Starting phenix.real_space_refine on Sun Mar 24 08:07:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/03_2024/6pee_20315_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/03_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_20315/03_2024/6pee_20315.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/03_2024/6pee_20315.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/03_2024/6pee_20315_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pee_20315/03_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-5265/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: 19.25, 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: 14.74 Conformation dependent library (CDL) restraints added in 7.4 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: 8.36 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: 14.05 Time building geometry restraints manager: 15.92 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.770 Check model and map are aligned: 0.580 Set scattering table: 0.390 Process input model: 97.660 Find NCS groups from input model: 3.210 Set up NCS constraints: 0.410 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.600 ------------------------------------------------------------------------------- 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 : 4.717 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: 0.5602 time to fit residues: 418.5951 Evaluate side-chains 329 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 321 time to evaluate : 4.667 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 421 GLN A 432 ASN B 432 ASN C 421 GLN C 432 ASN D 421 GLN D 432 ASN F 432 ASN G 432 ASN H 432 ASN I 421 GLN I 432 ASN J 432 ASN ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 432 ASN L 432 ASN M 341 GLN M 432 ASN N 341 GLN N 432 ASN O 432 ASN P 432 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40995 Z= 0.156 Angle : 0.515 6.289 55470 Z= 0.272 Chirality : 0.045 0.169 6525 Planarity : 0.005 0.066 7035 Dihedral : 6.904 55.074 5933 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.99 % Allowed : 11.12 % Favored : 87.89 % 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: -2.82 (0.11), residues: 5115 helix: -4.05 (0.11), residues: 675 sheet: -0.86 (0.10), residues: 2760 loop : -2.40 (0.12), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 309 HIS 0.002 0.000 HIS P 303 PHE 0.015 0.001 PHE H 486 TYR 0.013 0.001 TYR P 195 ARG 0.005 0.000 ARG B 387 *********************** REFINEMENT MACRO_CYCLE 2 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 425 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 381 time to evaluate : 4.762 Fit side-chains REVERT: A 183 MET cc_start: 0.8592 (mtt) cc_final: 0.8246 (mtt) REVERT: A 289 PHE cc_start: 0.8339 (t80) cc_final: 0.8054 (t80) REVERT: A 292 MET cc_start: 0.7804 (mmp) cc_final: 0.7566 (mmm) REVERT: A 361 GLU cc_start: 0.7288 (tt0) cc_final: 0.7033 (tt0) REVERT: A 512 MET cc_start: 0.8709 (mtm) cc_final: 0.8370 (mtt) REVERT: A 540 TRP cc_start: 0.8796 (t60) cc_final: 0.8327 (t60) REVERT: B 177 ARG cc_start: 0.6862 (mmm-85) cc_final: 0.6457 (mmm-85) REVERT: B 212 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 289 PHE cc_start: 0.8414 (t80) cc_final: 0.7809 (t80) REVERT: B 298 ASP cc_start: 0.7908 (t0) cc_final: 0.7574 (t0) REVERT: B 410 ILE cc_start: 0.8635 (mt) cc_final: 0.8287 (tt) REVERT: B 424 MET cc_start: 0.8702 (mtm) cc_final: 0.8121 (mtm) REVERT: B 496 LEU cc_start: 0.8858 (mp) cc_final: 0.8620 (mt) REVERT: B 536 GLN cc_start: 0.8705 (mt0) cc_final: 0.8381 (tt0) REVERT: C 389 PHE cc_start: 0.7313 (t80) cc_final: 0.7062 (t80) REVERT: D 361 GLU cc_start: 0.7330 (tt0) cc_final: 0.6924 (tm-30) REVERT: D 432 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8532 (p0) REVERT: D 513 ILE cc_start: 0.9418 (mm) cc_final: 0.9175 (mm) REVERT: F 202 MET cc_start: 0.8101 (mmm) cc_final: 0.7622 (mmm) REVERT: F 512 MET cc_start: 0.8292 (mtm) cc_final: 0.7984 (mtm) REVERT: G 183 MET cc_start: 0.8682 (mtt) cc_final: 0.8385 (mtm) REVERT: G 312 ASP cc_start: 0.7625 (t70) cc_final: 0.7411 (t0) REVERT: G 424 MET cc_start: 0.8496 (mtm) cc_final: 0.8247 (mtm) REVERT: I 202 MET cc_start: 0.7948 (mmm) cc_final: 0.7712 (mtp) REVERT: I 512 MET cc_start: 0.8390 (mtm) cc_final: 0.7857 (mtt) REVERT: J 272 TYR cc_start: 0.8536 (t80) cc_final: 0.8243 (t80) REVERT: J 486 PHE cc_start: 0.7612 (t80) cc_final: 0.7357 (t80) REVERT: K 272 TYR cc_start: 0.8754 (t80) cc_final: 0.8530 (t80) REVERT: K 413 LEU cc_start: 0.9453 (tp) cc_final: 0.9033 (tt) REVERT: K 424 MET cc_start: 0.7452 (mtp) cc_final: 0.7247 (mtp) REVERT: K 429 GLU cc_start: 0.7758 (tt0) cc_final: 0.7396 (tt0) REVERT: K 454 LEU cc_start: 0.8753 (mt) cc_final: 0.8520 (mp) REVERT: K 482 GLN cc_start: 0.8107 (mt0) cc_final: 0.7898 (mt0) REVERT: L 512 MET cc_start: 0.8156 (mtm) cc_final: 0.7274 (mtp) REVERT: L 540 TRP cc_start: 0.8368 (t60) cc_final: 0.8046 (t60) REVERT: M 177 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6325 (mtp85) REVERT: M 200 GLN cc_start: 0.7996 (pt0) cc_final: 0.7701 (pt0) REVERT: M 289 PHE cc_start: 0.8135 (t80) cc_final: 0.7899 (t80) REVERT: M 409 MET cc_start: 0.7327 (ttt) cc_final: 0.6838 (ttm) REVERT: M 424 MET cc_start: 0.8473 (mtm) cc_final: 0.8211 (mtp) REVERT: N 212 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7401 (tm-30) REVERT: N 312 ASP cc_start: 0.7468 (t70) cc_final: 0.7006 (t0) REVERT: N 360 GLU cc_start: 0.7382 (tt0) cc_final: 0.7035 (tt0) REVERT: N 363 LYS cc_start: 0.7905 (tttt) cc_final: 0.7638 (mtpp) REVERT: N 410 ILE cc_start: 0.8731 (mt) cc_final: 0.8462 (mm) REVERT: O 200 GLN cc_start: 0.7430 (pt0) cc_final: 0.6954 (pt0) REVERT: O 274 ASP cc_start: 0.8732 (t0) cc_final: 0.8044 (t0) REVERT: O 389 PHE cc_start: 0.7194 (t80) cc_final: 0.6733 (t80) REVERT: O 432 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8176 (p0) REVERT: P 202 MET cc_start: 0.8132 (mmm) cc_final: 0.7806 (mmt) REVERT: P 486 PHE cc_start: 0.7329 (t80) cc_final: 0.6980 (t80) outliers start: 44 outliers final: 16 residues processed: 406 average time/residue: 0.5167 time to fit residues: 342.9362 Evaluate side-chains 327 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 309 time to evaluate : 4.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain O residue 277 SER Chi-restraints excluded: chain O residue 432 ASN Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 493 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 chunk 315 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 463 optimal weight: 2.9990 chunk 501 optimal weight: 4.9990 chunk 413 optimal weight: 6.9990 chunk 460 optimal weight: 0.0980 chunk 158 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN B 432 ASN ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS G 536 GLN H 482 GLN H 506 ASN I 266 ASN I 506 ASN J 432 ASN K 536 GLN L 266 ASN M 303 HIS M 421 GLN M 482 GLN N 341 GLN N 506 ASN O 266 ASN P 432 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40995 Z= 0.290 Angle : 0.554 5.549 55470 Z= 0.293 Chirality : 0.045 0.161 6525 Planarity : 0.005 0.070 7035 Dihedral : 6.555 59.702 5925 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.17 % Allowed : 11.93 % Favored : 85.90 % 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: -2.16 (0.11), residues: 5115 helix: -3.27 (0.14), residues: 675 sheet: -0.43 (0.10), residues: 2640 loop : -2.05 (0.13), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 309 HIS 0.004 0.001 HIS O 303 PHE 0.021 0.002 PHE O 511 TYR 0.017 0.002 TYR M 195 ARG 0.007 0.000 ARG D 411 *********************** REFINEMENT MACRO_CYCLE 3 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 426 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 330 time to evaluate : 4.186 Fit side-chains REVERT: A 183 MET cc_start: 0.8691 (mtt) cc_final: 0.8326 (mtt) REVERT: A 200 GLN cc_start: 0.7480 (pt0) cc_final: 0.7165 (pt0) REVERT: B 298 ASP cc_start: 0.7695 (t0) cc_final: 0.7482 (t0) REVERT: B 496 LEU cc_start: 0.8885 (mp) cc_final: 0.8633 (mt) REVERT: B 523 THR cc_start: 0.9377 (OUTLIER) cc_final: 0.8997 (p) REVERT: B 536 GLN cc_start: 0.8678 (mt0) cc_final: 0.8269 (tt0) REVERT: C 177 ARG cc_start: 0.6715 (mmm-85) cc_final: 0.6299 (mmm-85) REVERT: C 389 PHE cc_start: 0.7320 (t80) cc_final: 0.7069 (t80) REVERT: C 402 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7009 (mm-30) REVERT: D 406 TYR cc_start: 0.8708 (p90) cc_final: 0.8196 (p90) REVERT: F 177 ARG cc_start: 0.6588 (mtp85) cc_final: 0.6332 (mtp85) REVERT: F 382 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8291 (pt) REVERT: F 512 MET cc_start: 0.8450 (mtm) cc_final: 0.8207 (mtm) REVERT: G 183 MET cc_start: 0.8840 (mtt) cc_final: 0.8378 (mtm) REVERT: G 197 LEU cc_start: 0.8618 (mp) cc_final: 0.8321 (mp) REVERT: G 424 MET cc_start: 0.8523 (mtm) cc_final: 0.8253 (mtm) REVERT: I 361 GLU cc_start: 0.7805 (tt0) cc_final: 0.7576 (tt0) REVERT: I 512 MET cc_start: 0.8332 (mtm) cc_final: 0.7745 (mtt) REVERT: J 272 TYR cc_start: 0.8555 (t80) cc_final: 0.8320 (t80) REVERT: K 200 GLN cc_start: 0.7965 (pt0) cc_final: 0.7529 (pt0) REVERT: K 413 LEU cc_start: 0.9429 (tp) cc_final: 0.9225 (tt) REVERT: K 429 GLU cc_start: 0.7731 (tt0) cc_final: 0.7419 (tt0) REVERT: K 482 GLN cc_start: 0.8363 (mt0) cc_final: 0.8159 (mt0) REVERT: K 536 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8529 (mt0) REVERT: L 177 ARG cc_start: 0.6707 (mmm-85) cc_final: 0.6125 (ttt-90) REVERT: L 540 TRP cc_start: 0.8520 (t60) cc_final: 0.8022 (t60) REVERT: M 177 ARG cc_start: 0.6912 (mtp85) cc_final: 0.6645 (mtp85) REVERT: M 200 GLN cc_start: 0.8000 (pt0) cc_final: 0.7735 (pt0) REVERT: M 409 MET cc_start: 0.7312 (ttt) cc_final: 0.6822 (ttm) REVERT: M 424 MET cc_start: 0.8473 (mtm) cc_final: 0.8239 (mtp) REVERT: N 293 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8767 (tp) REVERT: N 360 GLU cc_start: 0.7429 (tt0) cc_final: 0.7036 (tt0) REVERT: N 363 LYS cc_start: 0.8252 (tttt) cc_final: 0.8013 (mtpp) REVERT: N 410 ILE cc_start: 0.8643 (mt) cc_final: 0.8430 (mm) REVERT: N 536 GLN cc_start: 0.8579 (mt0) cc_final: 0.8274 (mm-40) REVERT: O 200 GLN cc_start: 0.7424 (pt0) cc_final: 0.6956 (pt0) REVERT: O 274 ASP cc_start: 0.8728 (t0) cc_final: 0.8057 (t0) REVERT: O 389 PHE cc_start: 0.7208 (t80) cc_final: 0.6776 (t80) REVERT: O 540 TRP cc_start: 0.8298 (t60) cc_final: 0.7798 (t-100) REVERT: P 202 MET cc_start: 0.7887 (mmm) cc_final: 0.7584 (mmm) REVERT: P 486 PHE cc_start: 0.7338 (t80) cc_final: 0.7031 (t80) REVERT: P 510 VAL cc_start: 0.8842 (OUTLIER) cc_final: 0.8621 (m) outliers start: 96 outliers final: 64 residues processed: 400 average time/residue: 0.5104 time to fit residues: 336.5851 Evaluate side-chains 376 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 307 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 382 ILE Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 266 ASN Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 432 ASN Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 432 ASN Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 536 GLN Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 419 ASP Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 0.5980 chunk 348 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 311 optimal weight: 2.9990 chunk 465 optimal weight: 6.9990 chunk 492 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 441 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN B 266 ASN D 506 ASN F 266 ASN F 341 GLN F 398 ASN G 266 ASN H 266 ASN H 398 ASN K 398 ASN K 536 GLN L 266 ASN M 506 ASN N 341 GLN N 421 GLN O 341 GLN O 398 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 40995 Z= 0.328 Angle : 0.568 10.189 55470 Z= 0.298 Chirality : 0.045 0.160 6525 Planarity : 0.005 0.073 7035 Dihedral : 6.224 59.988 5925 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 3.57 % Allowed : 12.72 % Favored : 83.71 % 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: -1.90 (0.11), residues: 5115 helix: -2.78 (0.16), residues: 675 sheet: -0.19 (0.10), residues: 2565 loop : -2.09 (0.12), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 309 HIS 0.004 0.001 HIS O 303 PHE 0.029 0.002 PHE L 289 TYR 0.020 0.002 TYR M 195 ARG 0.006 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 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 479 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 321 time to evaluate : 4.611 Fit side-chains REVERT: A 183 MET cc_start: 0.8652 (mtt) cc_final: 0.8400 (mtt) REVERT: A 200 GLN cc_start: 0.7519 (pt0) cc_final: 0.7179 (pt0) REVERT: B 212 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7648 (tm-30) REVERT: B 266 ASN cc_start: 0.7895 (OUTLIER) cc_final: 0.7498 (p0) REVERT: B 298 ASP cc_start: 0.7793 (t0) cc_final: 0.7449 (t0) REVERT: B 447 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7852 (tt) REVERT: B 496 LEU cc_start: 0.8940 (mp) cc_final: 0.8661 (mt) REVERT: B 523 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.8978 (p) REVERT: B 536 GLN cc_start: 0.8685 (mt0) cc_final: 0.8272 (tt0) REVERT: C 177 ARG cc_start: 0.6667 (mmm-85) cc_final: 0.6336 (mmm-85) REVERT: C 341 GLN cc_start: 0.7647 (mt0) cc_final: 0.7344 (mt0) REVERT: C 389 PHE cc_start: 0.7200 (t80) cc_final: 0.6918 (t80) REVERT: D 361 GLU cc_start: 0.7494 (tt0) cc_final: 0.7085 (tm-30) REVERT: D 406 TYR cc_start: 0.8715 (p90) cc_final: 0.8178 (p90) REVERT: F 512 MET cc_start: 0.8465 (mtm) cc_final: 0.8159 (mtm) REVERT: F 523 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9001 (p) REVERT: G 183 MET cc_start: 0.8830 (mtt) cc_final: 0.8361 (mtm) REVERT: G 197 LEU cc_start: 0.8606 (mp) cc_final: 0.8298 (mp) REVERT: G 289 PHE cc_start: 0.7932 (t80) cc_final: 0.7555 (t80) REVERT: G 389 PHE cc_start: 0.7765 (t80) cc_final: 0.7331 (t80) REVERT: G 424 MET cc_start: 0.8554 (mtm) cc_final: 0.8259 (mtm) REVERT: I 293 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8429 (tp) REVERT: I 319 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7635 (tm-30) REVERT: I 447 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7683 (tp) REVERT: I 512 MET cc_start: 0.8345 (mtm) cc_final: 0.7887 (mtt) REVERT: J 183 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7758 (ptp) REVERT: J 274 ASP cc_start: 0.8503 (t0) cc_final: 0.8265 (m-30) REVERT: K 289 PHE cc_start: 0.7533 (t80) cc_final: 0.7321 (t80) REVERT: K 429 GLU cc_start: 0.7717 (tt0) cc_final: 0.7391 (tt0) REVERT: K 482 GLN cc_start: 0.8441 (mt0) cc_final: 0.8227 (mt0) REVERT: L 540 TRP cc_start: 0.8367 (t60) cc_final: 0.7834 (t60) REVERT: M 177 ARG cc_start: 0.6934 (mtp85) cc_final: 0.6547 (mtp85) REVERT: M 200 GLN cc_start: 0.8064 (pt0) cc_final: 0.7782 (pt0) REVERT: M 402 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7284 (mm-30) REVERT: M 409 MET cc_start: 0.7104 (ttt) cc_final: 0.6636 (ttm) REVERT: M 424 MET cc_start: 0.8354 (mtm) cc_final: 0.8092 (mtp) REVERT: N 289 PHE cc_start: 0.8129 (t80) cc_final: 0.7829 (t80) REVERT: N 360 GLU cc_start: 0.7391 (tt0) cc_final: 0.7048 (tt0) REVERT: N 363 LYS cc_start: 0.8248 (tttt) cc_final: 0.7994 (mtpp) REVERT: N 410 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8471 (mm) REVERT: N 536 GLN cc_start: 0.8635 (mt0) cc_final: 0.8259 (mm-40) REVERT: O 200 GLN cc_start: 0.7302 (pt0) cc_final: 0.6795 (pt0) REVERT: O 274 ASP cc_start: 0.8690 (t0) cc_final: 0.8081 (t0) REVERT: O 341 GLN cc_start: 0.7708 (mt0) cc_final: 0.7268 (mt0) REVERT: O 389 PHE cc_start: 0.7235 (t80) cc_final: 0.6791 (t80) REVERT: O 540 TRP cc_start: 0.8373 (t60) cc_final: 0.7898 (t-100) REVERT: P 202 MET cc_start: 0.7852 (mmm) cc_final: 0.7563 (mmm) REVERT: P 289 PHE cc_start: 0.7694 (t80) cc_final: 0.7494 (t80) REVERT: P 540 TRP cc_start: 0.8924 (t60) cc_final: 0.8599 (t60) outliers start: 158 outliers final: 108 residues processed: 450 average time/residue: 0.4761 time to fit residues: 361.6913 Evaluate side-chains 418 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 302 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 266 ASN Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 555 ASP Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 409 MET Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 432 ASN Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 419 ASP Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 0.9990 chunk 279 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 367 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 420 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 442 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 GLN I 341 GLN J 421 GLN N 341 GLN O 506 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 40995 Z= 0.246 Angle : 0.520 8.244 55470 Z= 0.275 Chirality : 0.045 0.152 6525 Planarity : 0.004 0.071 7035 Dihedral : 5.811 59.844 5925 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.62 % Allowed : 13.63 % Favored : 82.76 % 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: -1.61 (0.11), residues: 5115 helix: -2.15 (0.18), residues: 645 sheet: -0.05 (0.10), residues: 2565 loop : -2.02 (0.12), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 309 HIS 0.003 0.001 HIS O 303 PHE 0.028 0.002 PHE F 289 TYR 0.014 0.001 TYR M 195 ARG 0.006 0.000 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 5 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 480 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 320 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8656 (mtt) cc_final: 0.8415 (mtt) REVERT: A 200 GLN cc_start: 0.7501 (pt0) cc_final: 0.7169 (pt0) REVERT: B 177 ARG cc_start: 0.7292 (mmm-85) cc_final: 0.7087 (mmm-85) REVERT: B 298 ASP cc_start: 0.7777 (t0) cc_final: 0.7392 (t0) REVERT: B 447 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7778 (tt) REVERT: B 496 LEU cc_start: 0.8936 (mp) cc_final: 0.8642 (mt) REVERT: B 523 THR cc_start: 0.9364 (OUTLIER) cc_final: 0.9022 (p) REVERT: B 536 GLN cc_start: 0.8559 (mt0) cc_final: 0.8154 (tt0) REVERT: C 177 ARG cc_start: 0.6769 (mmm-85) cc_final: 0.6430 (mmm-85) REVERT: C 389 PHE cc_start: 0.7247 (t80) cc_final: 0.6984 (t80) REVERT: C 447 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8095 (tp) REVERT: D 361 GLU cc_start: 0.7505 (tt0) cc_final: 0.7081 (tm-30) REVERT: D 406 TYR cc_start: 0.8703 (p90) cc_final: 0.8207 (p90) REVERT: D 447 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7558 (tp) REVERT: F 512 MET cc_start: 0.8419 (mtm) cc_final: 0.8116 (mtm) REVERT: G 183 MET cc_start: 0.8837 (mtt) cc_final: 0.8304 (mtm) REVERT: G 289 PHE cc_start: 0.7874 (t80) cc_final: 0.7508 (t80) REVERT: G 424 MET cc_start: 0.8550 (mtm) cc_final: 0.8228 (mtm) REVERT: G 502 LYS cc_start: 0.7960 (mttt) cc_final: 0.7746 (mtmm) REVERT: H 202 MET cc_start: 0.8209 (mmm) cc_final: 0.7708 (mtt) REVERT: I 293 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8406 (tp) REVERT: I 319 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7606 (tm-30) REVERT: I 447 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7633 (tp) REVERT: I 512 MET cc_start: 0.8314 (mtm) cc_final: 0.7824 (mtt) REVERT: J 202 MET cc_start: 0.8360 (mmm) cc_final: 0.8141 (mmm) REVERT: J 274 ASP cc_start: 0.8525 (t0) cc_final: 0.8217 (m-30) REVERT: J 364 GLN cc_start: 0.8175 (tt0) cc_final: 0.7716 (tt0) REVERT: K 429 GLU cc_start: 0.7700 (tt0) cc_final: 0.7383 (tt0) REVERT: K 482 GLN cc_start: 0.8405 (mt0) cc_final: 0.8168 (mt0) REVERT: L 447 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7894 (tt) REVERT: L 540 TRP cc_start: 0.8347 (t60) cc_final: 0.7797 (t60) REVERT: M 177 ARG cc_start: 0.6939 (mtp85) cc_final: 0.6563 (mtp85) REVERT: M 200 GLN cc_start: 0.8017 (pt0) cc_final: 0.7714 (pt0) REVERT: M 409 MET cc_start: 0.7061 (ttt) cc_final: 0.6661 (ttm) REVERT: M 424 MET cc_start: 0.8328 (mtm) cc_final: 0.8111 (mtm) REVERT: N 289 PHE cc_start: 0.8241 (t80) cc_final: 0.7929 (t80) REVERT: N 293 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8771 (tp) REVERT: N 341 GLN cc_start: 0.7921 (mt0) cc_final: 0.7671 (mt0) REVERT: N 360 GLU cc_start: 0.7333 (tt0) cc_final: 0.7028 (tt0) REVERT: N 363 LYS cc_start: 0.8212 (tttt) cc_final: 0.7957 (mtpp) REVERT: N 410 ILE cc_start: 0.8838 (mt) cc_final: 0.8577 (mm) REVERT: N 536 GLN cc_start: 0.8653 (mt0) cc_final: 0.8282 (mm-40) REVERT: O 200 GLN cc_start: 0.7327 (pt0) cc_final: 0.6684 (pt0) REVERT: O 274 ASP cc_start: 0.8687 (t0) cc_final: 0.8091 (t0) REVERT: O 341 GLN cc_start: 0.7646 (OUTLIER) cc_final: 0.7375 (mt0) REVERT: O 540 TRP cc_start: 0.8395 (t60) cc_final: 0.7932 (t-100) REVERT: P 202 MET cc_start: 0.7799 (mmm) cc_final: 0.7540 (mmm) REVERT: P 289 PHE cc_start: 0.7494 (t80) cc_final: 0.7253 (t80) REVERT: P 510 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8527 (m) REVERT: P 540 TRP cc_start: 0.8905 (t60) cc_final: 0.8521 (t60) outliers start: 160 outliers final: 117 residues processed: 452 average time/residue: 0.5174 time to fit residues: 391.2924 Evaluate side-chains 428 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 301 time to evaluate : 4.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 397 ARG Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 266 ASN Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 555 ASP Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 432 ASN Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 397 ARG Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 513 ILE Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 1.9990 chunk 443 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 289 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 493 optimal weight: 4.9990 chunk 409 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 398 ASN C 421 GLN I 341 GLN L 266 ASN L 398 ASN M 266 ASN N 398 ASN N 531 ASN O 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40995 Z= 0.265 Angle : 0.536 7.298 55470 Z= 0.282 Chirality : 0.045 0.149 6525 Planarity : 0.005 0.071 7035 Dihedral : 5.732 59.772 5925 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.18 % Allowed : 13.97 % Favored : 81.85 % 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: -1.50 (0.11), residues: 5115 helix: -1.93 (0.19), residues: 645 sheet: 0.01 (0.10), residues: 2565 loop : -1.99 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 309 HIS 0.003 0.001 HIS P 303 PHE 0.020 0.002 PHE F 389 TYR 0.016 0.001 TYR M 195 ARG 0.007 0.000 ARG O 397 *********************** REFINEMENT MACRO_CYCLE 6 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 486 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 301 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8624 (mtt) cc_final: 0.8417 (mtt) REVERT: A 200 GLN cc_start: 0.7509 (pt0) cc_final: 0.7201 (pt0) REVERT: B 177 ARG cc_start: 0.7328 (mmm-85) cc_final: 0.7125 (mmm-85) REVERT: B 298 ASP cc_start: 0.7773 (t0) cc_final: 0.7394 (t0) REVERT: B 447 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7776 (tt) REVERT: B 496 LEU cc_start: 0.8909 (mp) cc_final: 0.8604 (mt) REVERT: B 523 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9008 (p) REVERT: B 536 GLN cc_start: 0.8550 (mt0) cc_final: 0.8149 (tt0) REVERT: C 177 ARG cc_start: 0.6732 (mmm-85) cc_final: 0.6399 (mmm-85) REVERT: C 389 PHE cc_start: 0.7266 (t80) cc_final: 0.6979 (t80) REVERT: C 399 VAL cc_start: 0.4506 (OUTLIER) cc_final: 0.4128 (m) REVERT: C 447 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (tp) REVERT: D 361 GLU cc_start: 0.7411 (tt0) cc_final: 0.7059 (tm-30) REVERT: D 406 TYR cc_start: 0.8740 (p90) cc_final: 0.8235 (p90) REVERT: D 447 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7647 (tt) REVERT: G 183 MET cc_start: 0.8833 (mtt) cc_final: 0.8289 (mtm) REVERT: G 212 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7463 (tt0) REVERT: G 289 PHE cc_start: 0.7892 (t80) cc_final: 0.7528 (t80) REVERT: G 424 MET cc_start: 0.8555 (mtm) cc_final: 0.8221 (mtm) REVERT: H 202 MET cc_start: 0.8197 (mmm) cc_final: 0.7721 (mtt) REVERT: I 293 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8408 (tp) REVERT: I 319 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7641 (tm-30) REVERT: I 447 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7622 (tp) REVERT: I 512 MET cc_start: 0.8328 (mtm) cc_final: 0.7892 (mtt) REVERT: J 272 TYR cc_start: 0.8554 (t80) cc_final: 0.8279 (t80) REVERT: J 274 ASP cc_start: 0.8511 (t0) cc_final: 0.7432 (p0) REVERT: J 364 GLN cc_start: 0.8206 (tt0) cc_final: 0.7735 (tt0) REVERT: K 429 GLU cc_start: 0.7694 (tt0) cc_final: 0.7375 (tt0) REVERT: K 482 GLN cc_start: 0.8412 (mt0) cc_final: 0.8174 (mt0) REVERT: L 447 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7856 (tt) REVERT: L 540 TRP cc_start: 0.8343 (t60) cc_final: 0.7795 (t60) REVERT: M 200 GLN cc_start: 0.8036 (pt0) cc_final: 0.7748 (pt0) REVERT: M 409 MET cc_start: 0.7088 (ttt) cc_final: 0.6667 (ttm) REVERT: M 424 MET cc_start: 0.8309 (mtm) cc_final: 0.8091 (mtm) REVERT: N 289 PHE cc_start: 0.8258 (t80) cc_final: 0.7946 (t80) REVERT: N 293 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (tp) REVERT: N 312 ASP cc_start: 0.7701 (t0) cc_final: 0.7224 (t0) REVERT: N 360 GLU cc_start: 0.7314 (tt0) cc_final: 0.7022 (tt0) REVERT: N 363 LYS cc_start: 0.8243 (tttt) cc_final: 0.8005 (mtpp) REVERT: N 410 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8499 (mm) REVERT: N 536 GLN cc_start: 0.8661 (mt0) cc_final: 0.8284 (mm-40) REVERT: O 183 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8326 (mpp) REVERT: O 274 ASP cc_start: 0.8678 (t0) cc_final: 0.8091 (t0) REVERT: O 285 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7400 (tm-30) REVERT: O 341 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: O 389 PHE cc_start: 0.7198 (t80) cc_final: 0.6799 (t80) REVERT: O 540 TRP cc_start: 0.8396 (t60) cc_final: 0.7930 (t-100) REVERT: P 202 MET cc_start: 0.7796 (mmm) cc_final: 0.7577 (mmm) REVERT: P 289 PHE cc_start: 0.7508 (t80) cc_final: 0.7276 (t80) REVERT: P 510 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8533 (m) REVERT: P 540 TRP cc_start: 0.8908 (t60) cc_final: 0.8484 (t60) outliers start: 185 outliers final: 148 residues processed: 454 average time/residue: 0.4789 time to fit residues: 366.3655 Evaluate side-chains 452 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 291 time to evaluate : 5.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 536 GLN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 512 MET Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain H residue 555 ASP Chi-restraints excluded: chain I residue 293 LEU Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 493 ILE Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 432 ASN Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 410 ILE Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 424 MET Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 397 ARG Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 419 ASP Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 377 GLU Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 412 VAL Chi-restraints excluded: chain O residue 427 ASP Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 382 ILE Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 281 optimal weight: 0.9980 chunk 360 optimal weight: 0.0570 chunk 279 optimal weight: 0.7980 chunk 415 optimal weight: 1.9990 chunk 275 optimal weight: 0.4980 chunk 491 optimal weight: 2.9990 chunk 307 optimal weight: 5.9990 chunk 299 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN D 432 ASN I 341 GLN J 432 ASN L 421 GLN M 266 ASN O 432 ASN P 398 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40995 Z= 0.155 Angle : 0.491 8.190 55470 Z= 0.258 Chirality : 0.044 0.144 6525 Planarity : 0.004 0.065 7035 Dihedral : 5.272 50.427 5925 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.21 % Allowed : 15.07 % Favored : 81.72 % 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: -1.30 (0.12), residues: 5115 helix: -1.52 (0.21), residues: 645 sheet: 0.07 (0.10), residues: 2700 loop : -1.99 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 309 HIS 0.001 0.000 HIS G 403 PHE 0.018 0.001 PHE C 486 TYR 0.011 0.001 TYR P 195 ARG 0.010 0.000 ARG N 397 *********************** REFINEMENT MACRO_CYCLE 7 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 472 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 330 time to evaluate : 4.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8616 (mtt) cc_final: 0.8402 (mtt) REVERT: A 200 GLN cc_start: 0.7448 (pt0) cc_final: 0.7100 (pt0) REVERT: A 447 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7543 (tt) REVERT: B 298 ASP cc_start: 0.7730 (t0) cc_final: 0.7313 (t0) REVERT: B 405 THR cc_start: 0.9309 (m) cc_final: 0.9091 (p) REVERT: B 447 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7769 (tt) REVERT: B 496 LEU cc_start: 0.8891 (mp) cc_final: 0.8588 (mt) REVERT: B 536 GLN cc_start: 0.8639 (mt0) cc_final: 0.8301 (tt0) REVERT: C 389 PHE cc_start: 0.7252 (t80) cc_final: 0.6949 (t80) REVERT: D 361 GLU cc_start: 0.7502 (tt0) cc_final: 0.7064 (tm-30) REVERT: D 406 TYR cc_start: 0.8727 (p90) cc_final: 0.8348 (p90) REVERT: D 432 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7917 (p0) REVERT: D 447 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7655 (tt) REVERT: G 183 MET cc_start: 0.8821 (mtt) cc_final: 0.8174 (mtm) REVERT: G 424 MET cc_start: 0.8534 (mtm) cc_final: 0.8184 (mtm) REVERT: H 177 ARG cc_start: 0.7356 (tpp-160) cc_final: 0.7004 (tpp-160) REVERT: H 202 MET cc_start: 0.8133 (mmm) cc_final: 0.7919 (mtp) REVERT: H 454 LEU cc_start: 0.9198 (mt) cc_final: 0.8955 (mp) REVERT: I 319 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7555 (tm-30) REVERT: I 447 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7745 (tp) REVERT: I 512 MET cc_start: 0.8196 (mtm) cc_final: 0.7690 (mtt) REVERT: J 272 TYR cc_start: 0.8559 (t80) cc_final: 0.8164 (t80) REVERT: J 274 ASP cc_start: 0.8563 (t0) cc_final: 0.7442 (p0) REVERT: J 364 GLN cc_start: 0.8157 (tt0) cc_final: 0.7680 (tt0) REVERT: K 429 GLU cc_start: 0.7524 (tt0) cc_final: 0.7185 (tt0) REVERT: K 482 GLN cc_start: 0.8354 (mt0) cc_final: 0.8070 (mt0) REVERT: L 447 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7804 (tt) REVERT: L 540 TRP cc_start: 0.8470 (t60) cc_final: 0.8000 (t60) REVERT: M 200 GLN cc_start: 0.7947 (pt0) cc_final: 0.7651 (pt0) REVERT: M 409 MET cc_start: 0.7199 (ttt) cc_final: 0.6814 (ttm) REVERT: N 289 PHE cc_start: 0.8156 (t80) cc_final: 0.7831 (t80) REVERT: N 363 LYS cc_start: 0.8170 (tttt) cc_final: 0.7949 (mtpp) REVERT: N 410 ILE cc_start: 0.8796 (mt) cc_final: 0.8557 (mm) REVERT: N 536 GLN cc_start: 0.8649 (mt0) cc_final: 0.8424 (mm-40) REVERT: O 183 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8335 (mpp) REVERT: O 274 ASP cc_start: 0.8737 (t0) cc_final: 0.8072 (t0) REVERT: O 341 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7344 (mt0) REVERT: O 389 PHE cc_start: 0.7142 (t80) cc_final: 0.6734 (t80) REVERT: O 540 TRP cc_start: 0.8383 (t60) cc_final: 0.7940 (t-100) REVERT: P 510 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8468 (m) REVERT: P 540 TRP cc_start: 0.8891 (t60) cc_final: 0.8485 (t60) outliers start: 142 outliers final: 104 residues processed: 441 average time/residue: 0.4710 time to fit residues: 350.0424 Evaluate side-chains 421 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 308 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 536 GLN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 266 ASN Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 397 ARG Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 294 VAL Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 510 VAL Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 304 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 312 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 386 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN G 506 ASN I 178 GLN I 341 GLN J 432 ASN K 536 GLN L 266 ASN L 421 GLN M 266 ASN M 482 GLN O 432 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 40995 Z= 0.401 Angle : 0.615 8.697 55470 Z= 0.323 Chirality : 0.046 0.157 6525 Planarity : 0.005 0.074 7035 Dihedral : 5.889 51.496 5925 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 4.07 % Allowed : 14.71 % Favored : 81.22 % 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: -1.43 (0.12), residues: 5115 helix: -1.84 (0.20), residues: 645 sheet: 0.06 (0.10), residues: 2565 loop : -1.97 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP O 309 HIS 0.004 0.001 HIS M 288 PHE 0.027 0.002 PHE O 511 TYR 0.016 0.002 TYR M 195 ARG 0.009 0.001 ARG F 397 *********************** REFINEMENT MACRO_CYCLE 8 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 472 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 292 time to evaluate : 4.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8648 (mtt) cc_final: 0.8445 (mtt) REVERT: A 447 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7676 (tt) REVERT: B 298 ASP cc_start: 0.7848 (t0) cc_final: 0.7456 (t0) REVERT: B 496 LEU cc_start: 0.8984 (mp) cc_final: 0.8656 (mt) REVERT: B 523 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9052 (p) REVERT: B 536 GLN cc_start: 0.8561 (mt0) cc_final: 0.8181 (tt0) REVERT: C 389 PHE cc_start: 0.7275 (t80) cc_final: 0.7006 (t80) REVERT: D 361 GLU cc_start: 0.7417 (tt0) cc_final: 0.7061 (tm-30) REVERT: D 406 TYR cc_start: 0.8794 (p90) cc_final: 0.8291 (p90) REVERT: D 447 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7663 (tt) REVERT: F 177 ARG cc_start: 0.6523 (mtp85) cc_final: 0.6188 (mtp85) REVERT: G 183 MET cc_start: 0.8812 (mtt) cc_final: 0.8323 (mtm) REVERT: G 424 MET cc_start: 0.8581 (mtm) cc_final: 0.8237 (mtm) REVERT: H 177 ARG cc_start: 0.7419 (tpp-160) cc_final: 0.7043 (tpp-160) REVERT: H 188 THR cc_start: 0.9475 (OUTLIER) cc_final: 0.9254 (m) REVERT: I 319 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7596 (tm-30) REVERT: I 447 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7738 (tp) REVERT: I 512 MET cc_start: 0.8360 (mtm) cc_final: 0.7924 (mtt) REVERT: K 429 GLU cc_start: 0.7580 (tt0) cc_final: 0.7215 (tt0) REVERT: K 482 GLN cc_start: 0.8459 (mt0) cc_final: 0.8200 (mt0) REVERT: L 447 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7872 (tt) REVERT: L 540 TRP cc_start: 0.8324 (t60) cc_final: 0.7819 (t60) REVERT: M 200 GLN cc_start: 0.8113 (pt0) cc_final: 0.7855 (pt0) REVERT: M 409 MET cc_start: 0.7120 (ttt) cc_final: 0.6679 (ttm) REVERT: N 289 PHE cc_start: 0.7719 (t80) cc_final: 0.7404 (t80) REVERT: N 293 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8715 (tp) REVERT: N 410 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8490 (mm) REVERT: N 536 GLN cc_start: 0.8673 (mt0) cc_final: 0.8389 (mm-40) REVERT: O 183 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8213 (mpp) REVERT: O 274 ASP cc_start: 0.8643 (t0) cc_final: 0.8070 (t0) REVERT: O 341 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: O 540 TRP cc_start: 0.8411 (t60) cc_final: 0.7903 (t-100) REVERT: P 540 TRP cc_start: 0.8918 (t60) cc_final: 0.8469 (t60) outliers start: 180 outliers final: 151 residues processed: 443 average time/residue: 0.4614 time to fit residues: 348.1863 Evaluate side-chains 447 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 286 time to evaluate : 4.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 478 THR Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 536 GLN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 419 ASP Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 199 ASP Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 430 ASP Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 323 THR Chi-restraints excluded: chain H residue 378 ASN Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 419 ASP Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 323 THR Chi-restraints excluded: chain I residue 366 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 410 ILE Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 183 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 323 THR Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 409 MET Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 384 ASP Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 323 THR Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 266 ASN Chi-restraints excluded: chain M residue 294 VAL Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 419 ASP Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 177 ARG Chi-restraints excluded: chain N residue 293 LEU Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 410 ILE Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 550 VAL Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 294 VAL Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 377 GLU Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 401 LEU Chi-restraints excluded: chain P residue 410 ILE Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 478 THR Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 447 optimal weight: 4.9990 chunk 470 optimal weight: 0.3980 chunk 429 optimal weight: 0.6980 chunk 458 optimal weight: 0.8980 chunk 275 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 359 optimal weight: 0.9980 chunk 140 optimal weight: 0.3980 chunk 413 optimal weight: 0.9990 chunk 433 optimal weight: 2.9990 chunk 456 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 ASN I 341 GLN J 432 ASN K 536 GLN L 341 GLN L 421 GLN M 266 ASN M 482 GLN O 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40995 Z= 0.156 Angle : 0.507 9.091 55470 Z= 0.266 Chirality : 0.044 0.143 6525 Planarity : 0.004 0.067 7035 Dihedral : 5.238 57.842 5925 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.23 % Allowed : 16.07 % Favored : 80.70 % 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: -1.20 (0.12), residues: 5115 helix: -1.35 (0.21), residues: 645 sheet: 0.13 (0.10), residues: 2700 loop : -1.97 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 309 HIS 0.002 0.000 HIS C 288 PHE 0.040 0.001 PHE F 289 TYR 0.012 0.001 TYR P 195 ARG 0.008 0.000 ARG A 397 *********************** REFINEMENT MACRO_CYCLE 9 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 467 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 324 time to evaluate : 5.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8607 (mtt) cc_final: 0.8403 (mtt) REVERT: A 555 ASP cc_start: 0.7509 (m-30) cc_final: 0.7303 (t0) REVERT: B 298 ASP cc_start: 0.7722 (t0) cc_final: 0.7295 (t0) REVERT: B 405 THR cc_start: 0.9308 (m) cc_final: 0.9101 (p) REVERT: B 447 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7774 (tt) REVERT: B 496 LEU cc_start: 0.9042 (mp) cc_final: 0.8668 (mt) REVERT: B 523 THR cc_start: 0.9378 (OUTLIER) cc_final: 0.9000 (p) REVERT: B 536 GLN cc_start: 0.8633 (mt0) cc_final: 0.8304 (tt0) REVERT: C 389 PHE cc_start: 0.7242 (t80) cc_final: 0.6950 (t80) REVERT: C 399 VAL cc_start: 0.4654 (OUTLIER) cc_final: 0.4300 (m) REVERT: D 361 GLU cc_start: 0.7481 (tt0) cc_final: 0.7065 (tm-30) REVERT: D 406 TYR cc_start: 0.8786 (p90) cc_final: 0.8400 (p90) REVERT: D 447 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7701 (tt) REVERT: F 177 ARG cc_start: 0.6565 (mtp85) cc_final: 0.6173 (mtp85) REVERT: G 183 MET cc_start: 0.8811 (mtt) cc_final: 0.8164 (mtm) REVERT: G 289 PHE cc_start: 0.7944 (t80) cc_final: 0.7527 (t80) REVERT: G 293 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8212 (tp) REVERT: G 424 MET cc_start: 0.8556 (mtm) cc_final: 0.8197 (mtm) REVERT: G 449 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7062 (tt0) REVERT: H 177 ARG cc_start: 0.7392 (tpp-160) cc_final: 0.6988 (tpp-160) REVERT: H 202 MET cc_start: 0.8241 (mmm) cc_final: 0.7946 (mtp) REVERT: H 454 LEU cc_start: 0.9248 (mt) cc_final: 0.8991 (mp) REVERT: I 319 GLU cc_start: 0.7906 (tm-30) cc_final: 0.7575 (tm-30) REVERT: I 447 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7453 (tp) REVERT: I 512 MET cc_start: 0.8197 (mtm) cc_final: 0.7705 (mtt) REVERT: J 272 TYR cc_start: 0.8551 (t80) cc_final: 0.8220 (t80) REVERT: J 364 GLN cc_start: 0.8166 (tt0) cc_final: 0.7927 (tt0) REVERT: K 429 GLU cc_start: 0.7539 (tt0) cc_final: 0.7132 (tt0) REVERT: K 454 LEU cc_start: 0.8875 (mt) cc_final: 0.8659 (mp) REVERT: K 482 GLN cc_start: 0.8307 (mt0) cc_final: 0.8025 (mt0) REVERT: L 447 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7363 (tt) REVERT: L 482 GLN cc_start: 0.8019 (mt0) cc_final: 0.7818 (mt0) REVERT: L 540 TRP cc_start: 0.8464 (t60) cc_final: 0.8004 (t60) REVERT: M 200 GLN cc_start: 0.8006 (pt0) cc_final: 0.7701 (pt0) REVERT: M 409 MET cc_start: 0.7230 (ttt) cc_final: 0.6738 (ttm) REVERT: N 289 PHE cc_start: 0.8161 (t80) cc_final: 0.7856 (t80) REVERT: N 363 LYS cc_start: 0.8142 (tttt) cc_final: 0.7924 (mtpp) REVERT: N 410 ILE cc_start: 0.8820 (mt) cc_final: 0.8571 (mm) REVERT: N 536 GLN cc_start: 0.8641 (mt0) cc_final: 0.8416 (mm-40) REVERT: O 274 ASP cc_start: 0.8722 (t0) cc_final: 0.8062 (t0) REVERT: O 341 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: O 540 TRP cc_start: 0.8379 (t60) cc_final: 0.7930 (t-100) REVERT: P 360 GLU cc_start: 0.7587 (tt0) cc_final: 0.7335 (tt0) REVERT: P 540 TRP cc_start: 0.8877 (t60) cc_final: 0.8467 (t60) outliers start: 143 outliers final: 116 residues processed: 445 average time/residue: 0.4597 time to fit residues: 346.4775 Evaluate side-chains 436 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 311 time to evaluate : 5.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 513 ILE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 394 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 404 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 536 GLN Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 449 GLU Chi-restraints excluded: chain F residue 473 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 293 LEU Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 419 ASP Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain G residue 510 VAL Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 473 THR Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 523 THR Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 404 VAL Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 377 GLU Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 300 optimal weight: 7.9990 chunk 484 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 229 optimal weight: 4.9990 chunk 336 optimal weight: 0.0970 chunk 508 optimal weight: 0.0470 chunk 467 optimal weight: 4.9990 chunk 404 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 312 optimal weight: 0.7980 chunk 248 optimal weight: 0.9980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN C 421 GLN D 536 GLN G 398 ASN G 421 GLN I 341 GLN J 398 ASN J 432 ASN K 536 GLN L 266 ASN L 536 GLN M 482 GLN O 432 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40995 Z= 0.146 Angle : 0.499 11.000 55470 Z= 0.261 Chirality : 0.044 0.144 6525 Planarity : 0.004 0.060 7035 Dihedral : 4.924 53.015 5925 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.98 % Allowed : 16.29 % Favored : 80.72 % 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: -0.98 (0.12), residues: 5115 helix: -1.13 (0.21), residues: 645 sheet: 0.30 (0.10), residues: 2700 loop : -1.90 (0.13), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 309 HIS 0.002 0.000 HIS C 288 PHE 0.031 0.001 PHE O 289 TYR 0.012 0.001 TYR P 195 ARG 0.012 0.000 ARG G 397 ********************** REFINEMENT MACRO_CYCLE 10 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 463 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 331 time to evaluate : 4.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8562 (mtt) cc_final: 0.8339 (mtt) REVERT: A 202 MET cc_start: 0.7938 (mmm) cc_final: 0.7685 (mmm) REVERT: A 555 ASP cc_start: 0.7509 (m-30) cc_final: 0.7292 (t0) REVERT: B 298 ASP cc_start: 0.7788 (t0) cc_final: 0.7331 (t0) REVERT: B 405 THR cc_start: 0.9326 (m) cc_final: 0.9124 (p) REVERT: B 496 LEU cc_start: 0.9048 (mp) cc_final: 0.8664 (mt) REVERT: B 523 THR cc_start: 0.9368 (OUTLIER) cc_final: 0.8970 (p) REVERT: B 536 GLN cc_start: 0.8636 (mt0) cc_final: 0.8308 (tt0) REVERT: C 399 VAL cc_start: 0.4151 (OUTLIER) cc_final: 0.3771 (m) REVERT: D 307 SER cc_start: 0.9256 (t) cc_final: 0.8687 (m) REVERT: D 361 GLU cc_start: 0.7493 (tt0) cc_final: 0.7039 (tm-30) REVERT: D 406 TYR cc_start: 0.8742 (p90) cc_final: 0.8404 (p90) REVERT: D 447 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7722 (tt) REVERT: D 513 ILE cc_start: 0.9426 (mm) cc_final: 0.9206 (mm) REVERT: F 177 ARG cc_start: 0.6562 (mtp85) cc_final: 0.6177 (mtp85) REVERT: G 183 MET cc_start: 0.8822 (mtt) cc_final: 0.8350 (mtm) REVERT: G 289 PHE cc_start: 0.7952 (t80) cc_final: 0.7522 (t80) REVERT: G 424 MET cc_start: 0.8633 (mtm) cc_final: 0.8283 (mtm) REVERT: G 449 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6915 (tt0) REVERT: H 177 ARG cc_start: 0.7368 (tpp-160) cc_final: 0.6986 (tpp-160) REVERT: H 454 LEU cc_start: 0.9209 (mt) cc_final: 0.8970 (mp) REVERT: I 319 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7576 (tm-30) REVERT: I 447 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7468 (tp) REVERT: I 512 MET cc_start: 0.8153 (mtm) cc_final: 0.7638 (mtt) REVERT: J 272 TYR cc_start: 0.8476 (t80) cc_final: 0.8084 (t80) REVERT: K 429 GLU cc_start: 0.7530 (tt0) cc_final: 0.7141 (tt0) REVERT: K 454 LEU cc_start: 0.8850 (mt) cc_final: 0.8642 (mp) REVERT: K 482 GLN cc_start: 0.8354 (mt0) cc_final: 0.8063 (mt0) REVERT: L 447 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7389 (tt) REVERT: L 482 GLN cc_start: 0.7957 (mt0) cc_final: 0.7753 (mt0) REVERT: L 540 TRP cc_start: 0.8458 (t60) cc_final: 0.7993 (t60) REVERT: M 200 GLN cc_start: 0.7915 (pt0) cc_final: 0.7646 (pt0) REVERT: M 409 MET cc_start: 0.7161 (ttt) cc_final: 0.6735 (ttm) REVERT: N 177 ARG cc_start: 0.7359 (mtp-110) cc_final: 0.6790 (ttp80) REVERT: N 289 PHE cc_start: 0.8106 (t80) cc_final: 0.7771 (t80) REVERT: N 363 LYS cc_start: 0.8152 (tttt) cc_final: 0.7946 (mtpp) REVERT: N 410 ILE cc_start: 0.8870 (mt) cc_final: 0.8641 (mm) REVERT: N 536 GLN cc_start: 0.8631 (mt0) cc_final: 0.8413 (mm-40) REVERT: O 183 MET cc_start: 0.8213 (mpp) cc_final: 0.7992 (mtm) REVERT: O 274 ASP cc_start: 0.8718 (t0) cc_final: 0.8076 (t0) REVERT: O 341 GLN cc_start: 0.7710 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: O 496 LEU cc_start: 0.9042 (mp) cc_final: 0.8836 (mp) REVERT: O 540 TRP cc_start: 0.8360 (t60) cc_final: 0.7921 (t-100) REVERT: P 360 GLU cc_start: 0.7550 (tt0) cc_final: 0.7234 (tt0) REVERT: P 540 TRP cc_start: 0.8872 (t60) cc_final: 0.8467 (t60) outliers start: 132 outliers final: 110 residues processed: 444 average time/residue: 0.4712 time to fit residues: 355.9253 Evaluate side-chains 432 residues out of total 4470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 315 time to evaluate : 5.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 399 VAL Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 512 MET Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 419 ASP Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain C residue 266 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 382 ILE Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 382 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 447 LEU Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 510 VAL Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 346 THR Chi-restraints excluded: chain F residue 394 ILE Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 493 ILE Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain G residue 266 ASN Chi-restraints excluded: chain G residue 267 ILE Chi-restraints excluded: chain G residue 294 VAL Chi-restraints excluded: chain G residue 298 ASP Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 399 VAL Chi-restraints excluded: chain G residue 409 MET Chi-restraints excluded: chain G residue 449 GLU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain H residue 399 VAL Chi-restraints excluded: chain H residue 412 VAL Chi-restraints excluded: chain H residue 461 VAL Chi-restraints excluded: chain H residue 523 THR Chi-restraints excluded: chain H residue 550 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 397 ARG Chi-restraints excluded: chain I residue 399 VAL Chi-restraints excluded: chain I residue 424 MET Chi-restraints excluded: chain I residue 427 ASP Chi-restraints excluded: chain I residue 447 LEU Chi-restraints excluded: chain I residue 473 THR Chi-restraints excluded: chain I residue 478 THR Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 269 ILE Chi-restraints excluded: chain J residue 294 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 375 THR Chi-restraints excluded: chain J residue 399 VAL Chi-restraints excluded: chain J residue 478 THR Chi-restraints excluded: chain J residue 523 THR Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain K residue 177 ARG Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain K residue 294 VAL Chi-restraints excluded: chain K residue 346 THR Chi-restraints excluded: chain K residue 399 VAL Chi-restraints excluded: chain K residue 419 ASP Chi-restraints excluded: chain K residue 478 THR Chi-restraints excluded: chain K residue 493 ILE Chi-restraints excluded: chain K residue 505 SER Chi-restraints excluded: chain K residue 550 VAL Chi-restraints excluded: chain L residue 266 ASN Chi-restraints excluded: chain L residue 294 VAL Chi-restraints excluded: chain L residue 298 ASP Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 375 THR Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 419 ASP Chi-restraints excluded: chain L residue 447 LEU Chi-restraints excluded: chain L residue 478 THR Chi-restraints excluded: chain L residue 493 ILE Chi-restraints excluded: chain L residue 536 GLN Chi-restraints excluded: chain M residue 346 THR Chi-restraints excluded: chain M residue 399 VAL Chi-restraints excluded: chain M residue 404 VAL Chi-restraints excluded: chain M residue 478 THR Chi-restraints excluded: chain M residue 513 ILE Chi-restraints excluded: chain M residue 523 THR Chi-restraints excluded: chain N residue 346 THR Chi-restraints excluded: chain N residue 399 VAL Chi-restraints excluded: chain N residue 450 VAL Chi-restraints excluded: chain N residue 473 THR Chi-restraints excluded: chain N residue 478 THR Chi-restraints excluded: chain O residue 266 ASN Chi-restraints excluded: chain O residue 341 GLN Chi-restraints excluded: chain O residue 346 THR Chi-restraints excluded: chain O residue 377 GLU Chi-restraints excluded: chain O residue 399 VAL Chi-restraints excluded: chain O residue 475 ASP Chi-restraints excluded: chain O residue 493 ILE Chi-restraints excluded: chain O residue 512 MET Chi-restraints excluded: chain O residue 523 THR Chi-restraints excluded: chain P residue 183 MET Chi-restraints excluded: chain P residue 190 VAL Chi-restraints excluded: chain P residue 294 VAL Chi-restraints excluded: chain P residue 346 THR Chi-restraints excluded: chain P residue 399 VAL Chi-restraints excluded: chain P residue 419 ASP Chi-restraints excluded: chain P residue 493 ILE Chi-restraints excluded: chain P residue 550 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 321 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 373 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 405 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 416 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 266 ASN C 421 GLN H 482 GLN I 341 GLN J 432 ASN K 536 GLN L 266 ASN L 536 GLN M 482 GLN O 432 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.124734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.084634 restraints weight = 55698.673| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.05 r_work: 0.2802 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40995 Z= 0.221 Angle : 0.533 11.420 55470 Z= 0.278 Chirality : 0.044 0.159 6525 Planarity : 0.004 0.066 7035 Dihedral : 5.056 49.981 5925 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.16 % Allowed : 16.29 % Favored : 80.54 % 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: -1.04 (0.12), residues: 5115 helix: -1.38 (0.21), residues: 675 sheet: 0.30 (0.10), residues: 2700 loop : -1.92 (0.13), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 309 HIS 0.002 0.001 HIS C 288 PHE 0.035 0.002 PHE O 289 TYR 0.013 0.001 TYR M 195 ARG 0.012 0.000 ARG G 397 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7863.49 seconds wall clock time: 143 minutes 4.90 seconds (8584.90 seconds total)