid 551 through 554 No H-bonds generated for 'chain 'K' and resid 551 through 554' Processing helix chain 'L' and resid 207 through 214 removed outlier: 3.518A pdb=" N ILE L 211 " --> pdb=" O ILE L 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU L 212 " --> pdb=" O ALA L 208 " (cutoff:3.500A) Processing helix chain 'L' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS L 288 " --> pdb=" O ALA L 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU L 293 " --> pdb=" O PHE L 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS L 295 " --> pdb=" O GLU L 291 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 296 " --> pdb=" O MET L 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 443 No H-bonds generated for 'chain 'L' and resid 441 through 443' Processing helix chain 'L' and resid 487 through 489 No H-bonds generated for 'chain 'L' and resid 487 through 489' Processing helix chain 'L' and resid 494 through 496 No H-bonds generated for 'chain 'L' and resid 494 through 496' Processing helix chain 'L' and resid 526 through 537 removed outlier: 3.583A pdb=" N VAL L 530 " --> pdb=" O ALA L 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN L 531 " --> pdb=" O SER L 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 532 " --> pdb=" O GLU L 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS L 535 " --> pdb=" O ASN L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 547 through 549 No H-bonds generated for 'chain 'L' and resid 547 through 549' Processing helix chain 'L' and resid 551 through 554 No H-bonds generated for 'chain 'L' and resid 551 through 554' Processing helix chain 'M' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE M 211 " --> pdb=" O ILE M 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU M 212 " --> pdb=" O ALA M 208 " (cutoff:3.500A) Processing helix chain 'M' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS M 288 " --> pdb=" O ALA M 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU M 293 " --> pdb=" O PHE M 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS M 295 " --> pdb=" O GLU M 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA M 296 " --> pdb=" O MET M 292 " (cutoff:3.500A) Processing helix chain 'M' and resid 441 through 443 No H-bonds generated for 'chain 'M' and resid 441 through 443' Processing helix chain 'M' and resid 487 through 489 No H-bonds generated for 'chain 'M' and resid 487 through 489' Processing helix chain 'M' and resid 494 through 496 No H-bonds generated for 'chain 'M' and resid 494 through 496' Processing helix chain 'M' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL M 530 " --> pdb=" O ALA M 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN M 531 " --> pdb=" O SER M 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN M 532 " --> pdb=" O GLU M 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS M 535 " --> pdb=" O ASN M 531 " (cutoff:3.500A) Processing helix chain 'M' and resid 547 through 549 No H-bonds generated for 'chain 'M' and resid 547 through 549' Processing helix chain 'M' and resid 551 through 554 No H-bonds generated for 'chain 'M' and resid 551 through 554' Processing helix chain 'N' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE N 211 " --> pdb=" O ILE N 207 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU N 212 " --> pdb=" O ALA N 208 " (cutoff:3.500A) Processing helix chain 'N' and resid 284 through 296 removed outlier: 3.973A pdb=" N HIS N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU N 293 " --> pdb=" O PHE N 289 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS N 295 " --> pdb=" O GLU N 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA N 296 " --> pdb=" O MET N 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 441 through 443 No H-bonds generated for 'chain 'N' and resid 441 through 443' Processing helix chain 'N' and resid 487 through 489 No H-bonds generated for 'chain 'N' and resid 487 through 489' Processing helix chain 'N' and resid 494 through 496 No H-bonds generated for 'chain 'N' and resid 494 through 496' Processing helix chain 'N' and resid 526 through 537 removed outlier: 3.581A pdb=" N VAL N 530 " --> pdb=" O ALA N 526 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN N 531 " --> pdb=" O SER N 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN N 532 " --> pdb=" O GLU N 528 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS N 535 " --> pdb=" O ASN N 531 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 549 No H-bonds generated for 'chain 'N' and resid 547 through 549' Processing helix chain 'N' and resid 551 through 554 No H-bonds generated for 'chain 'N' and resid 551 through 554' Processing helix chain 'O' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE O 211 " --> pdb=" O ILE O 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU O 212 " --> pdb=" O ALA O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 284 through 296 removed outlier: 3.974A pdb=" N HIS O 288 " --> pdb=" O ALA O 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU O 293 " --> pdb=" O PHE O 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS O 295 " --> pdb=" O GLU O 291 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA O 296 " --> pdb=" O MET O 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 441 through 443 No H-bonds generated for 'chain 'O' and resid 441 through 443' Processing helix chain 'O' and resid 487 through 489 No H-bonds generated for 'chain 'O' and resid 487 through 489' Processing helix chain 'O' and resid 494 through 496 No H-bonds generated for 'chain 'O' and resid 494 through 496' Processing helix chain 'O' and resid 526 through 537 removed outlier: 3.583A pdb=" N VAL O 530 " --> pdb=" O ALA O 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN O 531 " --> pdb=" O SER O 527 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN O 532 " --> pdb=" O GLU O 528 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS O 535 " --> pdb=" O ASN O 531 " (cutoff:3.500A) Processing helix chain 'O' and resid 547 through 549 No H-bonds generated for 'chain 'O' and resid 547 through 549' Processing helix chain 'O' and resid 551 through 554 No H-bonds generated for 'chain 'O' and resid 551 through 554' Processing helix chain 'P' and resid 207 through 214 removed outlier: 3.517A pdb=" N ILE P 211 " --> pdb=" O ILE P 207 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU P 212 " --> pdb=" O ALA P 208 " (cutoff:3.500A) Processing helix chain 'P' and resid 284 through 296 removed outlier: 3.975A pdb=" N HIS P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU P 293 " --> pdb=" O PHE P 289 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS P 295 " --> pdb=" O GLU P 291 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA P 296 " --> pdb=" O MET P 292 " (cutoff:3.500A) Processing helix chain 'P' and resid 441 through 443 No H-bonds generated for 'chain 'P' and resid 441 through 443' Processing helix chain 'P' and resid 487 through 489 No H-bonds generated for 'chain 'P' and resid 487 through 489' Processing helix chain 'P' and resid 494 through 496 No H-bonds generated for 'chain 'P' and resid 494 through 496' Processing helix chain 'P' and resid 526 through 537 removed outlier: 3.582A pdb=" N VAL P 530 " --> pdb=" O ALA P 526 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN P 531 " --> pdb=" O SER P 527 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN P 532 " --> pdb=" O GLU P 528 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS P 535 " --> pdb=" O ASN P 531 " (cutoff:3.500A) Processing helix chain 'P' and resid 547 through 549 No H-bonds generated for 'chain 'P' and resid 547 through 549' Processing helix chain 'P' and resid 551 through 554 No H-bonds generated for 'chain 'P' and resid 551 through 554' Processing sheet with id= A, first strand: chain 'A' and resid 179 through 184 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN A 200 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS A 363 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA A 365 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS A 303 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 319 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE A 511 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY A 470 " --> pdb=" O PHE A 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE A 513 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU A 468 " --> pdb=" O ILE A 513 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 316 through 322 removed outlier: 3.861A pdb=" N GLU A 319 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 380 through 393 removed outlier: 3.781A pdb=" N GLU A 402 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 393 " --> pdb=" O ALA A 400 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA A 400 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 413 " --> pdb=" O SER A 425 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 425 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 457 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 179 through 184 Processing sheet with id= G, first strand: chain 'B' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN B 200 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 354 through 376 removed outlier: 3.802A pdb=" N LYS B 363 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 365 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS B 303 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU B 319 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B 511 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY B 470 " --> pdb=" O PHE B 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE B 513 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 468 " --> pdb=" O ILE B 513 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 316 through 322 removed outlier: 3.862A pdb=" N GLU B 319 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU B 402 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU B 393 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA B 400 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 413 " --> pdb=" O SER B 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 425 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR B 457 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 179 through 184 Processing sheet with id= L, first strand: chain 'C' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN C 200 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 354 through 376 removed outlier: 3.802A pdb=" N LYS C 363 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 365 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS C 303 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C 319 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE C 511 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY C 470 " --> pdb=" O PHE C 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 513 " --> pdb=" O LEU C 468 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C 468 " --> pdb=" O ILE C 513 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 316 through 322 removed outlier: 3.859A pdb=" N GLU C 319 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU C 402 " --> pdb=" O THR C 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU C 393 " --> pdb=" O ALA C 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA C 400 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 413 " --> pdb=" O SER C 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER C 425 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR C 457 " --> pdb=" O LEU C 426 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 179 through 184 Processing sheet with id= Q, first strand: chain 'D' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN D 200 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS D 363 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 365 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS D 303 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU D 319 " --> pdb=" O LYS D 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE D 511 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY D 470 " --> pdb=" O PHE D 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE D 513 " --> pdb=" O LEU D 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU D 468 " --> pdb=" O ILE D 513 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU D 319 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 380 through 393 removed outlier: 3.783A pdb=" N GLU D 402 " --> pdb=" O THR D 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU D 393 " --> pdb=" O ALA D 400 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA D 400 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU D 413 " --> pdb=" O SER D 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER D 425 " --> pdb=" O LEU D 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR D 457 " --> pdb=" O LEU D 426 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 179 through 184 Processing sheet with id= V, first strand: chain 'F' and resid 193 through 197 removed outlier: 3.671A pdb=" N GLN F 200 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 354 through 376 removed outlier: 3.800A pdb=" N LYS F 363 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA F 365 " --> pdb=" O ASN F 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS F 303 " --> pdb=" O ILE F 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU F 319 " --> pdb=" O LYS F 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE F 511 " --> pdb=" O GLY F 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 470 " --> pdb=" O PHE F 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE F 513 " --> pdb=" O LEU F 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU F 468 " --> pdb=" O ILE F 513 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 316 through 322 removed outlier: 3.861A pdb=" N GLU F 319 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 380 through 393 removed outlier: 3.781A pdb=" N GLU F 402 " --> pdb=" O THR F 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU F 393 " --> pdb=" O ALA F 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA F 400 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU F 413 " --> pdb=" O SER F 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER F 425 " --> pdb=" O LEU F 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 457 " --> pdb=" O LEU F 426 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 179 through 184 Processing sheet with id= AA, first strand: chain 'G' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN G 200 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 354 through 376 removed outlier: 3.802A pdb=" N LYS G 363 " --> pdb=" O SER G 316 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA G 365 " --> pdb=" O ASN G 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS G 303 " --> pdb=" O ILE G 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU G 319 " --> pdb=" O LYS G 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE G 511 " --> pdb=" O GLY G 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY G 470 " --> pdb=" O PHE G 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE G 513 " --> pdb=" O LEU G 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU G 468 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'G' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU G 319 " --> pdb=" O LYS G 502 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'G' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU G 402 " --> pdb=" O THR G 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU G 393 " --> pdb=" O ALA G 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA G 400 " --> pdb=" O LEU G 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU G 413 " --> pdb=" O SER G 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER G 425 " --> pdb=" O LEU G 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR G 457 " --> pdb=" O LEU G 426 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 179 through 184 Processing sheet with id= AF, first strand: chain 'H' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN H 200 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'H' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS H 363 " --> pdb=" O SER H 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA H 365 " --> pdb=" O ASN H 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS H 303 " --> pdb=" O ILE H 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU H 319 " --> pdb=" O LYS H 502 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE H 511 " --> pdb=" O GLY H 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY H 470 " --> pdb=" O PHE H 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE H 513 " --> pdb=" O LEU H 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU H 468 " --> pdb=" O ILE H 513 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 316 through 322 removed outlier: 3.861A pdb=" N GLU H 319 " --> pdb=" O LYS H 502 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU H 402 " --> pdb=" O THR H 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU H 393 " --> pdb=" O ALA H 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA H 400 " --> pdb=" O LEU H 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU H 413 " --> pdb=" O SER H 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER H 425 " --> pdb=" O LEU H 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR H 457 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 179 through 184 Processing sheet with id= AK, first strand: chain 'I' and resid 193 through 197 removed outlier: 3.671A pdb=" N GLN I 200 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS I 363 " --> pdb=" O SER I 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA I 365 " --> pdb=" O ASN I 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS I 303 " --> pdb=" O ILE I 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU I 319 " --> pdb=" O LYS I 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE I 511 " --> pdb=" O GLY I 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY I 470 " --> pdb=" O PHE I 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE I 513 " --> pdb=" O LEU I 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU I 468 " --> pdb=" O ILE I 513 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'I' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU I 319 " --> pdb=" O LYS I 502 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU I 402 " --> pdb=" O THR I 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU I 393 " --> pdb=" O ALA I 400 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA I 400 " --> pdb=" O LEU I 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU I 413 " --> pdb=" O SER I 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER I 425 " --> pdb=" O LEU I 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR I 457 " --> pdb=" O LEU I 426 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'J' and resid 179 through 184 Processing sheet with id= AP, first strand: chain 'J' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN J 200 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'J' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS J 363 " --> pdb=" O SER J 316 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA J 365 " --> pdb=" O ASN J 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS J 303 " --> pdb=" O ILE J 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU J 319 " --> pdb=" O LYS J 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE J 511 " --> pdb=" O GLY J 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY J 470 " --> pdb=" O PHE J 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE J 513 " --> pdb=" O LEU J 468 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU J 468 " --> pdb=" O ILE J 513 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'J' and resid 316 through 322 removed outlier: 3.862A pdb=" N GLU J 319 " --> pdb=" O LYS J 502 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'J' and resid 380 through 393 removed outlier: 3.780A pdb=" N GLU J 402 " --> pdb=" O THR J 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU J 393 " --> pdb=" O ALA J 400 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA J 400 " --> pdb=" O LEU J 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU J 413 " --> pdb=" O SER J 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER J 425 " --> pdb=" O LEU J 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR J 457 " --> pdb=" O LEU J 426 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'K' and resid 179 through 184 Processing sheet with id= AU, first strand: chain 'K' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN K 200 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'K' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS K 363 " --> pdb=" O SER K 316 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA K 365 " --> pdb=" O ASN K 314 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N HIS K 303 " --> pdb=" O ILE K 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU K 319 " --> pdb=" O LYS K 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE K 511 " --> pdb=" O GLY K 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY K 470 " --> pdb=" O PHE K 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE K 513 " --> pdb=" O LEU K 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU K 468 " --> pdb=" O ILE K 513 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'K' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU K 319 " --> pdb=" O LYS K 502 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'K' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU K 402 " --> pdb=" O THR K 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU K 393 " --> pdb=" O ALA K 400 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA K 400 " --> pdb=" O LEU K 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU K 413 " --> pdb=" O SER K 425 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER K 425 " --> pdb=" O LEU K 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR K 457 " --> pdb=" O LEU K 426 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'L' and resid 179 through 184 Processing sheet with id= AZ, first strand: chain 'L' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN L 200 " --> pdb=" O LEU L 197 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'L' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS L 363 " --> pdb=" O SER L 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 365 " --> pdb=" O ASN L 314 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS L 303 " --> pdb=" O ILE L 518 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU L 319 " --> pdb=" O LYS L 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE L 511 " --> pdb=" O GLY L 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 470 " --> pdb=" O PHE L 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE L 513 " --> pdb=" O LEU L 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU L 468 " --> pdb=" O ILE L 513 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'L' and resid 316 through 322 removed outlier: 3.861A pdb=" N GLU L 319 " --> pdb=" O LYS L 502 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'L' and resid 380 through 393 removed outlier: 3.783A pdb=" N GLU L 402 " --> pdb=" O THR L 391 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU L 393 " --> pdb=" O ALA L 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA L 400 " --> pdb=" O LEU L 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU L 413 " --> pdb=" O SER L 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER L 425 " --> pdb=" O LEU L 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR L 457 " --> pdb=" O LEU L 426 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'M' and resid 179 through 184 Processing sheet with id= BE, first strand: chain 'M' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN M 200 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'M' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS M 363 " --> pdb=" O SER M 316 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA M 365 " --> pdb=" O ASN M 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS M 303 " --> pdb=" O ILE M 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU M 319 " --> pdb=" O LYS M 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE M 511 " --> pdb=" O GLY M 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY M 470 " --> pdb=" O PHE M 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE M 513 " --> pdb=" O LEU M 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU M 468 " --> pdb=" O ILE M 513 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'M' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU M 319 " --> pdb=" O LYS M 502 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'M' and resid 380 through 393 removed outlier: 3.781A pdb=" N GLU M 402 " --> pdb=" O THR M 391 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU M 393 " --> pdb=" O ALA M 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA M 400 " --> pdb=" O LEU M 393 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU M 413 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER M 425 " --> pdb=" O LEU M 413 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR M 457 " --> pdb=" O LEU M 426 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'N' and resid 179 through 184 Processing sheet with id= BJ, first strand: chain 'N' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN N 200 " --> pdb=" O LEU N 197 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'N' and resid 354 through 376 removed outlier: 3.802A pdb=" N LYS N 363 " --> pdb=" O SER N 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA N 365 " --> pdb=" O ASN N 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS N 303 " --> pdb=" O ILE N 518 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU N 319 " --> pdb=" O LYS N 502 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE N 511 " --> pdb=" O GLY N 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY N 470 " --> pdb=" O PHE N 511 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE N 513 " --> pdb=" O LEU N 468 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU N 468 " --> pdb=" O ILE N 513 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'N' and resid 316 through 322 removed outlier: 3.859A pdb=" N GLU N 319 " --> pdb=" O LYS N 502 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'N' and resid 380 through 393 removed outlier: 3.783A pdb=" N GLU N 402 " --> pdb=" O THR N 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU N 393 " --> pdb=" O ALA N 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA N 400 " --> pdb=" O LEU N 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU N 413 " --> pdb=" O SER N 425 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER N 425 " --> pdb=" O LEU N 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR N 457 " --> pdb=" O LEU N 426 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'O' and resid 179 through 184 Processing sheet with id= BO, first strand: chain 'O' and resid 193 through 197 removed outlier: 3.672A pdb=" N GLN O 200 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'O' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS O 363 " --> pdb=" O SER O 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA O 365 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS O 303 " --> pdb=" O ILE O 518 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU O 319 " --> pdb=" O LYS O 502 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N PHE O 511 " --> pdb=" O GLY O 470 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY O 470 " --> pdb=" O PHE O 511 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE O 513 " --> pdb=" O LEU O 468 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU O 468 " --> pdb=" O ILE O 513 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'O' and resid 316 through 322 removed outlier: 3.860A pdb=" N GLU O 319 " --> pdb=" O LYS O 502 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'O' and resid 380 through 393 removed outlier: 3.781A pdb=" N GLU O 402 " --> pdb=" O THR O 391 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU O 393 " --> pdb=" O ALA O 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA O 400 " --> pdb=" O LEU O 393 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU O 413 " --> pdb=" O SER O 425 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER O 425 " --> pdb=" O LEU O 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR O 457 " --> pdb=" O LEU O 426 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'P' and resid 179 through 184 Processing sheet with id= BT, first strand: chain 'P' and resid 193 through 197 removed outlier: 3.673A pdb=" N GLN P 200 " --> pdb=" O LEU P 197 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'P' and resid 354 through 376 removed outlier: 3.801A pdb=" N LYS P 363 " --> pdb=" O SER P 316 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA P 365 " --> pdb=" O ASN P 314 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS P 303 " --> pdb=" O ILE P 518 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU P 319 " --> pdb=" O LYS P 502 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE P 511 " --> pdb=" O GLY P 470 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY P 470 " --> pdb=" O PHE P 511 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE P 513 " --> pdb=" O LEU P 468 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU P 468 " --> pdb=" O ILE P 513 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'P' and resid 316 through 322 removed outlier: 3.862A pdb=" N GLU P 319 " --> pdb=" O LYS P 502 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'P' and resid 380 through 393 removed outlier: 3.782A pdb=" N GLU P 402 " --> pdb=" O THR P 391 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU P 393 " --> pdb=" O ALA P 400 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ALA P 400 " --> pdb=" O LEU P 393 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU P 413 " --> pdb=" O SER P 425 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER P 425 " --> pdb=" O LEU P 413 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR P 457 " --> pdb=" O LEU P 426 " (cutoff:3.500A) 1560 hydrogen bonds defined for protein. 4410 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: 15.84 Time building geometry restraints manager: 14.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13307 1.34 - 1.46: 4919 1.46 - 1.57: 22589 1.57 - 1.69: 0 1.69 - 1.80: 180 Bond restraints: 40995 Sorted by residual: bond pdb=" N1 LDA D1001 " pdb=" O1 LDA D1001 " ideal model delta sigma weight residual 1.354 1.248 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" N1 LDA C1001 " pdb=" O1 LDA C1001 " ideal model delta sigma weight residual 1.354 1.248 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" N1 LDA I1001 " pdb=" O1 LDA I1001 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N1 LDA G1002 " pdb=" O1 LDA G1002 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" N1 LDA O1001 " pdb=" O1 LDA O1001 " ideal model delta sigma weight residual 1.354 1.249 0.105 2.00e-02 2.50e+03 2.78e+01 ... (remaining 40990 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.98: 1138 106.98 - 113.73: 24103 113.73 - 120.49: 14495 120.49 - 127.24: 15395 127.24 - 133.99: 339 Bond angle restraints: 55470 Sorted by residual: angle pdb=" C GLY O 332 " pdb=" N ASP O 333 " pdb=" CA ASP O 333 " ideal model delta sigma weight residual 122.08 128.54 -6.46 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C GLY L 332 " pdb=" N ASP L 333 " pdb=" CA ASP L 333 " ideal model delta sigma weight residual 122.08 128.53 -6.45 1.47e+00 4.63e-01 1.93e+01 angle pdb=" C GLY B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta sigma weight residual 122.08 128.51 -6.43 1.47e+00 4.63e-01 1.91e+01 angle pdb=" C GLY K 332 " pdb=" N ASP K 333 " pdb=" CA ASP K 333 " ideal model delta sigma weight residual 122.08 128.49 -6.41 1.47e+00 4.63e-01 1.90e+01 angle pdb=" C GLY C 332 " pdb=" N ASP C 333 " pdb=" CA ASP C 333 " ideal model delta sigma weight residual 122.08 128.48 -6.40 1.47e+00 4.63e-01 1.90e+01 ... (remaining 55465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 22519 16.98 - 33.96: 1961 33.96 - 50.94: 390 50.94 - 67.93: 120 67.93 - 84.91: 45 Dihedral angle restraints: 25035 sinusoidal: 10215 harmonic: 14820 Sorted by residual: dihedral pdb=" CA GLY K 217 " pdb=" C GLY K 217 " pdb=" N GLU K 218 " pdb=" CA GLU K 218 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY M 217 " pdb=" C GLY M 217 " pdb=" N GLU M 218 " pdb=" CA GLU M 218 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA GLY I 217 " pdb=" C GLY I 217 " pdb=" N GLU I 218 " pdb=" CA GLU I 218 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 25032 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4406 0.044 - 0.088: 1353 0.088 - 0.132: 530 0.132 - 0.177: 176 0.177 - 0.221: 60 Chirality restraints: 6525 Sorted by residual: chirality pdb=" CA ASP D 333 " pdb=" N ASP D 333 " pdb=" C ASP D 333 " pdb=" CB ASP D 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASP I 333 " pdb=" N ASP I 333 " pdb=" C ASP I 333 " pdb=" CB ASP I 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA ASP M 333 " pdb=" N ASP M 333 " pdb=" C ASP M 333 " pdb=" CB ASP M 333 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 6522 not shown) Planarity restraints: 7035 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG N 370 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.42e+00 pdb=" N PRO N 371 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO N 371 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 371 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 370 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO L 371 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO L 371 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO L 371 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG P 370 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO P 371 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO P 371 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO P 371 " -0.037 5.00e-02 4.00e+02 ... (remaining 7032 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2257 2.73 - 3.27: 33178 3.27 - 3.81: 58841 3.81 - 4.36: 70675 4.36 - 4.90: 131889 Nonbonded interactions: 296840 Sorted by model distance: nonbonded pdb=" O SER I 537 " pdb=" ND2 ASN K 477 " model vdw 2.186 2.520 nonbonded pdb=" O LYS I 301 " pdb=" NH2 ARG J 460 " model vdw 2.276 2.520 nonbonded pdb=" O SER H 537 " pdb=" ND2 ASN J 477 " model vdw 2.305 2.520 nonbonded pdb=" OG1 THR N 323 " pdb=" O LEU N 496 " model vdw 2.343 2.440 nonbonded pdb=" OG1 THR K 323 " pdb=" O LEU K 496 " model vdw 2.343 2.440 ... (remaining 296835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'B' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'C' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'D' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'F' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'G' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'H' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'I' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'J' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'K' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'L' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'M' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'N' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'O' and (resid 175 through 557 or (resid 1001 through 1003 and (name C1 o \ r name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or n \ ame C9 or name CM1 or name CM2 or name N1 or name O1 )))) selection = (chain 'P' and (resid 175 through 557 or (resid 601 through 603 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 or name C7 or name C8 or nam \ e C9 or name CM1 or name CM2 or name N1 or name O1 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.670 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: 0.040 Extract box with map and model: 5.630 Check model and map are aligned: 0.530 Set scattering table: 0.340 Process input model: 100.440 Find NCS groups from input model: 3.800 Set up NCS constraints: 0.430 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 40995 Z= 0.437 Angle : 0.867 8.315 55470 Z= 0.467 Chirality : 0.055 0.221 6525 Planarity : 0.006 0.068 7035 Dihedral : 13.951 84.906 15465 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.34 % Allowed : 8.20 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.10), residues: 5115 helix: -5.10 (0.04), residues: 855 sheet: -1.53 (0.09), residues: 2700 loop : -2.67 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 309 HIS 0.001 0.000 HIS G 463 PHE 0.012 0.002 PHE B 511 TYR 0.008 0.001 TYR N 406 ARG 0.003 0.000 ARG M 474 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10230 Ramachandran restraints generated. 5115 Oldfield, 0 Emsley, 5115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 455 time to evaluate : 4.968 Fit side-chains REVERT: A 183 MET cc_start: 0.8597 (mtt) cc_final: 0.8341 (mtt) REVERT: A 200 GLN cc_start: 0.7573 (pt0) cc_final: 0.7212 (pt0) REVERT: A 289 PHE cc_start: 0.8271 (t80) cc_final: 0.8043 (t80) REVERT: A 292 MET cc_start: 0.8253 (mmp) cc_final: 0.8049 (mmm) REVERT: A 361 GLU cc_start: 0.7450 (tt0) cc_final: 0.7207 (tt0) REVERT: A 512 MET cc_start: 0.8778 (mtm) cc_final: 0.8213 (mtt) REVERT: A 536 GLN cc_start: 0.8493 (mt0) cc_final: 0.8174 (mt0) REVERT: B 183 MET cc_start: 0.8619 (mtt) cc_final: 0.8229 (mpp) REVERT: B 289 PHE cc_start: 0.8512 (t80) cc_final: 0.7782 (t80) REVERT: B 298 ASP cc_start: 0.7935 (t0) cc_final: 0.7555 (t0) REVERT: B 320 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7216 (mtt90) REVERT: B 424 MET cc_start: 0.8706 (mtm) cc_final: 0.8225 (mtm) REVERT: B 496 LEU cc_start: 0.8873 (mp) cc_final: 0.8662 (mt) REVERT: C 328 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8214 (p) REVERT: D 331 ILE cc_start: 0.8044 (mm) cc_final: 0.7771 (tt) REVERT: F 200 GLN cc_start: 0.8366 (pt0) cc_final: 0.8119 (pt0) REVERT: F 202 MET cc_start: 0.8384 (mmm) cc_final: 0.8044 (mmm) REVERT: F 512 MET cc_start: 0.8356 (mtm) cc_final: 0.7956 (mtm) REVERT: G 183 MET cc_start: 0.8862 (mtt) cc_final: 0.8299 (mtm) REVERT: G 289 PHE cc_start: 0.8081 (t80) cc_final: 0.7787 (t80) REVERT: G 424 MET cc_start: 0.8240 (mtm) cc_final: 0.7840 (mtm) REVERT: I 328 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8238 (p) REVERT: I 475 ASP cc_start: 0.8297 (m-30) cc_final: 0.8024 (m-30) REVERT: I 512 MET cc_start: 0.8443 (mtm) cc_final: 0.8001 (mtt) REVERT: J 199 ASP cc_start: 0.7962 (p0) cc_final: 0.7761 (p0) REVERT: J 292 MET cc_start: 0.8271 (mmp) cc_final: 0.8065 (mmp) REVERT: J 424 MET cc_start: 0.8888 (mtm) cc_final: 0.8305 (mtp) REVERT: J 486 PHE cc_start: 0.7573 (t80) cc_final: 0.7367 (t80) REVERT: K 272 TYR cc_start: 0.8890 (t80) cc_final: 0.8469 (t80) REVERT: K 429 GLU cc_start: 0.7704 (tt0) cc_final: 0.7387 (tt0) REVERT: L 200 GLN cc_start: 0.8315 (pt0) cc_final: 0.8056 (pt0) REVERT: L 292 MET cc_start: 0.8304 (mmp) cc_final: 0.7963 (mmm) REVERT: L 328 SER cc_start: 0.8458 (OUTLIER) cc_final: 0.8160 (p) REVERT: L 512 MET cc_start: 0.8451 (mtm) cc_final: 0.7569 (mtp) REVERT: L 540 TRP cc_start: 0.8377 (t60) cc_final: 0.7985 (t60) REVERT: M 402 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6904 (mm-30) REVERT: M 409 MET cc_start: 0.7672 (ttt) cc_final: 0.6983 (ttm) REVERT: M 424 MET cc_start: 0.8681 (mtm) cc_final: 0.8394 (mtp) REVERT: N 216 GLN cc_start: 0.7931 (tt0) cc_final: 0.7718 (tt0) REVERT: N 328 SER cc_start: 0.8072 (OUTLIER) cc_final: 0.7779 (p) REVERT: N 360 GLU cc_start: 0.7576 (tt0) cc_final: 0.7252 (tt0) REVERT: O 183 MET cc_start: 0.8413 (mtt) cc_final: 0.8163 (mtm) REVERT: O 200 GLN cc_start: 0.7870 (pt0) cc_final: 0.7343 (pt0) REVERT: O 272 TYR cc_start: 0.8727 (t80) cc_final: 0.8320 (t80) REVERT: O 274 ASP cc_start: 0.8662 (t0) cc_final: 0.7936 (t0) REVERT: O 292 MET cc_start: 0.8456 (mmp) cc_final: 0.8138 (mmm) REVERT: P 202 MET cc_start: 0.8246 (mmm) cc_final: 0.7771 (mmt) REVERT: P 274 ASP cc_start: 0.8446 (t0) cc_final: 0.8217 (t0) REVERT: P 389 PHE cc_start: 0.7430 (t80) cc_final: 0.7078 (t80) REVERT: P 424 MET cc_start: 0.8530 (mtm) cc_final: 0.8295 (mtm) REVERT: P 486 PHE cc_start: 0.7426 (t80) cc_final: 0.7113 (t80) REVERT: P 512 MET cc_start: 0.8384 (mtm) cc_final: 0.8171 (mtp) outliers start: 15 outliers final: 4 residues processed: 470 average time/residue: 0.5361 time to fit residues: 400.1343 Evaluate side-chains 329 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 321 time to evaluate : 3.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 328 SER Chi-restraints excluded: chain F residue 328 SER Chi-restraints excluded: chain I residue 328 SER Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain M residue 328 SER Chi-restraints excluded: chain N residue 328 SER Chi-restraints excluded: chain O residue 328 SER Chi-restraints excluded: chain P residue 328 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 430 optimal weight: 0.0970 chunk 386 optimal weight: 7.9990 chunk 214 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 260 optimal weight: 0.0270 chunk 206 optimal weight: 0.9980 chunk 399 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 243 optimal weight: 0.9990 chunk 297 optimal weight: 3.9990 chunk 463 optimal weight: 4.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: