Starting phenix.real_space_refine on Mon Mar 18 06:31:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nqd_0485/03_2024/6nqd_0485.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 114 5.16 5 C 12645 2.51 5 N 3273 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 327": "NH1" <-> "NH2" Residue "C ARG 66": "NH1" <-> "NH2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "G ARG 66": "NH1" <-> "NH2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 327": "NH1" <-> "NH2" Residue "K ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20175 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "F" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "G" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3399 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 23, 'TRANS': 415} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 50 Chain: "J" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 944 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "K" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 976 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 125} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 793 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "N" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "Y" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "j" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.02, per 1000 atoms: 0.55 Number of scatterers: 20175 At special positions: 0 Unit cell: (150, 145, 120, 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 114 16.00 O 4143 8.00 N 3273 7.00 C 12645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.11 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.05 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.02 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.11 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.03 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.05 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.04 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.02 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.02 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 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 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN M 5 " - " MAN M 6 " " MAN M 8 " - " MAN M 9 " " MAN N 4 " - " MAN N 5 " " MAN X 4 " - " MAN X 5 " " MAN X 5 " - " MAN X 6 " " MAN X 8 " - " MAN X 9 " " MAN Y 4 " - " MAN Y 5 " " MAN i 4 " - " MAN i 5 " " MAN i 5 " - " MAN i 6 " " MAN i 8 " - " MAN i 9 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 7 " - " MAN M 10 " " BMA N 3 " - " MAN N 4 " " BMA W 3 " - " MAN W 4 " " BMA X 3 " - " MAN X 4 " " MAN X 7 " - " MAN X 10 " " BMA Y 3 " - " MAN Y 4 " " BMA h 3 " - " MAN h 4 " " BMA i 3 " - " MAN i 4 " " MAN i 7 " - " MAN i 10 " " BMA j 3 " - " MAN j 4 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA M 3 " - " MAN M 7 " " MAN M 7 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " BMA X 3 " - " MAN X 7 " " MAN X 7 " - " MAN X 8 " " BMA Y 3 " - " MAN Y 6 " " BMA i 3 " - " MAN i 7 " " MAN i 7 " - " MAN i 8 " " BMA j 3 " - " MAN j 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 619 " - " ASN A 160 " " NAG A 620 " - " ASN A 241 " " NAG A 623 " - " ASN A 295 " " NAG A 624 " - " ASN A 301 " " NAG A 627 " - " ASN A 355 " " NAG A 632 " - " ASN A 448 " " NAG B 705 " - " ASN B 611 " " NAG B 706 " - " ASN B 616 " " NAG B 707 " - " ASN B 625 " " NAG C 301 " - " ASN C 82B" " NAG E 619 " - " ASN E 160 " " NAG E 620 " - " ASN E 241 " " NAG E 623 " - " ASN E 295 " " NAG E 624 " - " ASN E 301 " " NAG E 627 " - " ASN E 355 " " NAG E 632 " - " ASN E 448 " " NAG F 705 " - " ASN F 611 " " NAG F 706 " - " ASN F 616 " " NAG F 707 " - " ASN F 625 " " NAG G 301 " - " ASN G 82B" " NAG I 619 " - " ASN I 160 " " NAG I 620 " - " ASN I 241 " " NAG I 623 " - " ASN I 295 " " NAG I 624 " - " ASN I 301 " " NAG I 627 " - " ASN I 355 " " NAG I 632 " - " ASN I 448 " " NAG J 705 " - " ASN J 611 " " NAG J 706 " - " ASN J 616 " " NAG J 707 " - " ASN J 625 " " NAG K 301 " - " ASN K 82B" " NAG M 1 " - " ASN A 234 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 156 " " NAG P 1 " - " ASN A 289 " " NAG Q 1 " - " ASN A 332 " " NAG R 1 " - " ASN A 386 " " NAG S 1 " - " ASN A 392 " " NAG T 1 " - " ASN A 197 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 262 " " NAG W 1 " - " ASN B 637 " " NAG X 1 " - " ASN E 234 " " NAG Y 1 " - " ASN E 276 " " NAG Z 1 " - " ASN E 156 " " NAG a 1 " - " ASN E 289 " " NAG b 1 " - " ASN E 332 " " NAG c 1 " - " ASN E 386 " " NAG d 1 " - " ASN E 392 " " NAG e 1 " - " ASN E 197 " " NAG f 1 " - " ASN E 130 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN F 637 " " NAG i 1 " - " ASN I 234 " " NAG j 1 " - " ASN I 276 " " NAG k 1 " - " ASN I 156 " " NAG l 1 " - " ASN I 289 " " NAG m 1 " - " ASN I 332 " " NAG n 1 " - " ASN I 386 " " NAG o 1 " - " ASN I 392 " " NAG p 1 " - " ASN I 197 " " NAG q 1 " - " ASN I 130 " " NAG r 1 " - " ASN I 262 " " NAG s 1 " - " ASN J 637 " Time building additional restraints: 9.97 Conformation dependent library (CDL) restraints added in 3.3 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 45 sheets defined 16.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 114 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 593 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 114 Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 476 through 481 removed outlier: 4.043A pdb=" N ASN E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE F 535 " --> pdb=" O GLY F 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 593 Processing helix chain 'F' and resid 618 through 624 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 660 Processing helix chain 'H' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE H 83 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 98 No H-bonds generated for 'chain 'I' and resid 96 through 98' Processing helix chain 'I' and resid 99 through 114 Processing helix chain 'I' and resid 335 through 353 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 476 through 481 removed outlier: 4.042A pdb=" N ASN I 481 " --> pdb=" O ASP I 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 548 removed outlier: 4.494A pdb=" N ILE J 535 " --> pdb=" O GLY J 531 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER J 546 " --> pdb=" O ARG J 542 " (cutoff:3.500A) Processing helix chain 'J' and resid 573 through 593 Processing helix chain 'J' and resid 618 through 624 Processing helix chain 'J' and resid 627 through 635 Processing helix chain 'J' and resid 638 through 660 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.004A pdb=" N PHE L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN A 170 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER A 334 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O CYS A 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 12.087A pdb=" N LEU A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN A 301 " --> pdb=" O ILE A 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 100E through 100F Processing sheet with id=AB5, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 496 removed outlier: 4.453A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR F 606 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 46 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN E 170 " --> pdb=" O MET E 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER E 334 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 295 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS E 374 " --> pdb=" O CYS E 385 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU E 453 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 300 through 312 removed outlier: 6.632A pdb=" N ASN E 301 " --> pdb=" O ILE E 322 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ILE E 322 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 393 through 395 Processing sheet with id=AC7, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC8, first strand: chain 'G' and resid 3 through 5 Processing sheet with id=AC9, first strand: chain 'G' and resid 58 through 59 removed outlier: 5.086A pdb=" N TYR G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG G 38 " --> pdb=" O TYR G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 100E through 100F Processing sheet with id=AD2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 494 through 496 removed outlier: 4.452A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 45 through 46 Processing sheet with id=AD6, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD7, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AD8, first strand: chain 'I' and resid 169 through 174 removed outlier: 3.688A pdb=" N GLN I 170 " --> pdb=" O MET I 161 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 271 through 273 removed outlier: 6.938A pdb=" N LYS I 293 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N SER I 334 " --> pdb=" O LYS I 293 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 295 " --> pdb=" O ASN I 332 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS I 374 " --> pdb=" O CYS I 385 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 271 through 273 removed outlier: 12.223A pdb=" N PHE I 288 " --> pdb=" O LEU I 453 " (cutoff:3.500A) removed outlier: 12.088A pdb=" N LEU I 453 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLU I 290 " --> pdb=" O GLY I 451 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY I 451 " --> pdb=" O GLU I 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 300 through 312 removed outlier: 6.631A pdb=" N ASN I 301 " --> pdb=" O ILE I 322 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE I 322 " --> pdb=" O ASN I 301 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N THR I 303 " --> pdb=" O GLY I 321 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN I 315 " --> pdb=" O ILE I 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 393 through 395 Processing sheet with id=AE4, first strand: chain 'I' and resid 423 through 424 Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 5 Processing sheet with id=AE6, first strand: chain 'K' and resid 58 through 59 removed outlier: 5.087A pdb=" N TYR K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ARG K 38 " --> pdb=" O TYR K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 100E through 100F Processing sheet with id=AE8, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.872A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) 681 hydrogen bonds defined for protein. 1782 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: 6.67 Time building geometry restraints manager: 10.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6141 1.35 - 1.48: 5862 1.48 - 1.61: 8430 1.61 - 1.74: 0 1.74 - 1.87: 150 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 NAG o 1 " pdb=" O5 NAG o 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.498 -0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" C1 NAG J 706 " pdb=" O5 NAG J 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C1 NAG F 706 " pdb=" O5 NAG F 706 " ideal model delta sigma weight residual 1.406 1.497 -0.091 2.00e-02 2.50e+03 2.06e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 97.24 - 104.68: 331 104.68 - 112.13: 10706 112.13 - 119.57: 7456 119.57 - 127.02: 9195 127.02 - 134.46: 317 Bond angle restraints: 28005 Sorted by residual: angle pdb=" N GLY B 516 " pdb=" CA GLY B 516 " pdb=" C GLY B 516 " ideal model delta sigma weight residual 112.51 124.41 -11.90 1.53e+00 4.27e-01 6.04e+01 angle pdb=" N GLY J 516 " pdb=" CA GLY J 516 " pdb=" C GLY J 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" N GLY F 516 " pdb=" CA GLY F 516 " pdb=" C GLY F 516 " ideal model delta sigma weight residual 112.51 124.39 -11.88 1.53e+00 4.27e-01 6.03e+01 angle pdb=" C ALA F 517 " pdb=" N MET F 518 " pdb=" CA MET F 518 " ideal model delta sigma weight residual 122.07 110.71 11.36 1.71e+00 3.42e-01 4.41e+01 angle pdb=" C ALA J 517 " pdb=" N MET J 518 " pdb=" CA MET J 518 " ideal model delta sigma weight residual 122.07 110.72 11.35 1.71e+00 3.42e-01 4.40e+01 ... (remaining 28000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.44: 12819 24.44 - 48.87: 816 48.87 - 73.31: 189 73.31 - 97.74: 96 97.74 - 122.18: 39 Dihedral angle restraints: 13959 sinusoidal: 7092 harmonic: 6867 Sorted by residual: dihedral pdb=" CB CYS I 501 " pdb=" SG CYS I 501 " pdb=" SG CYS J 605 " pdb=" CB CYS J 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.70 -69.30 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS A 501 " pdb=" SG CYS A 501 " pdb=" SG CYS B 605 " pdb=" CB CYS B 605 " ideal model delta sinusoidal sigma weight residual -86.00 -16.73 -69.27 1 1.00e+01 1.00e-02 6.20e+01 ... (remaining 13956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.177: 3479 0.177 - 0.354: 106 0.354 - 0.531: 9 0.531 - 0.708: 6 0.708 - 0.885: 3 Chirality restraints: 3603 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN A 289 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.51 -0.89 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN E 289 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 chirality pdb=" C1 NAG l 1 " pdb=" ND2 ASN I 289 " pdb=" C2 NAG l 1 " pdb=" O5 NAG l 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.96e+01 ... (remaining 3600 not shown) Planarity restraints: 3405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 123 " -0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO E 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO E 124 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 123 " 0.056 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO I 124 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO I 124 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 124 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 123 " -0.056 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO A 124 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " -0.049 5.00e-02 4.00e+02 ... (remaining 3402 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3185 2.75 - 3.29: 18917 3.29 - 3.83: 34025 3.83 - 4.36: 37626 4.36 - 4.90: 64547 Nonbonded interactions: 158300 Sorted by model distance: nonbonded pdb=" O ASN E 67 " pdb=" OG1 THR E 71 " model vdw 2.213 2.440 nonbonded pdb=" O ASN A 67 " pdb=" OG1 THR A 71 " model vdw 2.213 2.440 nonbonded pdb=" O ASN I 67 " pdb=" OG1 THR I 71 " model vdw 2.213 2.440 nonbonded pdb=" OG1 THR E 283 " pdb=" O GLY E 472 " model vdw 2.285 2.440 nonbonded pdb=" OG1 THR I 283 " pdb=" O GLY I 472 " model vdw 2.285 2.440 ... (remaining 158295 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' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'X' selection = chain 'i' } ncs_group { reference = chain 'N' selection = chain 'Y' selection = chain 'j' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'V' selection = chain 'g' selection = chain 'r' } ncs_group { reference = chain 'W' selection = chain 'h' selection = chain 's' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.010 Extract box with map and model: 7.010 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.940 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.420 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.012 0.114 20583 Z= 0.787 Angle : 1.404 11.895 28005 Z= 0.738 Chirality : 0.085 0.885 3603 Planarity : 0.008 0.083 3342 Dihedral : 18.647 122.175 9426 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.77 % Allowed : 10.88 % Favored : 88.35 % Rotamer: Outliers : 8.15 % Allowed : 8.05 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -3.70 (0.15), residues: 2343 helix: -3.03 (0.18), residues: 378 sheet: -1.65 (0.22), residues: 555 loop : -2.74 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.007 TRP L 35 HIS 0.010 0.002 HIS E 287 PHE 0.043 0.005 PHE A 382 TYR 0.046 0.005 TYR L 91 ARG 0.018 0.002 ARG E 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 545 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 SER cc_start: 0.7851 (p) cc_final: 0.7587 (t) REVERT: A 169 GLN cc_start: 0.7573 (tm-30) cc_final: 0.7101 (mp10) REVERT: A 207 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8292 (ptpp) REVERT: A 217 TYR cc_start: 0.8851 (m-80) cc_final: 0.8369 (m-10) REVERT: A 218 CYS cc_start: 0.6565 (OUTLIER) cc_final: 0.6364 (m) REVERT: A 362 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6878 (tmtt) REVERT: C 52 TRP cc_start: 0.8814 (t60) cc_final: 0.8531 (t60) REVERT: E 82 GLN cc_start: 0.6928 (pt0) cc_final: 0.6698 (mp10) REVERT: E 207 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8183 (ptpp) REVERT: E 305 THR cc_start: 0.8104 (t) cc_final: 0.7858 (m) REVERT: E 362 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6353 (tmtt) REVERT: H 92 ASP cc_start: 0.7861 (m-30) cc_final: 0.7327 (m-30) REVERT: I 133 SER cc_start: 0.7617 (p) cc_final: 0.7265 (t) REVERT: I 169 GLN cc_start: 0.7749 (tm-30) cc_final: 0.7467 (mp10) REVERT: I 207 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8289 (ptpp) REVERT: I 218 CYS cc_start: 0.6589 (OUTLIER) cc_final: 0.6286 (m) REVERT: I 362 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6998 (tmtt) REVERT: L 24 ARG cc_start: 0.7968 (ttm110) cc_final: 0.7695 (mtp85) outliers start: 160 outliers final: 49 residues processed: 654 average time/residue: 0.3104 time to fit residues: 309.2952 Evaluate side-chains 481 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 424 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 362 LYS Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 469 ARG Chi-restraints excluded: chain A residue 485 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 22 SER Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 71 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 362 LYS Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 469 ARG Chi-restraints excluded: chain E residue 485 LYS Chi-restraints excluded: chain E residue 489 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 469 ARG Chi-restraints excluded: chain I residue 485 LYS Chi-restraints excluded: chain K residue 45 LEU Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 101 SER Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.8980 chunk 177 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 111 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN A 249 HIS A 308 HIS A 354 ASN A 375 HIS B 590 GLN C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 249 HIS E 308 HIS E 354 ASN E 374 HIS E 375 HIS E 478 ASN F 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 ASN I 249 HIS I 308 HIS I 354 ASN I 374 HIS I 375 HIS I 478 ASN J 590 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20583 Z= 0.244 Angle : 0.842 12.427 28005 Z= 0.407 Chirality : 0.055 0.561 3603 Planarity : 0.006 0.054 3342 Dihedral : 15.734 110.718 5515 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 6.68 % Allowed : 14.22 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.75 (0.16), residues: 2343 helix: -1.55 (0.22), residues: 393 sheet: -1.14 (0.23), residues: 549 loop : -2.28 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP J 628 HIS 0.008 0.001 HIS G 3 PHE 0.029 0.002 PHE E 382 TYR 0.031 0.002 TYR I 484 ARG 0.006 0.001 ARG H 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 505 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8332 (ptpp) REVERT: A 217 TYR cc_start: 0.8631 (m-80) cc_final: 0.8261 (m-10) REVERT: A 259 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8145 (pp) REVERT: A 305 THR cc_start: 0.8104 (t) cc_final: 0.7759 (m) REVERT: A 377 ASN cc_start: 0.7782 (t0) cc_final: 0.7493 (t0) REVERT: A 484 TYR cc_start: 0.9032 (p90) cc_final: 0.8802 (p90) REVERT: B 603 ILE cc_start: 0.8116 (mm) cc_final: 0.7618 (mt) REVERT: B 616 ASN cc_start: 0.6881 (p0) cc_final: 0.6662 (p0) REVERT: C 54 ARG cc_start: 0.8690 (mpp80) cc_final: 0.8487 (mpp80) REVERT: C 94 THR cc_start: 0.8383 (p) cc_final: 0.8144 (p) REVERT: D 24 ARG cc_start: 0.7921 (mmt-90) cc_final: 0.7721 (mtp85) REVERT: E 82 GLN cc_start: 0.6981 (pt0) cc_final: 0.6690 (mp-120) REVERT: E 207 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8200 (mttp) REVERT: E 259 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8441 (pp) REVERT: E 384 TYR cc_start: 0.6649 (m-10) cc_final: 0.6155 (m-10) REVERT: E 455 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7943 (t) REVERT: E 484 TYR cc_start: 0.8866 (p90) cc_final: 0.8621 (p90) REVERT: F 603 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.7856 (mt) REVERT: G 66 ARG cc_start: 0.7552 (ptt180) cc_final: 0.6937 (ptt180) REVERT: H 47 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (pt) REVERT: H 86 PHE cc_start: 0.6252 (m-10) cc_final: 0.5962 (m-10) REVERT: I 207 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8327 (mttp) REVERT: I 259 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8417 (pp) REVERT: I 305 THR cc_start: 0.8184 (t) cc_final: 0.7870 (m) REVERT: I 370 GLU cc_start: 0.8303 (tt0) cc_final: 0.8013 (tt0) REVERT: I 384 TYR cc_start: 0.6877 (m-10) cc_final: 0.6456 (m-10) REVERT: J 603 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7612 (mt) REVERT: K 66 ARG cc_start: 0.7710 (ptt180) cc_final: 0.7440 (ptt180) REVERT: L 24 ARG cc_start: 0.8056 (ttm110) cc_final: 0.7621 (mtp85) outliers start: 131 outliers final: 68 residues processed: 588 average time/residue: 0.3002 time to fit residues: 271.7864 Evaluate side-chains 507 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 429 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 26 SER Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 207 LYS Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 207 LYS Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 259 LEU Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 474 ASN Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain K residue 69 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 212 optimal weight: 6.9990 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 170 optimal weight: 8.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 35AASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 35AASN K 43 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20583 Z= 0.283 Angle : 0.803 13.157 28005 Z= 0.387 Chirality : 0.054 0.483 3603 Planarity : 0.005 0.047 3342 Dihedral : 13.232 108.224 5442 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 6.37 % Allowed : 17.28 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.38 (0.17), residues: 2343 helix: -0.66 (0.25), residues: 396 sheet: -1.04 (0.23), residues: 552 loop : -2.16 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP D 35 HIS 0.004 0.001 HIS E 339 PHE 0.026 0.003 PHE C 30 TYR 0.028 0.002 TYR I 484 ARG 0.006 0.001 ARG J 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 462 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8540 (m-80) cc_final: 0.8250 (m-10) REVERT: A 259 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 265 LEU cc_start: 0.8625 (mp) cc_final: 0.8337 (tp) REVERT: A 305 THR cc_start: 0.8041 (t) cc_final: 0.7787 (m) REVERT: B 603 ILE cc_start: 0.8359 (mm) cc_final: 0.8040 (mt) REVERT: B 616 ASN cc_start: 0.6911 (p0) cc_final: 0.6602 (p0) REVERT: B 658 LYS cc_start: 0.8336 (ptmt) cc_final: 0.7961 (ttpt) REVERT: C 52 TRP cc_start: 0.8872 (t60) cc_final: 0.8303 (t60) REVERT: C 54 ARG cc_start: 0.8822 (mpp80) cc_final: 0.8086 (mpp80) REVERT: C 74 LEU cc_start: 0.8435 (tp) cc_final: 0.8224 (tp) REVERT: E 87 LYS cc_start: 0.7896 (mmtt) cc_final: 0.7661 (mmtt) REVERT: E 384 TYR cc_start: 0.6736 (m-10) cc_final: 0.6280 (m-10) REVERT: F 530 MET cc_start: 0.6534 (mmt) cc_final: 0.6206 (mmt) REVERT: F 603 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8177 (mt) REVERT: F 628 TRP cc_start: 0.7764 (OUTLIER) cc_final: 0.7480 (m-10) REVERT: G 100 LEU cc_start: 0.9032 (mt) cc_final: 0.8828 (mt) REVERT: H 92 ASP cc_start: 0.7720 (m-30) cc_final: 0.7291 (m-30) REVERT: I 181 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8581 (mp) REVERT: I 209 SER cc_start: 0.8386 (t) cc_final: 0.7940 (m) REVERT: I 305 THR cc_start: 0.8130 (t) cc_final: 0.7858 (m) REVERT: J 603 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7948 (mt) REVERT: L 24 ARG cc_start: 0.8123 (ttm110) cc_final: 0.7670 (mtp85) outliers start: 125 outliers final: 92 residues processed: 533 average time/residue: 0.2913 time to fit residues: 241.6698 Evaluate side-chains 524 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 427 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 523 LEU Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain G residue 101 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 474 ASN Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 9.9990 chunk 160 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 213 optimal weight: 8.9990 chunk 226 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 202 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20583 Z= 0.274 Angle : 0.788 12.889 28005 Z= 0.378 Chirality : 0.054 0.459 3603 Planarity : 0.005 0.049 3342 Dihedral : 11.825 107.833 5427 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 7.44 % Allowed : 19.11 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.21 (0.17), residues: 2343 helix: -0.02 (0.26), residues: 378 sheet: -1.00 (0.23), residues: 534 loop : -2.16 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 628 HIS 0.006 0.001 HIS G 100E PHE 0.033 0.002 PHE D 71 TYR 0.032 0.002 TYR E 484 ARG 0.010 0.001 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 452 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7387 (OUTLIER) cc_final: 0.7136 (p0) REVERT: A 209 SER cc_start: 0.8310 (t) cc_final: 0.7842 (m) REVERT: A 217 TYR cc_start: 0.8591 (m-80) cc_final: 0.8368 (m-80) REVERT: A 259 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8085 (pp) REVERT: A 265 LEU cc_start: 0.8585 (mp) cc_final: 0.8306 (tp) REVERT: A 304 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7820 (ttp80) REVERT: A 305 THR cc_start: 0.8082 (t) cc_final: 0.7840 (m) REVERT: A 456 ARG cc_start: 0.7951 (ptm-80) cc_final: 0.7650 (ptm-80) REVERT: A 483 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8824 (mm) REVERT: A 484 TYR cc_start: 0.9101 (p90) cc_final: 0.8806 (p90) REVERT: B 603 ILE cc_start: 0.8342 (mm) cc_final: 0.8018 (mt) REVERT: B 616 ASN cc_start: 0.6649 (p0) cc_final: 0.6349 (p0) REVERT: C 32 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8093 (pp) REVERT: C 54 ARG cc_start: 0.8906 (mpp80) cc_final: 0.8367 (mpp80) REVERT: D 37 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: D 45 ARG cc_start: 0.8337 (ttp80) cc_final: 0.7832 (ttp80) REVERT: E 82 GLN cc_start: 0.7555 (pm20) cc_final: 0.6797 (pt0) REVERT: E 217 TYR cc_start: 0.8507 (m-80) cc_final: 0.8236 (m-10) REVERT: E 377 ASN cc_start: 0.7658 (t0) cc_final: 0.7435 (t0) REVERT: E 411 ASN cc_start: 0.7119 (p0) cc_final: 0.6786 (p0) REVERT: F 603 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8112 (mt) REVERT: F 628 TRP cc_start: 0.7980 (OUTLIER) cc_final: 0.7363 (m-90) REVERT: G 54 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8150 (mtm180) REVERT: H 32 TRP cc_start: 0.8692 (m100) cc_final: 0.7976 (m100) REVERT: H 89 GLN cc_start: 0.7306 (tt0) cc_final: 0.7048 (tt0) REVERT: I 181 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8566 (mp) REVERT: I 209 SER cc_start: 0.8211 (t) cc_final: 0.7729 (m) REVERT: I 395 TRP cc_start: 0.5616 (m-10) cc_final: 0.5381 (m-10) REVERT: I 456 ARG cc_start: 0.7153 (ttp80) cc_final: 0.6861 (ttp80) REVERT: I 483 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8931 (mm) REVERT: J 591 LYS cc_start: 0.8273 (ptmt) cc_final: 0.8034 (pttt) REVERT: J 603 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8133 (mt) REVERT: J 624 ASN cc_start: 0.9073 (m-40) cc_final: 0.8582 (m-40) REVERT: K 30 PHE cc_start: 0.8369 (m-80) cc_final: 0.8106 (m-80) REVERT: K 100 MET cc_start: 0.7598 (OUTLIER) cc_final: 0.6701 (ptp) REVERT: L 37 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.7839 (pp30) outliers start: 146 outliers final: 99 residues processed: 541 average time/residue: 0.2938 time to fit residues: 252.3403 Evaluate side-chains 541 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 430 time to evaluate : 2.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 583 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain G residue 77 SER Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 219 THR Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 265 LEU Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 430 VAL Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 474 ASN Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 583 VAL Chi-restraints excluded: chain J residue 603 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 4.9990 chunk 128 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20583 Z= 0.363 Angle : 0.826 15.263 28005 Z= 0.400 Chirality : 0.055 0.458 3603 Planarity : 0.005 0.048 3342 Dihedral : 11.482 110.771 5426 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 8.15 % Allowed : 19.37 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.22 (0.17), residues: 2343 helix: -0.21 (0.25), residues: 396 sheet: -1.16 (0.22), residues: 591 loop : -2.08 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 35 HIS 0.005 0.001 HIS E 339 PHE 0.031 0.003 PHE D 71 TYR 0.032 0.002 TYR E 484 ARG 0.006 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 460 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7200 (p0) REVERT: A 209 SER cc_start: 0.8186 (t) cc_final: 0.7616 (m) REVERT: A 259 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8087 (pp) REVERT: A 265 LEU cc_start: 0.8650 (mp) cc_final: 0.8331 (tp) REVERT: A 373 MET cc_start: 0.8168 (mmm) cc_final: 0.7873 (mmm) REVERT: A 483 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.8893 (mm) REVERT: B 591 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8476 (ttpt) REVERT: B 603 ILE cc_start: 0.8340 (mm) cc_final: 0.8092 (mt) REVERT: B 616 ASN cc_start: 0.6854 (p0) cc_final: 0.6532 (p0) REVERT: C 32 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7432 (pp) REVERT: C 54 ARG cc_start: 0.8894 (mpp80) cc_final: 0.8318 (mpp80) REVERT: C 74 LEU cc_start: 0.8555 (tp) cc_final: 0.8298 (tp) REVERT: D 24 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7383 (mtp85) REVERT: D 37 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8180 (pm20) REVERT: D 45 ARG cc_start: 0.8306 (ttp80) cc_final: 0.7825 (ttp80) REVERT: E 181 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8567 (tp) REVERT: E 217 TYR cc_start: 0.8584 (m-80) cc_final: 0.8311 (m-10) REVERT: E 377 ASN cc_start: 0.7630 (t0) cc_final: 0.7403 (t0) REVERT: E 384 TYR cc_start: 0.7156 (m-10) cc_final: 0.6955 (m-80) REVERT: E 411 ASN cc_start: 0.7187 (p0) cc_final: 0.6850 (p0) REVERT: F 603 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8179 (mt) REVERT: F 628 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7314 (m-90) REVERT: F 634 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7978 (mm-30) REVERT: G 32 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7053 (pp) REVERT: H 6 GLN cc_start: 0.6965 (pm20) cc_final: 0.6732 (mt0) REVERT: H 24 ARG cc_start: 0.8104 (ttm110) cc_final: 0.7840 (mtm110) REVERT: H 32 TRP cc_start: 0.8910 (m100) cc_final: 0.8018 (m100) REVERT: H 92 ASP cc_start: 0.7694 (m-30) cc_final: 0.7490 (m-30) REVERT: I 209 SER cc_start: 0.8171 (t) cc_final: 0.7708 (m) REVERT: I 483 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9043 (mm) REVERT: J 616 ASN cc_start: 0.7163 (p0) cc_final: 0.6812 (p0) REVERT: J 617 LYS cc_start: 0.8051 (mtpp) cc_final: 0.7402 (mtmm) REVERT: J 624 ASN cc_start: 0.9153 (m-40) cc_final: 0.8708 (m-40) REVERT: J 632 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8194 (mm-30) REVERT: K 100 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.6666 (ptp) REVERT: L 35 TRP cc_start: 0.6608 (m-10) cc_final: 0.6245 (m-10) outliers start: 160 outliers final: 108 residues processed: 550 average time/residue: 0.2866 time to fit residues: 250.9115 Evaluate side-chains 551 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 432 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 33 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 218 CYS Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 345 VAL Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain I residue 474 ASN Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 646 LEU Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 81 GLU Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 3.9990 chunk 203 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 226 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 118 optimal weight: 0.4980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 100EHIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35AASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20583 Z= 0.357 Angle : 0.817 13.927 28005 Z= 0.396 Chirality : 0.055 0.429 3603 Planarity : 0.005 0.046 3342 Dihedral : 11.286 110.274 5424 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 8.36 % Allowed : 20.13 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.26 (0.17), residues: 2343 helix: -0.38 (0.25), residues: 408 sheet: -1.16 (0.22), residues: 591 loop : -2.08 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 35 HIS 0.005 0.001 HIS E 339 PHE 0.029 0.002 PHE D 71 TYR 0.033 0.002 TYR A 484 ARG 0.007 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 461 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 SER cc_start: 0.8206 (t) cc_final: 0.7621 (m) REVERT: A 259 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8045 (pp) REVERT: A 265 LEU cc_start: 0.8669 (mp) cc_final: 0.8344 (tp) REVERT: A 373 MET cc_start: 0.8116 (mmm) cc_final: 0.7893 (mmm) REVERT: A 483 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.8894 (mm) REVERT: B 603 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8160 (mt) REVERT: C 32 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7727 (pp) REVERT: C 54 ARG cc_start: 0.8838 (mpp80) cc_final: 0.8336 (mpp80) REVERT: C 74 LEU cc_start: 0.8497 (tp) cc_final: 0.8278 (tp) REVERT: D 24 ARG cc_start: 0.8024 (mmt-90) cc_final: 0.7509 (mtp85) REVERT: D 37 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8130 (pm20) REVERT: D 45 ARG cc_start: 0.8377 (ttp80) cc_final: 0.7945 (ttp80) REVERT: E 82 GLN cc_start: 0.7552 (pm20) cc_final: 0.6894 (pt0) REVERT: E 181 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8637 (tp) REVERT: E 384 TYR cc_start: 0.7235 (m-10) cc_final: 0.6933 (m-80) REVERT: E 395 TRP cc_start: 0.5288 (m-10) cc_final: 0.4932 (m-10) REVERT: E 411 ASN cc_start: 0.7201 (p0) cc_final: 0.6857 (p0) REVERT: F 628 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.7515 (m-90) REVERT: F 632 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8066 (mm-30) REVERT: F 634 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8040 (mm-30) REVERT: G 36 TRP cc_start: 0.8095 (m100) cc_final: 0.7127 (m100) REVERT: H 24 ARG cc_start: 0.8100 (ttm110) cc_final: 0.7820 (mtm110) REVERT: H 32 TRP cc_start: 0.8979 (m100) cc_final: 0.8031 (m100) REVERT: H 89 GLN cc_start: 0.7691 (tt0) cc_final: 0.7359 (tt0) REVERT: I 209 SER cc_start: 0.8150 (t) cc_final: 0.7743 (m) REVERT: J 616 ASN cc_start: 0.7057 (p0) cc_final: 0.6818 (p0) REVERT: J 617 LYS cc_start: 0.7862 (mtpp) cc_final: 0.7380 (mtmm) REVERT: J 624 ASN cc_start: 0.9198 (m-40) cc_final: 0.8927 (m-40) REVERT: K 54 ARG cc_start: 0.8813 (mtm180) cc_final: 0.8566 (mtm110) REVERT: K 100 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6617 (ptp) outliers start: 164 outliers final: 112 residues processed: 554 average time/residue: 0.2862 time to fit residues: 250.3417 Evaluate side-chains 565 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 445 time to evaluate : 2.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 416 ILE Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 83 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 33 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 165 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 375 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35AASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN I 375 HIS K 39 GLN ** K 100EHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20583 Z= 0.220 Angle : 0.754 13.862 28005 Z= 0.362 Chirality : 0.052 0.417 3603 Planarity : 0.005 0.048 3342 Dihedral : 10.676 106.140 5419 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.37 % Favored : 91.63 % Rotamer: Outliers : 6.12 % Allowed : 22.58 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -2.09 (0.17), residues: 2343 helix: -0.02 (0.26), residues: 396 sheet: -1.15 (0.23), residues: 549 loop : -1.97 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP L 35 HIS 0.004 0.001 HIS A 374 PHE 0.025 0.002 PHE D 71 TYR 0.030 0.002 TYR E 484 ARG 0.007 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 457 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8858 (ttt) REVERT: A 209 SER cc_start: 0.8146 (t) cc_final: 0.7635 (m) REVERT: A 259 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8007 (pp) REVERT: A 265 LEU cc_start: 0.8592 (mp) cc_final: 0.8238 (tp) REVERT: A 373 MET cc_start: 0.7999 (mmm) cc_final: 0.7728 (mmm) REVERT: B 584 GLU cc_start: 0.8451 (tt0) cc_final: 0.8240 (tt0) REVERT: B 603 ILE cc_start: 0.8399 (mm) cc_final: 0.8195 (mt) REVERT: B 616 ASN cc_start: 0.6759 (p0) cc_final: 0.6404 (p0) REVERT: C 32 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7619 (pp) REVERT: C 52 TRP cc_start: 0.8933 (t60) cc_final: 0.8254 (t60) REVERT: C 54 ARG cc_start: 0.8828 (mpp80) cc_final: 0.7945 (mpp80) REVERT: C 74 LEU cc_start: 0.8466 (tp) cc_final: 0.8261 (tp) REVERT: C 100 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6695 (ptp) REVERT: D 24 ARG cc_start: 0.7913 (mmt-90) cc_final: 0.7504 (mtp85) REVERT: D 37 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8015 (pm20) REVERT: D 45 ARG cc_start: 0.8347 (ttp80) cc_final: 0.7863 (ttp80) REVERT: E 82 GLN cc_start: 0.7458 (pm20) cc_final: 0.6918 (pt0) REVERT: E 181 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8539 (tp) REVERT: E 209 SER cc_start: 0.8026 (t) cc_final: 0.7524 (m) REVERT: E 217 TYR cc_start: 0.8362 (m-80) cc_final: 0.8037 (m-10) REVERT: E 411 ASN cc_start: 0.7048 (p0) cc_final: 0.6738 (p0) REVERT: F 628 TRP cc_start: 0.8069 (OUTLIER) cc_final: 0.7636 (m-90) REVERT: H 24 ARG cc_start: 0.8035 (ttm110) cc_final: 0.7788 (mtm110) REVERT: I 209 SER cc_start: 0.8086 (t) cc_final: 0.7639 (m) REVERT: I 362 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7057 (tttm) REVERT: I 411 ASN cc_start: 0.6908 (p0) cc_final: 0.6477 (p0) REVERT: J 616 ASN cc_start: 0.6897 (p0) cc_final: 0.6634 (p0) REVERT: J 624 ASN cc_start: 0.9153 (m-40) cc_final: 0.8850 (m-40) REVERT: K 54 ARG cc_start: 0.8792 (mtm180) cc_final: 0.8484 (mtm180) REVERT: K 100 MET cc_start: 0.7336 (OUTLIER) cc_final: 0.6485 (ptp) REVERT: L 35 TRP cc_start: 0.6397 (m-10) cc_final: 0.6155 (m-10) outliers start: 120 outliers final: 93 residues processed: 523 average time/residue: 0.2856 time to fit residues: 234.9347 Evaluate side-chains 532 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 430 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.8980 chunk 134 optimal weight: 0.0060 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS D 27 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100EHIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20583 Z= 0.221 Angle : 0.763 13.811 28005 Z= 0.370 Chirality : 0.053 0.418 3603 Planarity : 0.005 0.055 3342 Dihedral : 10.427 104.323 5419 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 6.07 % Allowed : 23.24 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.91 (0.18), residues: 2343 helix: 0.14 (0.26), residues: 396 sheet: -1.01 (0.22), residues: 576 loop : -1.87 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP H 35 HIS 0.004 0.001 HIS E 339 PHE 0.022 0.002 PHE D 71 TYR 0.026 0.002 TYR E 484 ARG 0.008 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 448 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8689 (ttp) REVERT: A 209 SER cc_start: 0.8056 (t) cc_final: 0.7494 (m) REVERT: A 227 ARG cc_start: 0.8637 (ttp-170) cc_final: 0.8324 (ttp-170) REVERT: A 259 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.8003 (pp) REVERT: A 265 LEU cc_start: 0.8548 (mp) cc_final: 0.8226 (tp) REVERT: A 362 LYS cc_start: 0.7345 (tttm) cc_final: 0.6697 (tmmt) REVERT: A 373 MET cc_start: 0.7963 (mmm) cc_final: 0.7674 (mmm) REVERT: B 584 GLU cc_start: 0.8446 (tt0) cc_final: 0.8221 (tt0) REVERT: B 616 ASN cc_start: 0.6815 (p0) cc_final: 0.6441 (p0) REVERT: C 32 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7652 (pp) REVERT: C 52 TRP cc_start: 0.8936 (t60) cc_final: 0.8268 (t60) REVERT: C 54 ARG cc_start: 0.8792 (mpp80) cc_final: 0.7954 (mpp80) REVERT: C 68 LEU cc_start: 0.8384 (tt) cc_final: 0.8021 (mm) REVERT: C 100 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6734 (ptp) REVERT: D 24 ARG cc_start: 0.7831 (mmt-90) cc_final: 0.7436 (mtp85) REVERT: D 37 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: D 45 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7884 (ttp80) REVERT: E 82 GLN cc_start: 0.7495 (pm20) cc_final: 0.7177 (pt0) REVERT: E 152 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6839 (p0) REVERT: E 169 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: E 181 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8470 (tp) REVERT: E 209 SER cc_start: 0.8022 (t) cc_final: 0.7689 (m) REVERT: E 362 LYS cc_start: 0.7252 (tttt) cc_final: 0.6591 (tmmt) REVERT: E 411 ASN cc_start: 0.6991 (p0) cc_final: 0.6655 (p0) REVERT: F 628 TRP cc_start: 0.8068 (OUTLIER) cc_final: 0.7668 (m-90) REVERT: G 36 TRP cc_start: 0.7699 (m100) cc_final: 0.6921 (m100) REVERT: H 24 ARG cc_start: 0.7994 (ttm110) cc_final: 0.7761 (mtm110) REVERT: I 209 SER cc_start: 0.8026 (t) cc_final: 0.7584 (m) REVERT: I 362 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.7010 (tttm) REVERT: I 384 TYR cc_start: 0.7510 (m-10) cc_final: 0.7227 (m-80) REVERT: I 411 ASN cc_start: 0.7001 (p0) cc_final: 0.6586 (p0) REVERT: J 616 ASN cc_start: 0.6846 (p0) cc_final: 0.6546 (p0) REVERT: J 624 ASN cc_start: 0.9150 (m-40) cc_final: 0.8813 (m-40) REVERT: K 100 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6405 (ptp) outliers start: 119 outliers final: 96 residues processed: 510 average time/residue: 0.2894 time to fit residues: 230.3391 Evaluate side-chains 530 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 423 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 300 SER Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 434 MET Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 210 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 198 optimal weight: 0.2980 chunk 209 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 375 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20583 Z= 0.212 Angle : 0.754 14.047 28005 Z= 0.363 Chirality : 0.055 1.038 3603 Planarity : 0.005 0.053 3342 Dihedral : 10.046 101.844 5419 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.76 % Allowed : 23.90 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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: -1.78 (0.18), residues: 2343 helix: 0.28 (0.26), residues: 396 sheet: -1.06 (0.22), residues: 624 loop : -1.74 (0.18), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP H 35 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.002 PHE D 71 TYR 0.027 0.002 TYR A 484 ARG 0.009 0.001 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 440 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6895 (mp10) REVERT: A 209 SER cc_start: 0.8021 (t) cc_final: 0.7527 (m) REVERT: A 227 ARG cc_start: 0.8648 (ttp-170) cc_final: 0.8335 (ttp-170) REVERT: A 259 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.8009 (pp) REVERT: A 265 LEU cc_start: 0.8482 (mp) cc_final: 0.8195 (tp) REVERT: A 362 LYS cc_start: 0.7165 (tttm) cc_final: 0.6568 (tmmt) REVERT: A 373 MET cc_start: 0.7947 (mmm) cc_final: 0.7672 (mmm) REVERT: B 584 GLU cc_start: 0.8437 (tt0) cc_final: 0.8223 (tt0) REVERT: C 30 PHE cc_start: 0.8407 (m-80) cc_final: 0.8197 (m-80) REVERT: C 52 TRP cc_start: 0.8926 (t60) cc_final: 0.8277 (t60) REVERT: C 54 ARG cc_start: 0.8782 (mpp80) cc_final: 0.7964 (mpp80) REVERT: C 100 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6675 (ptp) REVERT: D 24 ARG cc_start: 0.7815 (mmt-90) cc_final: 0.7447 (mtp85) REVERT: D 37 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8043 (pm20) REVERT: D 45 ARG cc_start: 0.8365 (ttp80) cc_final: 0.7924 (ttp80) REVERT: E 82 GLN cc_start: 0.7515 (pm20) cc_final: 0.7009 (mp10) REVERT: E 152 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6704 (p0) REVERT: E 169 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7208 (mp10) REVERT: E 181 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8396 (tp) REVERT: E 209 SER cc_start: 0.7923 (t) cc_final: 0.7373 (m) REVERT: E 362 LYS cc_start: 0.7075 (tttt) cc_final: 0.6350 (tmtt) REVERT: E 384 TYR cc_start: 0.7249 (m-80) cc_final: 0.6939 (m-80) REVERT: E 411 ASN cc_start: 0.6934 (p0) cc_final: 0.6627 (p0) REVERT: F 628 TRP cc_start: 0.8102 (OUTLIER) cc_final: 0.7692 (m-90) REVERT: G 36 TRP cc_start: 0.7503 (m100) cc_final: 0.6640 (m100) REVERT: H 20 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7904 (ptm-80) REVERT: H 24 ARG cc_start: 0.7990 (ttm110) cc_final: 0.7776 (mtm110) REVERT: I 209 SER cc_start: 0.7967 (t) cc_final: 0.7524 (m) REVERT: I 362 LYS cc_start: 0.7301 (OUTLIER) cc_final: 0.6984 (tttm) REVERT: I 411 ASN cc_start: 0.6894 (p0) cc_final: 0.6482 (p0) REVERT: J 624 ASN cc_start: 0.9096 (m-40) cc_final: 0.8782 (m-40) REVERT: K 100 MET cc_start: 0.7142 (OUTLIER) cc_final: 0.6386 (ptp) outliers start: 113 outliers final: 91 residues processed: 502 average time/residue: 0.2797 time to fit residues: 220.6583 Evaluate side-chains 519 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 418 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 153 ASP Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 169 GLN Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 201 ILE Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN D 27 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20583 Z= 0.424 Angle : 0.901 17.002 28005 Z= 0.443 Chirality : 0.075 2.712 3603 Planarity : 0.006 0.123 3342 Dihedral : 10.631 106.495 5419 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 6.22 % Allowed : 23.75 % Favored : 70.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % 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: -1.93 (0.18), residues: 2343 helix: -0.10 (0.25), residues: 399 sheet: -1.06 (0.21), residues: 648 loop : -1.81 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP C 36 HIS 0.004 0.001 HIS A 374 PHE 0.025 0.003 PHE J 592 TYR 0.033 0.003 TYR I 191 ARG 0.039 0.001 ARG A 304 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 437 time to evaluate : 2.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 169 GLN cc_start: 0.7703 (OUTLIER) cc_final: 0.7065 (mp10) REVERT: A 209 SER cc_start: 0.8190 (t) cc_final: 0.7593 (m) REVERT: A 259 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8134 (pp) REVERT: B 584 GLU cc_start: 0.8500 (tt0) cc_final: 0.8300 (tt0) REVERT: C 54 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8259 (mpp80) REVERT: D 24 ARG cc_start: 0.7983 (mmt-90) cc_final: 0.7565 (mtp85) REVERT: D 37 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8061 (pm20) REVERT: D 45 ARG cc_start: 0.8392 (ttp80) cc_final: 0.7954 (ttp80) REVERT: E 82 GLN cc_start: 0.7536 (pm20) cc_final: 0.7209 (pt0) REVERT: E 152 ASP cc_start: 0.7104 (OUTLIER) cc_final: 0.6843 (p0) REVERT: E 181 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (tp) REVERT: E 209 SER cc_start: 0.8165 (t) cc_final: 0.7606 (m) REVERT: E 362 LYS cc_start: 0.7187 (tttt) cc_final: 0.6813 (tttm) REVERT: E 411 ASN cc_start: 0.7098 (p0) cc_final: 0.6768 (p0) REVERT: F 632 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8206 (mm-30) REVERT: H 24 ARG cc_start: 0.8059 (ttm110) cc_final: 0.7807 (mtm110) REVERT: I 209 SER cc_start: 0.8111 (t) cc_final: 0.7673 (m) REVERT: I 362 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6954 (tttm) REVERT: I 411 ASN cc_start: 0.7185 (p0) cc_final: 0.6751 (p0) REVERT: J 591 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8391 (ttpt) REVERT: J 624 ASN cc_start: 0.9262 (m-40) cc_final: 0.8997 (m-40) REVERT: J 632 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8282 (mm-30) outliers start: 122 outliers final: 104 residues processed: 500 average time/residue: 0.2863 time to fit residues: 225.3684 Evaluate side-chains 532 residues out of total 2073 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 421 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 157 CYS Chi-restraints excluded: chain A residue 169 GLN Chi-restraints excluded: chain A residue 173 TYR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 522 PHE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 618 THR Chi-restraints excluded: chain B residue 628 TRP Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 99 ASP Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 37 GLN Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 152 ASP Chi-restraints excluded: chain E residue 157 CYS Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 200 VAL Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 420 ILE Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 474 ASN Chi-restraints excluded: chain F residue 522 PHE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 618 THR Chi-restraints excluded: chain F residue 628 TRP Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 651 THR Chi-restraints excluded: chain G residue 77 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 99 ASP Chi-restraints excluded: chain H residue 4 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 34 LEU Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 90 THR Chi-restraints excluded: chain I residue 113 ASP Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 125 LEU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 173 TYR Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 241 ASN Chi-restraints excluded: chain I residue 247 CYS Chi-restraints excluded: chain I residue 307 ILE Chi-restraints excluded: chain I residue 354 ASN Chi-restraints excluded: chain I residue 360 VAL Chi-restraints excluded: chain I residue 362 LYS Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 446 LEU Chi-restraints excluded: chain I residue 455 THR Chi-restraints excluded: chain J residue 522 PHE Chi-restraints excluded: chain J residue 535 ILE Chi-restraints excluded: chain J residue 591 LYS Chi-restraints excluded: chain J residue 606 THR Chi-restraints excluded: chain J residue 618 THR Chi-restraints excluded: chain J residue 628 TRP Chi-restraints excluded: chain J residue 639 THR Chi-restraints excluded: chain J residue 651 THR Chi-restraints excluded: chain K residue 58 SER Chi-restraints excluded: chain K residue 77 ILE Chi-restraints excluded: chain K residue 99 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 190 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 43 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.174221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.150181 restraints weight = 31006.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.153430 restraints weight = 19741.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154986 restraints weight = 13717.273| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20583 Z= 0.234 Angle : 0.791 14.241 28005 Z= 0.385 Chirality : 0.058 1.216 3603 Planarity : 0.005 0.083 3342 Dihedral : 10.196 102.426 5419 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 5.35 % Allowed : 24.67 % Favored : 69.98 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % 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: -1.72 (0.18), residues: 2343 helix: -0.07 (0.25), residues: 417 sheet: -0.97 (0.21), residues: 648 loop : -1.61 (0.18), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP K 36 HIS 0.005 0.001 HIS A 374 PHE 0.023 0.002 PHE D 71 TYR 0.028 0.002 TYR A 217 ARG 0.013 0.001 ARG E 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4575.58 seconds wall clock time: 83 minutes 53.52 seconds (5033.52 seconds total)