Starting phenix.real_space_refine on Sun Aug 11 08:15:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cue_7621/08_2024/6cue_7621_neut.cif" } resolution = 4.0 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= 0.015 sd= 0.141 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 174 5.16 5 C 19947 2.51 5 N 5289 2.21 5 O 6282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "c PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 62": "NH1" <-> "NH2" Residue "8 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 53": "NH1" <-> "NH2" Residue "Q ARG 62": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "q ARG 62": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31692 Number of models: 1 Model: "" Number of chains: 66 Chain: "c" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "2" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "C" Number of atoms: 3564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3564 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "1" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "3" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "4" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "5" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "6" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "7" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "H" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "L" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "N" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "Q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} Chain: "d" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1034 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "h" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 919 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "l" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 104} Chain: "m" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1047 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "n" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "q" Number of atoms: 1029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1029 Classifications: {'peptide': 129} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 121} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "r" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 802 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 97} 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: 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: "E" 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: "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: 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: "I" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" 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: "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: "O" 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: "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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "V" 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: "W" 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: "X" 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: "Y" 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: "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: 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: "g" 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: "i" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "j" 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: "k" 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: "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: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "w" 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: "x" 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: "y" 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: "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: "0" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "9" 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: "AA" 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: "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: "2" 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: "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 Time building chain proxies: 19.53, per 1000 atoms: 0.62 Number of scatterers: 31692 At special positions: 0 Unit cell: (154, 162.8, 156.2, 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 174 16.00 O 6282 8.00 N 5289 7.00 C 19947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS c 54 " - pdb=" SG CYS c 74 " distance=2.03 Simple disulfide: pdb=" SG CYS c 119 " - pdb=" SG CYS c 205 " distance=2.03 Simple disulfide: pdb=" SG CYS c 126 " - pdb=" SG CYS c 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 131 " - pdb=" SG CYS c 157 " distance=2.02 Simple disulfide: pdb=" SG CYS c 201 " - pdb=" SG CYS c 433 " distance=2.03 Simple disulfide: pdb=" SG CYS c 218 " - pdb=" SG CYS c 247 " distance=2.02 Simple disulfide: pdb=" SG CYS c 228 " - pdb=" SG CYS c 239 " distance=2.03 Simple disulfide: pdb=" SG CYS c 296 " - pdb=" SG CYS c 331 " distance=2.03 Simple disulfide: pdb=" SG CYS c 378 " - pdb=" SG CYS c 445 " distance=2.02 Simple disulfide: pdb=" SG CYS c 385 " - pdb=" SG CYS c 418 " distance=2.03 Simple disulfide: pdb=" SG CYS c 501 " - pdb=" SG CYS d 605 " distance=2.04 Simple disulfide: pdb=" SG CYS 2 54 " - pdb=" SG CYS 2 74 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 119 " - pdb=" SG CYS 2 205 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 126 " - pdb=" SG CYS 2 196 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 131 " - pdb=" SG CYS 2 157 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 201 " - pdb=" SG CYS 2 433 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 218 " - pdb=" SG CYS 2 247 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 228 " - pdb=" SG CYS 2 239 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 296 " - pdb=" SG CYS 2 331 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 378 " - pdb=" SG CYS 2 445 " distance=2.02 Simple disulfide: pdb=" SG CYS 2 385 " - pdb=" SG CYS 2 418 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 501 " - pdb=" SG CYS 1 605 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.10 Simple disulfide: pdb=" SG CYS 1 598 " - pdb=" SG CYS 1 604 " distance=1.91 Simple disulfide: pdb=" SG CYS 3 22 " - pdb=" SG CYS 3 96 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 23 " - pdb=" SG CYS 4 93 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 22 " - pdb=" SG CYS 5 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 23 " - pdb=" SG CYS 6 88 " distance=2.04 Simple disulfide: pdb=" SG CYS 7 22 " - pdb=" SG CYS 7 103 " distance=2.03 Simple disulfide: pdb=" SG CYS 7 109 " - pdb=" SG CYS 7 112 " distance=2.00 Simple disulfide: pdb=" SG CYS 8 23 " - pdb=" SG CYS 8 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=1.94 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 109 " - pdb=" SG CYS Q 112 " distance=2.00 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS d 598 " - pdb=" SG CYS d 604 " distance=2.00 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 93 " distance=2.03 Simple disulfide: pdb=" SG CYS m 22 " - pdb=" SG CYS m 92 " distance=2.03 Simple disulfide: pdb=" SG CYS n 23 " - pdb=" SG CYS n 88 " distance=2.03 Simple disulfide: pdb=" SG CYS q 22 " - pdb=" SG CYS q 103 " distance=2.03 Simple disulfide: pdb=" SG CYS q 109 " - pdb=" SG CYS q 112 " distance=1.98 Simple disulfide: pdb=" SG CYS r 23 " - pdb=" SG CYS r 88 " distance=2.04 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 0 4 " - " MAN 0 5 " " MAN S 4 " - " MAN S 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA 0 3 " - " MAN 0 4 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA a 3 " - " MAN a 4 " " BMA i 3 " - " MAN i 4 " " BMA k 3 " - " MAN k 4 " " BMA v 3 " - " MAN v 4 " " BMAAA 3 " - " MANAA 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA a 3 " - " MAN a 5 " " BMA v 3 " - " MAN v 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 9 1 " - " NAG 9 2 " " NAG A 1 " - " NAG A 2 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " 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 Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " 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 x 1 " - " NAG x 2 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAGAA 1 " - " NAGAA 2 " " NAGAA 2 " - " BMAAA 3 " NAG-ASN " NAG 0 1 " - " ASN C 332 " " NAG 2 611 " - " ASN 2 197 " " NAG 9 1 " - " ASN C 448 " " NAG A 1 " - " ASN c 133 " " NAG B 1 " - " ASN c 137 " " NAG C 611 " - " ASN C 197 " " NAG E 1 " - " ASN c 156 " " NAG F 1 " - " ASN c 160 " " NAG G 1 " - " ASN c 234 " " NAG I 1 " - " ASN c 262 " " NAG J 1 " - " ASN c 295 " " NAG K 1 " - " ASN c 301 " " NAG O 1 " - " ASN c 363 " " NAG P 1 " - " ASN c 386 " " NAG S 1 " - " ASN c 332 " " NAG T 1 " - " ASN c 448 " " NAG U 1 " - " ASN c 276 " " NAG V 1 " - " ASN 2 133 " " NAG W 1 " - " ASN 2 137 " " NAG X 1 " - " ASN 2 156 " " NAG Y 1 " - " ASN 2 160 " " NAG Z 1 " - " ASN 2 234 " " NAG a 1 " - " ASN 2 262 " " NAG b 1 " - " ASN 2 295 " " NAG c 611 " - " ASN c 197 " " NAG e 1 " - " ASN 2 301 " " NAG f 1 " - " ASN 2 363 " " NAG g 1 " - " ASN 2 386 " " NAG i 1 " - " ASN 2 332 " " NAG j 1 " - " ASN 2 448 " " NAG k 1 " - " ASN 2 276 " " NAG o 1 " - " ASN C 133 " " NAG p 1 " - " ASN C 137 " " NAG s 1 " - " ASN C 156 " " NAG t 1 " - " ASN C 160 " " NAG u 1 " - " ASN C 234 " " NAG v 1 " - " ASN C 262 " " NAG w 1 " - " ASN C 295 " " NAG x 1 " - " ASN C 301 " " NAG y 1 " - " ASN C 363 " " NAG z 1 " - " ASN C 386 " " NAGAA 1 " - " ASN C 276 " Time building additional restraints: 14.98 Conformation dependent library (CDL) restraints added in 5.8 seconds 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7056 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 84 sheets defined 13.7% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 Creating SS restraints... Processing helix chain 'c' and resid 101 through 115 removed outlier: 3.998A pdb=" N ILE c 109 " --> pdb=" O HIS c 105 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN c 114 " --> pdb=" O SER c 110 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 126 removed outlier: 3.773A pdb=" N CYS c 126 " --> pdb=" O THR c 123 " (cutoff:3.500A) Processing helix chain 'c' and resid 195 through 198 Processing helix chain 'c' and resid 335 through 350 Processing helix chain 'c' and resid 368 through 373 removed outlier: 3.500A pdb=" N THR c 372 " --> pdb=" O ASP c 368 " (cutoff:3.500A) Processing helix chain 'c' and resid 425 through 429 removed outlier: 4.271A pdb=" N ARG c 429 " --> pdb=" O MET c 426 " (cutoff:3.500A) Processing helix chain 'c' and resid 475 through 481 removed outlier: 3.684A pdb=" N TRP c 479 " --> pdb=" O MET c 475 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER c 481 " --> pdb=" O ASP c 477 " (cutoff:3.500A) Processing helix chain '2' and resid 101 through 115 removed outlier: 3.832A pdb=" N ILE 2 109 " --> pdb=" O HIS 2 105 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN 2 114 " --> pdb=" O SER 2 110 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER 2 115 " --> pdb=" O LEU 2 111 " (cutoff:3.500A) Processing helix chain '2' and resid 122 through 126 removed outlier: 3.535A pdb=" N LEU 2 125 " --> pdb=" O LEU 2 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS 2 126 " --> pdb=" O THR 2 123 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 122 through 126' Processing helix chain '2' and resid 195 through 198 Processing helix chain '2' and resid 335 through 350 Processing helix chain '2' and resid 368 through 373 Processing helix chain '2' and resid 425 through 429 removed outlier: 4.188A pdb=" N ARG 2 429 " --> pdb=" O MET 2 426 " (cutoff:3.500A) Processing helix chain '2' and resid 475 through 480 removed outlier: 3.671A pdb=" N TRP 2 479 " --> pdb=" O MET 2 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.728A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 114 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.576A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 removed outlier: 3.558A pdb=" N LYS C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.728A pdb=" N THR C 372 " --> pdb=" O ASP C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.002A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.810A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain '1' and resid 523 through 528 removed outlier: 4.017A pdb=" N GLY 1 527 " --> pdb=" O GLY 1 524 " (cutoff:3.500A) Processing helix chain '1' and resid 529 through 543 removed outlier: 3.807A pdb=" N ALA 1 533 " --> pdb=" O THR 1 529 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET 1 535 " --> pdb=" O GLY 1 531 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU 1 537 " --> pdb=" O ALA 1 533 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N THR 1 538 " --> pdb=" O SER 1 534 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL 1 539 " --> pdb=" O MET 1 535 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN 1 540 " --> pdb=" O THR 1 536 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA 1 541 " --> pdb=" O LEU 1 537 " (cutoff:3.500A) Processing helix chain '1' and resid 570 through 595 removed outlier: 3.704A pdb=" N LYS 1 574 " --> pdb=" O VAL 1 570 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 1 589 " --> pdb=" O ARG 1 585 " (cutoff:3.500A) Processing helix chain '1' and resid 611 through 616 removed outlier: 4.335A pdb=" N SER 1 615 " --> pdb=" O ASN 1 611 " (cutoff:3.500A) Processing helix chain '1' and resid 619 through 623 Processing helix chain '1' and resid 627 through 635 removed outlier: 3.914A pdb=" N LYS 1 633 " --> pdb=" O LEU 1 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU 1 634 " --> pdb=" O GLN 1 630 " (cutoff:3.500A) Processing helix chain '1' and resid 640 through 664 removed outlier: 3.702A pdb=" N GLU 1 647 " --> pdb=" O TYR 1 643 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU 1 648 " --> pdb=" O GLY 1 644 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN 1 650 " --> pdb=" O LEU 1 646 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 91 removed outlier: 3.511A pdb=" N SER 3 91 " --> pdb=" O SER 3 88 " (cutoff:3.500A) Processing helix chain '4' and resid 84 through 88 removed outlier: 3.540A pdb=" N ASP 4 87 " --> pdb=" O GLU 4 84 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 87 removed outlier: 3.731A pdb=" N SER 5 87 " --> pdb=" O ALA 5 84 " (cutoff:3.500A) Processing helix chain '5' and resid 100D through 100H removed outlier: 3.526A pdb=" N PHE 5 100G" --> pdb=" O VAL 5 100D" (cutoff:3.500A) Processing helix chain '7' and resid 62 through 65 Processing helix chain '7' and resid 94 through 98 removed outlier: 3.760A pdb=" N THR 7 98 " --> pdb=" O PRO 7 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 527 removed outlier: 4.095A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.629A pdb=" N ALA D 533 " --> pdb=" O THR D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 removed outlier: 4.048A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 611 through 616 removed outlier: 4.299A pdb=" N SER D 615 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 625 Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.767A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 664 removed outlier: 3.623A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.569A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'M' and resid 83 through 87 removed outlier: 3.891A pdb=" N SER M 87 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 100D through 100H Processing helix chain 'Q' and resid 62 through 65 Processing helix chain 'Q' and resid 94 through 98 removed outlier: 3.674A pdb=" N THR Q 98 " --> pdb=" O PRO Q 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 515 through 520 removed outlier: 3.752A pdb=" N PHE d 519 " --> pdb=" O ILE d 515 " (cutoff:3.500A) Processing helix chain 'd' and resid 523 through 528 removed outlier: 4.311A pdb=" N GLY d 527 " --> pdb=" O GLY d 524 " (cutoff:3.500A) Processing helix chain 'd' and resid 529 through 534 removed outlier: 3.842A pdb=" N ALA d 533 " --> pdb=" O THR d 529 " (cutoff:3.500A) Processing helix chain 'd' and resid 536 through 544 removed outlier: 4.081A pdb=" N GLN d 540 " --> pdb=" O THR d 536 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA d 541 " --> pdb=" O LEU d 537 " (cutoff:3.500A) Processing helix chain 'd' and resid 570 through 595 removed outlier: 3.702A pdb=" N LYS d 574 " --> pdb=" O VAL d 570 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP d 589 " --> pdb=" O ARG d 585 " (cutoff:3.500A) Processing helix chain 'd' and resid 611 through 616 removed outlier: 4.264A pdb=" N SER d 615 " --> pdb=" O ASN d 611 " (cutoff:3.500A) Processing helix chain 'd' and resid 620 through 625 Processing helix chain 'd' and resid 627 through 635 removed outlier: 3.949A pdb=" N LYS d 633 " --> pdb=" O LEU d 629 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU d 634 " --> pdb=" O GLN d 630 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE d 635 " --> pdb=" O TRP d 631 " (cutoff:3.500A) Processing helix chain 'd' and resid 640 through 663 removed outlier: 3.617A pdb=" N LYS d 655 " --> pdb=" O ASN d 651 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU d 663 " --> pdb=" O ASP d 659 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'l' and resid 84 through 88 removed outlier: 3.556A pdb=" N LEU l 88 " --> pdb=" O ALA l 85 " (cutoff:3.500A) Processing helix chain 'm' and resid 83 through 87 removed outlier: 3.680A pdb=" N SER m 87 " --> pdb=" O ALA m 84 " (cutoff:3.500A) Processing helix chain 'q' and resid 62 through 65 Processing helix chain 'q' and resid 94 through 98 removed outlier: 3.685A pdb=" N THR q 98 " --> pdb=" O PRO q 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'c' and resid 45 through 47 removed outlier: 3.949A pdb=" N ILE c 225 " --> pdb=" O VAL c 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'c' and resid 75 through 76 removed outlier: 3.854A pdb=" N VAL c 75 " --> pdb=" O CYS c 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'c' and resid 91 through 94 removed outlier: 4.120A pdb=" N GLU c 91 " --> pdb=" O CYS c 239 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS c 239 " --> pdb=" O GLU c 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY c 237 " --> pdb=" O PHE c 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'c' and resid 271 through 273 removed outlier: 7.516A pdb=" N GLN c 293 " --> pdb=" O SER c 334 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER c 334 " --> pdb=" O GLN c 293 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE c 376 " --> pdb=" O PHE c 383 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N HIS c 374 " --> pdb=" O CYS c 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'c' and resid 271 through 273 removed outlier: 11.197A pdb=" N VAL c 286 " --> pdb=" O THR c 455 " (cutoff:3.500A) removed outlier: 10.720A pdb=" N THR c 455 " --> pdb=" O VAL c 286 " (cutoff:3.500A) removed outlier: 11.862A pdb=" N PHE c 288 " --> pdb=" O ILE c 453 " (cutoff:3.500A) removed outlier: 11.412A pdb=" N ILE c 453 " --> pdb=" O PHE c 288 " (cutoff:3.500A) removed outlier: 10.782A pdb=" N THR c 290 " --> pdb=" O GLY c 451 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY c 451 " --> pdb=" O THR c 290 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'c' and resid 304 through 308 Processing sheet with id=AA9, first strand: chain 'c' and resid 359 through 360 Processing sheet with id=AB1, first strand: chain 'c' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain '2' and resid 495 through 499 removed outlier: 4.628A pdb=" N VAL 2 36 " --> pdb=" O THR 1 606 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR 1 606 " --> pdb=" O VAL 2 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N CYS 1 604 " --> pdb=" O VAL 2 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '2' and resid 45 through 47 removed outlier: 4.009A pdb=" N ILE 2 225 " --> pdb=" O VAL 2 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 75 through 76 removed outlier: 3.952A pdb=" N VAL 2 75 " --> pdb=" O CYS 2 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 91 through 94 removed outlier: 3.555A pdb=" N GLU 2 91 " --> pdb=" O CYS 2 239 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE 2 93 " --> pdb=" O GLY 2 237 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY 2 237 " --> pdb=" O PHE 2 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 169 through 177 Processing sheet with id=AB7, first strand: chain '2' and resid 202 through 203 removed outlier: 6.624A pdb=" N THR 2 202 " --> pdb=" O TYR 2 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 260 through 261 removed outlier: 7.138A pdb=" N LEU 2 260 " --> pdb=" O THR 2 450 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N GLN 2 293 " --> pdb=" O SER 2 334 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER 2 334 " --> pdb=" O GLN 2 293 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE 2 376 " --> pdb=" O PHE 2 383 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N HIS 2 374 " --> pdb=" O CYS 2 385 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 271 through 273 removed outlier: 11.321A pdb=" N VAL 2 286 " --> pdb=" O THR 2 455 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N THR 2 455 " --> pdb=" O VAL 2 286 " (cutoff:3.500A) removed outlier: 12.071A pdb=" N PHE 2 288 " --> pdb=" O ILE 2 453 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ILE 2 453 " --> pdb=" O PHE 2 288 " (cutoff:3.500A) removed outlier: 11.095A pdb=" N THR 2 290 " --> pdb=" O GLY 2 451 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLY 2 451 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE 2 443 " --> pdb=" O ARG 2 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 304 through 308 Processing sheet with id=AC2, first strand: chain '2' and resid 359 through 361 removed outlier: 3.510A pdb=" N PHE 2 361 " --> pdb=" O SER 2 393 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER 2 393 " --> pdb=" O PHE 2 361 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.837A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.557A pdb=" N PHE C 93 " --> pdb=" O GLY C 237 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.621A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 260 through 261 removed outlier: 7.200A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 376 " --> pdb=" O PHE C 383 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N HIS C 374 " --> pdb=" O CYS C 385 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 271 through 273 removed outlier: 11.292A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.754A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.907A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.477A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.049A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 304 through 307 Processing sheet with id=AD3, first strand: chain 'C' and resid 359 through 361 removed outlier: 3.550A pdb=" N ILE C 359 " --> pdb=" O TRP C 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C 361 " --> pdb=" O SER C 393 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER C 393 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '3' and resid 3 through 5 removed outlier: 4.005A pdb=" N THR 3 78 " --> pdb=" O ASP 3 73 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP 3 73 " --> pdb=" O THR 3 78 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR 3 71 " --> pdb=" O TYR 3 80 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 10 through 12 removed outlier: 7.301A pdb=" N MET 3 34 " --> pdb=" O ALA 3 50 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ALA 3 50 " --> pdb=" O MET 3 34 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N TRP 3 36 " --> pdb=" O ILE 3 48 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE 3 48 " --> pdb=" O TRP 3 36 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '3' and resid 10 through 12 removed outlier: 3.959A pdb=" N ARG 3 98 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N VAL 3 107 " --> pdb=" O ARG 3 98 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '4' and resid 5 through 7 removed outlier: 3.508A pdb=" N ASP 4 75 " --> pdb=" O SER 4 72 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '4' and resid 10 through 12 removed outlier: 6.607A pdb=" N LEU 4 11 " --> pdb=" O GLU 4 110 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY 4 89 " --> pdb=" O LEU 4 109 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR 4 92 " --> pdb=" O TYR 4 41 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '5' and resid 5 through 7 Processing sheet with id=AE1, first strand: chain '5' and resid 11 through 12 Processing sheet with id=AE2, first strand: chain '5' and resid 46 through 51 removed outlier: 6.401A pdb=" N TRP 5 36 " --> pdb=" O ILE 5 48 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR 5 50 " --> pdb=" O TRP 5 34 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP 5 34 " --> pdb=" O TYR 5 50 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR 5 33 " --> pdb=" O THR 5 95 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '5' and resid 99 through 100A Processing sheet with id=AE4, first strand: chain '6' and resid 18 through 23 Processing sheet with id=AE5, first strand: chain '6' and resid 44 through 48 removed outlier: 6.588A pdb=" N TRP 6 35 " --> pdb=" O ILE 6 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '7' and resid 3 through 5 Processing sheet with id=AE7, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ARG 7 38 " --> pdb=" O TRP 7 47 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TRP 7 47 " --> pdb=" O ARG 7 38 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE 7 40 " --> pdb=" O PHE 7 45 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N PHE 7 45 " --> pdb=" O ILE 7 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '7' and resid 10 through 12 removed outlier: 6.300A pdb=" N VAL 7 10 " --> pdb=" O VAL 7 127 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR 7 119 " --> pdb=" O ARG 7 105 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '8' and resid 4 through 7 removed outlier: 3.591A pdb=" N CYS 8 23 " --> pdb=" O PHE 8 71 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N PHE 8 71 " --> pdb=" O CYS 8 23 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '8' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain '8' and resid 53 through 54 removed outlier: 5.754A pdb=" N LEU 8 46 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN 8 37 " --> pdb=" O LEU 8 46 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ILE 8 48 " --> pdb=" O TRP 8 35 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AF4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.871A pdb=" N TRP H 36 " --> pdb=" O GLY H 49 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.360A pdb=" N CYS H 96 " --> pdb=" O TRP H 108 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP H 108 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG H 98 " --> pdb=" O ASP H 106 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 72 through 73 removed outlier: 4.133A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AF9, first strand: chain 'L' and resid 39 through 41 removed outlier: 6.683A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.696A pdb=" N VAL M 107 " --> pdb=" O ALA M 88 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA M 88 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR M 33 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TRP M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR M 50 " --> pdb=" O TRP M 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'M' and resid 99 through 100A Processing sheet with id=AG4, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG5, first strand: chain 'N' and resid 44 through 48 removed outlier: 6.547A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'Q' and resid 3 through 5 Processing sheet with id=AG7, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.693A pdb=" N ILE Q 34 " --> pdb=" O TRP Q 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TRP Q 50 " --> pdb=" O ILE Q 34 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP Q 36 " --> pdb=" O ILE Q 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE Q 40 " --> pdb=" O GLY Q 44 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY Q 44 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 57 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 10 through 12 removed outlier: 6.796A pdb=" N CYS Q 103 " --> pdb=" O TRP Q 120 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP Q 120 " --> pdb=" O CYS Q 103 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ARG Q 105 " --> pdb=" O GLN Q 118 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 4 through 7 removed outlier: 3.741A pdb=" N PHE R 71 " --> pdb=" O CYS R 23 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'R' and resid 10 through 12 Processing sheet with id=AH2, first strand: chain 'R' and resid 53 through 54 removed outlier: 5.702A pdb=" N LEU R 46 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLN R 37 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE R 48 " --> pdb=" O TRP R 35 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'h' and resid 3 through 5 Processing sheet with id=AH4, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER h 97 " --> pdb=" O HIS h 35 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET h 34 " --> pdb=" O ILE h 51 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY h 49 " --> pdb=" O TRP h 36 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 10 through 12 removed outlier: 6.723A pdb=" N GLU h 10 " --> pdb=" O THR h 115 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG h 98 " --> pdb=" O VAL h 107 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL h 107 " --> pdb=" O ARG h 98 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'h' and resid 39 through 40 Processing sheet with id=AH7, first strand: chain 'h' and resid 72 through 73 removed outlier: 3.980A pdb=" N ASP h 73 " --> pdb=" O THR h 78 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'l' and resid 5 through 7 removed outlier: 3.620A pdb=" N ASP l 75 " --> pdb=" O SER l 72 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'l' and resid 10 through 12 removed outlier: 6.438A pdb=" N LEU l 11 " --> pdb=" O GLU l 110 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'l' and resid 40 through 41 removed outlier: 6.575A pdb=" N TRP l 40 " --> pdb=" O LEU l 52 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'm' and resid 5 through 7 Processing sheet with id=AI3, first strand: chain 'm' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL m 107 " --> pdb=" O ALA m 88 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA m 88 " --> pdb=" O VAL m 107 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR m 33 " --> pdb=" O THR m 95 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP m 34 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N TYR m 50 " --> pdb=" O TRP m 34 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TRP m 36 " --> pdb=" O ILE m 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'm' and resid 99 through 100A Processing sheet with id=AI5, first strand: chain 'n' and resid 11 through 13 removed outlier: 3.657A pdb=" N VAL n 11 " --> pdb=" O THR n 103 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE n 105 " --> pdb=" O VAL n 11 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU n 104 " --> pdb=" O ALA n 84 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA n 84 " --> pdb=" O LEU n 104 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR n 87 " --> pdb=" O TYR n 36 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN n 37 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU n 46 " --> pdb=" O GLN n 37 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'n' and resid 18 through 23 Processing sheet with id=AI7, first strand: chain 'q' and resid 3 through 5 Processing sheet with id=AI8, first strand: chain 'q' and resid 10 through 12 removed outlier: 5.779A pdb=" N ARG q 38 " --> pdb=" O TRP q 47 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N TRP q 47 " --> pdb=" O ARG q 38 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE q 40 " --> pdb=" O PHE q 45 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE q 45 " --> pdb=" O ILE q 40 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'q' and resid 10 through 12 removed outlier: 6.958A pdb=" N CYS q 103 " --> pdb=" O TRP q 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N TRP q 120 " --> pdb=" O CYS q 103 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG q 105 " --> pdb=" O GLN q 118 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'r' and resid 4 through 7 removed outlier: 3.591A pdb=" N PHE r 71 " --> pdb=" O CYS r 23 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'r' and resid 10 through 13 Processing sheet with id=AJ3, first strand: chain 'r' and resid 53 through 54 removed outlier: 5.688A pdb=" N LEU r 46 " --> pdb=" O GLN r 37 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN r 37 " --> pdb=" O LEU r 46 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE r 48 " --> pdb=" O TRP r 35 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2454 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: 13.11 Time building geometry restraints manager: 16.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9798 1.34 - 1.46: 8565 1.46 - 1.59: 13804 1.59 - 1.71: 2 1.71 - 1.84: 234 Bond restraints: 32403 Sorted by residual: bond pdb=" C LYS C 252 " pdb=" N PRO C 253 " ideal model delta sigma weight residual 1.335 1.304 0.031 8.70e-03 1.32e+04 1.30e+01 bond pdb=" CA TYR L 54 " pdb=" CB TYR L 54 " ideal model delta sigma weight residual 1.530 1.602 -0.072 2.20e-02 2.07e+03 1.06e+01 bond pdb=" C1 BMA y 3 " pdb=" C2 BMA y 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 BMA O 3 " pdb=" C2 BMA O 3 " ideal model delta sigma weight residual 1.519 1.582 -0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.575 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 32398 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.81: 417 103.81 - 111.41: 14382 111.41 - 119.02: 12169 119.02 - 126.62: 16431 126.62 - 134.22: 626 Bond angle restraints: 44025 Sorted by residual: angle pdb=" C TYR r 49 " pdb=" N ASP r 50 " pdb=" CA ASP r 50 " ideal model delta sigma weight residual 121.54 132.47 -10.93 1.91e+00 2.74e-01 3.27e+01 angle pdb=" C ASN C 99 " pdb=" N MET C 100 " pdb=" CA MET C 100 " ideal model delta sigma weight residual 121.54 132.15 -10.61 1.91e+00 2.74e-01 3.09e+01 angle pdb=" C TYR R 49 " pdb=" N ASP R 50 " pdb=" CA ASP R 50 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.08e+01 angle pdb=" C ASN c 99 " pdb=" N MET c 100 " pdb=" CA MET c 100 " ideal model delta sigma weight residual 121.54 131.85 -10.31 1.91e+00 2.74e-01 2.91e+01 angle pdb=" C TYR 8 49 " pdb=" N ASP 8 50 " pdb=" CA ASP 8 50 " ideal model delta sigma weight residual 121.54 131.82 -10.28 1.91e+00 2.74e-01 2.90e+01 ... (remaining 44020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 19804 23.44 - 46.89: 570 46.89 - 70.33: 128 70.33 - 93.77: 93 93.77 - 117.22: 60 Dihedral angle restraints: 20655 sinusoidal: 9627 harmonic: 11028 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual 93.00 175.73 -82.73 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS 2 201 " pdb=" SG CYS 2 201 " pdb=" SG CYS 2 433 " pdb=" CB CYS 2 433 " ideal model delta sinusoidal sigma weight residual 93.00 169.42 -76.42 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" CA GLN r 90 " pdb=" C GLN r 90 " pdb=" N PHE r 91 " pdb=" CA PHE r 91 " ideal model delta harmonic sigma weight residual 180.00 -139.91 -40.09 0 5.00e+00 4.00e-02 6.43e+01 ... (remaining 20652 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 5157 0.244 - 0.488: 36 0.488 - 0.731: 3 0.731 - 0.975: 1 0.975 - 1.219: 2 Chirality restraints: 5199 Sorted by residual: chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN 2 363 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.71e+01 chirality pdb=" C1 NAG y 1 " pdb=" ND2 ASN C 363 " pdb=" C2 NAG y 1 " pdb=" O5 NAG y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN c 363 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.23e+01 ... (remaining 5196 not shown) Planarity restraints: 5490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 386 " 0.060 2.00e-02 2.50e+03 8.01e-02 8.03e+01 pdb=" CG ASN C 386 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 386 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 386 " -0.138 2.00e-02 2.50e+03 pdb=" C1 NAG z 1 " 0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 2 386 " -0.043 2.00e-02 2.50e+03 5.72e-02 4.09e+01 pdb=" CG ASN 2 386 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN 2 386 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN 2 386 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 386 " 0.036 2.00e-02 2.50e+03 5.00e-02 3.13e+01 pdb=" CG ASN c 386 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN c 386 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN c 386 " -0.088 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.058 2.00e-02 2.50e+03 ... (remaining 5487 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 869 2.68 - 3.23: 28028 3.23 - 3.79: 48079 3.79 - 4.34: 60139 4.34 - 4.90: 100563 Nonbonded interactions: 237678 Sorted by model distance: nonbonded pdb=" NH2 ARG D 542 " pdb=" OE2 GLU d 647 " model vdw 2.121 3.120 nonbonded pdb=" OD2 ASP c 457 " pdb=" NH1 ARG c 469 " model vdw 2.134 3.120 nonbonded pdb=" NH2 ARG 1 542 " pdb=" OE2 GLU D 647 " model vdw 2.174 3.120 nonbonded pdb=" OE2 GLU 1 647 " pdb=" NH2 ARG d 542 " model vdw 2.177 3.120 nonbonded pdb=" N THR M 83 " pdb=" OD2 ASP M 86 " model vdw 2.180 3.120 ... (remaining 237673 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain 'I' selection = chain 'S' selection = chain 'a' selection = chain 'i' selection = chain 'v' } ncs_group { reference = chain '1' selection = chain 'D' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain 'C' selection = chain 'c' } ncs_group { reference = chain '3' selection = chain 'H' selection = chain 'h' } ncs_group { reference = chain '4' selection = chain 'L' selection = chain 'l' } ncs_group { reference = chain '5' selection = chain 'M' selection = chain 'm' } ncs_group { reference = chain '6' selection = chain 'N' selection = chain 'n' } ncs_group { reference = chain '7' selection = chain 'Q' selection = chain 'q' } ncs_group { reference = chain '8' selection = chain 'R' selection = chain 'r' } ncs_group { reference = chain '9' selection = chain 'A' selection = chain 'F' selection = chain 'G' selection = chain 'J' selection = chain 'K' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'o' selection = chain 't' selection = chain 'u' selection = chain 'w' selection = chain 'x' selection = chain 'z' } ncs_group { reference = chain 'AA' selection = chain 'U' selection = chain 'k' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'O' selection = chain 'W' selection = chain 'X' selection = chain 'f' selection = chain 'p' selection = chain 's' selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.410 Check model and map are aligned: 0.270 Set scattering table: 0.330 Process input model: 93.140 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.008 0.083 32403 Z= 0.511 Angle : 1.032 11.437 44025 Z= 0.534 Chirality : 0.070 1.219 5199 Planarity : 0.007 0.070 5448 Dihedral : 14.562 117.216 13428 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.21 % Allowed : 3.36 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.55 (0.12), residues: 3783 helix: -3.21 (0.17), residues: 366 sheet: -1.85 (0.14), residues: 1236 loop : -2.57 (0.11), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP 1 614 HIS 0.012 0.003 HIS h 35 PHE 0.040 0.004 PHE 8 83 TYR 0.028 0.003 TYR D 638 ARG 0.010 0.001 ARG 2 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 647 time to evaluate : 3.579 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: 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: c 53 PHE cc_start: 0.6337 (t80) cc_final: 0.6130 (t80) REVERT: c 425 ASN cc_start: 0.8642 (t0) cc_final: 0.8306 (t0) REVERT: 2 259 LEU cc_start: 0.8867 (mp) cc_final: 0.8537 (pp) REVERT: 2 416 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8753 (pp) REVERT: 1 535 MET cc_start: 0.8399 (mpt) cc_final: 0.8087 (mpt) REVERT: 3 65 LYS cc_start: 0.8860 (tttt) cc_final: 0.8310 (pttt) REVERT: 4 40 TRP cc_start: 0.7833 (m100) cc_final: 0.7282 (m100) REVERT: 5 5 GLN cc_start: 0.8733 (tp40) cc_final: 0.8462 (mp10) REVERT: 5 32 ASN cc_start: 0.7408 (t0) cc_final: 0.6478 (p0) REVERT: 5 100 MET cc_start: 0.9470 (mpp) cc_final: 0.9212 (mmm) REVERT: 5 103 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8763 (mptt) REVERT: 7 43 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8548 (mmtm) REVERT: 7 80 ASP cc_start: 0.7888 (m-30) cc_final: 0.7600 (p0) REVERT: 7 88 MET cc_start: 0.8320 (ttp) cc_final: 0.7215 (ttp) REVERT: D 581 LEU cc_start: 0.9345 (tp) cc_final: 0.9130 (tt) REVERT: H 23 LYS cc_start: 0.8956 (mttt) cc_final: 0.8721 (tptt) REVERT: H 102 TYR cc_start: 0.8327 (m-80) cc_final: 0.8092 (m-10) REVERT: L 31 TYR cc_start: 0.7245 (t80) cc_final: 0.6823 (t80) REVERT: L 52 LEU cc_start: 0.7481 (mt) cc_final: 0.7226 (mm) REVERT: L 53 ILE cc_start: 0.6774 (mt) cc_final: 0.5762 (mt) REVERT: M 5 GLN cc_start: 0.9207 (tp40) cc_final: 0.8094 (mp10) REVERT: M 13 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8488 (mmtm) REVERT: M 100 MET cc_start: 0.9199 (mpp) cc_final: 0.8776 (mmm) REVERT: N 11 VAL cc_start: 0.7440 (t) cc_final: 0.7205 (t) REVERT: N 62 PHE cc_start: 0.7983 (m-80) cc_final: 0.7774 (m-80) REVERT: Q 88 MET cc_start: 0.8421 (ttp) cc_final: 0.7844 (ttp) REVERT: Q 110 ASP cc_start: 0.8082 (p0) cc_final: 0.7739 (p0) REVERT: Q 122 GLN cc_start: 0.8895 (pm20) cc_final: 0.8655 (pp30) REVERT: R 33 MET cc_start: 0.6922 (mtm) cc_final: 0.6637 (mtp) REVERT: R 83 PHE cc_start: 0.7714 (t80) cc_final: 0.7037 (t80) REVERT: d 633 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8760 (mttt) REVERT: h 81 MET cc_start: 0.6982 (mmm) cc_final: 0.5692 (tpp) REVERT: h 104 TYR cc_start: 0.8325 (p90) cc_final: 0.7717 (p90) REVERT: l 40 TRP cc_start: 0.7471 (m100) cc_final: 0.6815 (m100) REVERT: m 27 THR cc_start: 0.7440 (m) cc_final: 0.7212 (m) REVERT: m 31 ASP cc_start: 0.8695 (t0) cc_final: 0.8301 (t0) REVERT: m 32 ASN cc_start: 0.8357 (t0) cc_final: 0.7294 (p0) REVERT: m 86 ASP cc_start: 0.7549 (m-30) cc_final: 0.6764 (m-30) REVERT: m 100 MET cc_start: 0.9375 (mpp) cc_final: 0.8931 (mmm) REVERT: n 42 GLN cc_start: 0.7948 (mt0) cc_final: 0.7698 (mp10) REVERT: n 53 ASP cc_start: 0.8891 (m-30) cc_final: 0.8658 (m-30) REVERT: n 87 TYR cc_start: 0.8210 (m-80) cc_final: 0.7916 (m-80) REVERT: r 56 SER cc_start: 0.9077 (m) cc_final: 0.8764 (p) REVERT: r 70 ASP cc_start: 0.8385 (m-30) cc_final: 0.8068 (m-30) REVERT: r 106 VAL cc_start: 0.7778 (t) cc_final: 0.7139 (m) outliers start: 7 outliers final: 3 residues processed: 654 average time/residue: 0.4884 time to fit residues: 481.3986 Evaluate side-chains 294 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 290 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain C residue 373 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 6.9990 chunk 284 optimal weight: 0.5980 chunk 157 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 20.0000 chunk 218 optimal weight: 1.9990 chunk 340 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN c 315 GLN c 356 ASN 2 356 ASN C 33 ASN 1 625 ASN 4 27 GLN 4 58 ASN 5 52 HIS 7 3 GLN 7 6 GLN 7 118 GLN D 625 ASN L 27 GLN L 58 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN Q 6 GLN Q 118 GLN l 58 ASN l 95 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN q 6 GLN q 118 GLN r 90 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 32403 Z= 0.218 Angle : 0.750 12.648 44025 Z= 0.373 Chirality : 0.047 0.213 5199 Planarity : 0.005 0.053 5448 Dihedral : 12.988 81.127 6497 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.16 % Allowed : 9.88 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.71 (0.13), residues: 3783 helix: -1.06 (0.24), residues: 369 sheet: -1.58 (0.14), residues: 1278 loop : -2.10 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP 7 36 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.002 PHE C 353 TYR 0.031 0.001 TYR 6 87 ARG 0.008 0.001 ARG N 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 371 time to evaluate : 3.903 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: c 86 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8609 (tt) REVERT: c 100 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8641 (ptm) REVERT: c 125 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9217 (tt) REVERT: c 425 ASN cc_start: 0.8475 (t0) cc_final: 0.8217 (t0) REVERT: 2 425 ASN cc_start: 0.8634 (t0) cc_final: 0.8350 (t0) REVERT: 2 475 MET cc_start: 0.8180 (mmt) cc_final: 0.7935 (mmm) REVERT: 1 530 MET cc_start: 0.8811 (mmt) cc_final: 0.8576 (mmm) REVERT: 1 535 MET cc_start: 0.8464 (mpt) cc_final: 0.8109 (mpt) REVERT: 1 624 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8356 (p0) REVERT: 3 65 LYS cc_start: 0.8787 (tttt) cc_final: 0.8269 (pttt) REVERT: 4 40 TRP cc_start: 0.7662 (m100) cc_final: 0.7300 (m100) REVERT: 4 50 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7032 (mmtm) REVERT: 5 13 LYS cc_start: 0.8678 (tppp) cc_final: 0.8292 (mmmm) REVERT: 5 86 ASP cc_start: 0.7419 (m-30) cc_final: 0.7105 (m-30) REVERT: 5 100 LYS cc_start: 0.9309 (mmmt) cc_final: 0.9103 (mmmt) REVERT: 5 100 MET cc_start: 0.9589 (mpp) cc_final: 0.9256 (mmm) REVERT: 5 103 LYS cc_start: 0.9101 (mtpt) cc_final: 0.8749 (mptt) REVERT: 7 97 ASP cc_start: 0.8887 (m-30) cc_final: 0.8522 (m-30) REVERT: 8 89 GLN cc_start: 0.8949 (tt0) cc_final: 0.8704 (tt0) REVERT: D 589 ASP cc_start: 0.8544 (m-30) cc_final: 0.8339 (m-30) REVERT: D 632 ASP cc_start: 0.8119 (t0) cc_final: 0.7732 (t0) REVERT: D 633 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8410 (mmtt) REVERT: H 69 MET cc_start: 0.5791 (OUTLIER) cc_final: 0.5289 (tpt) REVERT: H 81 MET cc_start: 0.6393 (mmm) cc_final: 0.5786 (mmm) REVERT: H 100 ARG cc_start: 0.8853 (mtp180) cc_final: 0.8518 (mmt180) REVERT: H 102 TYR cc_start: 0.8365 (m-80) cc_final: 0.7957 (m-10) REVERT: L 4 MET cc_start: 0.5675 (tpp) cc_final: 0.5313 (tpp) REVERT: L 40 TRP cc_start: 0.7645 (m-90) cc_final: 0.7323 (m-10) REVERT: L 50 LYS cc_start: 0.6898 (mttt) cc_final: 0.6670 (tptp) REVERT: M 5 GLN cc_start: 0.9153 (tp40) cc_final: 0.8053 (mp10) REVERT: M 100 MET cc_start: 0.9453 (mpp) cc_final: 0.8983 (mmm) REVERT: N 42 GLN cc_start: 0.8669 (mt0) cc_final: 0.8463 (mp10) REVERT: N 61 ARG cc_start: 0.7871 (mtm110) cc_final: 0.7358 (mtm-85) REVERT: N 100 GLU cc_start: 0.8298 (pm20) cc_final: 0.7981 (pp20) REVERT: Q 80 ASP cc_start: 0.8487 (m-30) cc_final: 0.7966 (p0) REVERT: Q 97 ASP cc_start: 0.8666 (m-30) cc_final: 0.8435 (t70) REVERT: Q 110 ASP cc_start: 0.8204 (p0) cc_final: 0.7916 (p0) REVERT: R 36 TYR cc_start: 0.9262 (m-80) cc_final: 0.9009 (m-10) REVERT: d 595 ILE cc_start: 0.9538 (pt) cc_final: 0.9274 (mp) REVERT: d 621 GLU cc_start: 0.8008 (pt0) cc_final: 0.7628 (pp20) REVERT: h 81 MET cc_start: 0.6753 (mmm) cc_final: 0.5432 (tpp) REVERT: l 76 PHE cc_start: 0.6875 (m-80) cc_final: 0.6438 (m-10) REVERT: m 31 ASP cc_start: 0.8740 (t0) cc_final: 0.8332 (t0) REVERT: m 32 ASN cc_start: 0.8129 (t0) cc_final: 0.7210 (p0) REVERT: n 37 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7129 (tt0) REVERT: n 42 GLN cc_start: 0.7944 (mt0) cc_final: 0.7659 (mp10) REVERT: n 52 ASN cc_start: 0.9292 (t0) cc_final: 0.8958 (t0) REVERT: n 53 ASP cc_start: 0.8805 (m-30) cc_final: 0.8516 (m-30) REVERT: q 32 TYR cc_start: 0.8610 (m-80) cc_final: 0.8164 (m-10) REVERT: q 97 ASP cc_start: 0.8768 (m-30) cc_final: 0.8518 (m-30) REVERT: r 56 SER cc_start: 0.9007 (m) cc_final: 0.8671 (p) outliers start: 72 outliers final: 29 residues processed: 420 average time/residue: 0.4373 time to fit residues: 293.8096 Evaluate side-chains 320 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 284 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain 2 residue 95 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 624 ASP Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 95 GLN Chi-restraints excluded: chain 7 residue 11 ILE Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 283 optimal weight: 1.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 341 optimal weight: 0.7980 chunk 368 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 338 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 273 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN D 625 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN r 89 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32403 Z= 0.191 Angle : 0.689 11.975 44025 Z= 0.341 Chirality : 0.046 0.227 5199 Planarity : 0.005 0.085 5448 Dihedral : 10.708 72.469 6496 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.82 % Allowed : 10.90 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.28 (0.13), residues: 3783 helix: -0.23 (0.26), residues: 387 sheet: -1.23 (0.14), residues: 1377 loop : -1.97 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 2 427 HIS 0.005 0.001 HIS H 35 PHE 0.020 0.001 PHE Q 102 TYR 0.040 0.001 TYR 6 87 ARG 0.020 0.001 ARG H 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 324 time to evaluate : 3.949 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 86 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8560 (tt) REVERT: c 100 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8639 (ptm) REVERT: c 125 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9230 (tt) REVERT: c 425 ASN cc_start: 0.8406 (t0) cc_final: 0.8204 (t0) REVERT: 2 104 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7747 (tmm) REVERT: 2 125 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9229 (tt) REVERT: 2 255 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8883 (p) REVERT: 2 259 LEU cc_start: 0.8769 (mp) cc_final: 0.8502 (pp) REVERT: 2 475 MET cc_start: 0.8230 (mmt) cc_final: 0.7968 (mmm) REVERT: C 34 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7949 (mm) REVERT: C 100 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8595 (ppp) REVERT: C 416 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8808 (pp) REVERT: 1 624 ASP cc_start: 0.8718 (m-30) cc_final: 0.8387 (p0) REVERT: 3 65 LYS cc_start: 0.8925 (tttt) cc_final: 0.8447 (pttt) REVERT: 3 80 TYR cc_start: 0.7227 (m-80) cc_final: 0.6775 (m-80) REVERT: 4 4 MET cc_start: 0.5480 (tpt) cc_final: 0.5162 (tpt) REVERT: 4 29 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7103 (tp) REVERT: 4 40 TRP cc_start: 0.7658 (m100) cc_final: 0.7450 (m-10) REVERT: 4 50 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7402 (mmtm) REVERT: 5 86 ASP cc_start: 0.7415 (m-30) cc_final: 0.7131 (m-30) REVERT: 5 100 MET cc_start: 0.9612 (mpp) cc_final: 0.9282 (mmm) REVERT: 5 103 LYS cc_start: 0.9028 (mtpt) cc_final: 0.8725 (mptt) REVERT: 6 20 ARG cc_start: 0.6326 (mmm-85) cc_final: 0.6048 (mmm-85) REVERT: 6 25 GLU cc_start: 0.8722 (tp30) cc_final: 0.8512 (tp30) REVERT: 7 79 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7763 (t0) REVERT: 7 97 ASP cc_start: 0.8844 (m-30) cc_final: 0.8453 (m-30) REVERT: 8 89 GLN cc_start: 0.8995 (tt0) cc_final: 0.8791 (tt0) REVERT: H 69 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5543 (tpt) REVERT: L 4 MET cc_start: 0.6009 (tpp) cc_final: 0.5718 (tpp) REVERT: L 50 LYS cc_start: 0.6726 (mttt) cc_final: 0.6489 (tptp) REVERT: M 5 GLN cc_start: 0.9175 (tp40) cc_final: 0.8106 (mp10) REVERT: M 13 LYS cc_start: 0.8882 (mmtm) cc_final: 0.8517 (mmmm) REVERT: M 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7946 (t0) REVERT: M 75 LYS cc_start: 0.9427 (pttp) cc_final: 0.8720 (tptt) REVERT: M 81 ARG cc_start: 0.8809 (ttp-110) cc_final: 0.8455 (ptp90) REVERT: M 100 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9072 (mmmt) REVERT: M 100 MET cc_start: 0.9357 (mpp) cc_final: 0.8870 (mmm) REVERT: Q 80 ASP cc_start: 0.8446 (m-30) cc_final: 0.7969 (p0) REVERT: Q 97 ASP cc_start: 0.8677 (m-30) cc_final: 0.8459 (t0) REVERT: Q 110 ASP cc_start: 0.8245 (p0) cc_final: 0.7990 (p0) REVERT: h 81 MET cc_start: 0.6610 (mmm) cc_final: 0.5454 (tpp) REVERT: m 31 ASP cc_start: 0.8742 (t0) cc_final: 0.8315 (t0) REVERT: m 32 ASN cc_start: 0.8159 (t0) cc_final: 0.7254 (p0) REVERT: m 100 LYS cc_start: 0.9436 (mmmt) cc_final: 0.9082 (mmmt) REVERT: n 42 GLN cc_start: 0.7973 (mt0) cc_final: 0.7766 (mp10) REVERT: n 52 ASN cc_start: 0.9349 (t0) cc_final: 0.9027 (t0) REVERT: n 53 ASP cc_start: 0.8735 (m-30) cc_final: 0.8510 (m-30) REVERT: n 87 TYR cc_start: 0.7648 (m-80) cc_final: 0.7432 (m-80) REVERT: q 32 TYR cc_start: 0.8770 (m-80) cc_final: 0.8492 (m-10) REVERT: q 97 ASP cc_start: 0.8788 (m-30) cc_final: 0.8435 (m-30) REVERT: r 56 SER cc_start: 0.8957 (m) cc_final: 0.8654 (p) outliers start: 94 outliers final: 40 residues processed: 394 average time/residue: 0.4308 time to fit residues: 275.1253 Evaluate side-chains 331 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 278 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 86 LEU Chi-restraints excluded: chain c residue 100 MET Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 6 residue 23 CYS Chi-restraints excluded: chain 7 residue 79 ASP Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 7.9990 chunk 256 optimal weight: 0.0170 chunk 177 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 342 optimal weight: 8.9990 chunk 362 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN c 105 HIS ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN C 72 HIS C 183 GLN 4 35 ASN 5 44 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN d 625 ASN l 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN r 90 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 32403 Z= 0.323 Angle : 0.721 13.540 44025 Z= 0.355 Chirality : 0.046 0.228 5199 Planarity : 0.005 0.055 5448 Dihedral : 9.369 63.315 6496 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.48 % Allowed : 11.56 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.00 (0.13), residues: 3783 helix: 0.10 (0.26), residues: 393 sheet: -1.13 (0.14), residues: 1383 loop : -1.75 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP 3 47 HIS 0.005 0.001 HIS C 105 PHE 0.022 0.002 PHE N 62 TYR 0.024 0.002 TYR 6 87 ARG 0.007 0.001 ARG 2 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 290 time to evaluate : 3.663 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: c 125 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9262 (tt) REVERT: c 425 ASN cc_start: 0.8605 (t0) cc_final: 0.8358 (t0) REVERT: 2 104 MET cc_start: 0.8750 (ttp) cc_final: 0.7934 (tmm) REVERT: 2 125 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9189 (tt) REVERT: 2 255 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.9005 (p) REVERT: C 34 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8021 (mm) REVERT: C 100 MET cc_start: 0.8964 (ptm) cc_final: 0.8689 (ppp) REVERT: C 416 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8813 (pp) REVERT: 1 624 ASP cc_start: 0.8836 (m-30) cc_final: 0.8484 (p0) REVERT: 3 65 LYS cc_start: 0.8932 (tttt) cc_final: 0.8397 (pttt) REVERT: 4 4 MET cc_start: 0.5535 (tpt) cc_final: 0.5308 (tpp) REVERT: 4 50 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7578 (mmtp) REVERT: 5 86 ASP cc_start: 0.7334 (m-30) cc_final: 0.7016 (m-30) REVERT: 5 100 MET cc_start: 0.9617 (mpp) cc_final: 0.9307 (mmm) REVERT: 5 103 LYS cc_start: 0.8999 (mtpt) cc_final: 0.8736 (mptt) REVERT: 6 20 ARG cc_start: 0.6283 (mmm-85) cc_final: 0.6003 (mmm-85) REVERT: 6 104 LEU cc_start: 0.7091 (tp) cc_final: 0.6588 (tt) REVERT: 7 97 ASP cc_start: 0.8880 (m-30) cc_final: 0.8459 (m-30) REVERT: D 530 MET cc_start: 0.9025 (mmt) cc_final: 0.8394 (mmp) REVERT: D 657 GLU cc_start: 0.8986 (tp30) cc_final: 0.8484 (pt0) REVERT: H 81 MET cc_start: 0.6489 (mmm) cc_final: 0.5947 (mmm) REVERT: L 4 MET cc_start: 0.6148 (tpp) cc_final: 0.5866 (tpp) REVERT: L 29 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7828 (tp) REVERT: L 50 LYS cc_start: 0.6895 (mttt) cc_final: 0.6692 (tptp) REVERT: M 5 GLN cc_start: 0.9191 (tp40) cc_final: 0.8141 (mp10) REVERT: M 13 LYS cc_start: 0.8842 (mmtm) cc_final: 0.8477 (mmmm) REVERT: M 75 LYS cc_start: 0.9413 (pttp) cc_final: 0.8691 (tptt) REVERT: M 81 ARG cc_start: 0.8863 (ttp-110) cc_final: 0.8556 (ptp90) REVERT: M 100 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9111 (mmmt) REVERT: M 100 MET cc_start: 0.9360 (mpp) cc_final: 0.8848 (mmm) REVERT: N 42 GLN cc_start: 0.8683 (mt0) cc_final: 0.8282 (mm110) REVERT: N 87 TYR cc_start: 0.8060 (m-80) cc_final: 0.7589 (m-80) REVERT: Q 80 ASP cc_start: 0.8508 (m-30) cc_final: 0.7841 (p0) REVERT: Q 97 ASP cc_start: 0.8790 (m-30) cc_final: 0.8396 (t0) REVERT: Q 110 ASP cc_start: 0.8354 (p0) cc_final: 0.8098 (p0) REVERT: Q 122 GLN cc_start: 0.8725 (pm20) cc_final: 0.8497 (pp30) REVERT: h 27 TYR cc_start: 0.8969 (t80) cc_final: 0.8621 (t80) REVERT: h 81 MET cc_start: 0.6578 (mmm) cc_final: 0.5490 (tpp) REVERT: m 31 ASP cc_start: 0.8868 (t0) cc_final: 0.8438 (t0) REVERT: m 32 ASN cc_start: 0.8096 (t0) cc_final: 0.7106 (p0) REVERT: m 86 ASP cc_start: 0.6905 (t0) cc_final: 0.6543 (m-30) REVERT: m 100 MET cc_start: 0.9527 (mpp) cc_final: 0.8730 (mmm) REVERT: n 42 GLN cc_start: 0.8072 (mt0) cc_final: 0.7829 (mp10) REVERT: n 52 ASN cc_start: 0.9349 (t0) cc_final: 0.9034 (t0) REVERT: n 53 ASP cc_start: 0.8901 (m-30) cc_final: 0.8678 (m-30) REVERT: q 32 TYR cc_start: 0.8752 (m-80) cc_final: 0.8446 (m-10) REVERT: q 97 ASP cc_start: 0.8828 (m-30) cc_final: 0.8430 (m-30) REVERT: r 56 SER cc_start: 0.8984 (m) cc_final: 0.8733 (p) outliers start: 116 outliers final: 71 residues processed: 380 average time/residue: 0.4112 time to fit residues: 255.6803 Evaluate side-chains 340 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 262 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 67 LYS Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 48 ILE Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 0.9980 chunk 205 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 269 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 309 optimal weight: 0.0970 chunk 250 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 chunk 325 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 33 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN 6 89 HIS L 35 ASN l 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32403 Z= 0.240 Angle : 0.667 12.880 44025 Z= 0.328 Chirality : 0.045 0.224 5199 Planarity : 0.004 0.046 5448 Dihedral : 8.549 56.046 6496 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.30 % Allowed : 12.55 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.83 (0.13), residues: 3783 helix: 0.32 (0.26), residues: 396 sheet: -1.03 (0.14), residues: 1380 loop : -1.65 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 3 47 HIS 0.005 0.001 HIS c 85 PHE 0.022 0.002 PHE N 62 TYR 0.019 0.001 TYR 4 92 ARG 0.005 0.000 ARG n 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 287 time to evaluate : 3.892 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: symmetry clash REVERT: c 125 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9257 (tt) REVERT: 2 104 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8024 (tmm) REVERT: 2 125 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9204 (tt) REVERT: 2 255 VAL cc_start: 0.9280 (OUTLIER) cc_final: 0.9011 (p) REVERT: 2 259 LEU cc_start: 0.8861 (mp) cc_final: 0.8531 (pp) REVERT: C 34 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7988 (mm) REVERT: C 100 MET cc_start: 0.8926 (ptm) cc_final: 0.8603 (ppp) REVERT: C 104 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8401 (tpp) REVERT: C 416 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8815 (pp) REVERT: 3 47 TRP cc_start: 0.5093 (OUTLIER) cc_final: 0.4787 (t60) REVERT: 3 65 LYS cc_start: 0.8936 (tttt) cc_final: 0.8387 (pttt) REVERT: 3 81 MET cc_start: 0.6989 (mmm) cc_final: 0.6628 (mmm) REVERT: 4 29 ILE cc_start: 0.7857 (OUTLIER) cc_final: 0.7329 (tp) REVERT: 4 50 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7537 (mmtm) REVERT: 5 86 ASP cc_start: 0.7291 (m-30) cc_final: 0.7033 (m-30) REVERT: 5 100 MET cc_start: 0.9556 (mpp) cc_final: 0.9241 (mmm) REVERT: 5 103 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8740 (mptt) REVERT: 6 104 LEU cc_start: 0.7096 (tp) cc_final: 0.6608 (tt) REVERT: 7 97 ASP cc_start: 0.8849 (m-30) cc_final: 0.8415 (m-30) REVERT: D 530 MET cc_start: 0.8977 (mmt) cc_final: 0.8372 (mmp) REVERT: D 657 GLU cc_start: 0.8970 (tp30) cc_final: 0.8490 (pt0) REVERT: H 81 MET cc_start: 0.6648 (mmm) cc_final: 0.6148 (mmm) REVERT: L 29 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7704 (tp) REVERT: L 50 LYS cc_start: 0.6908 (mttt) cc_final: 0.6692 (tptp) REVERT: M 5 GLN cc_start: 0.9191 (tp40) cc_final: 0.8175 (mp10) REVERT: M 13 LYS cc_start: 0.8859 (mmtm) cc_final: 0.8562 (mmmm) REVERT: M 75 LYS cc_start: 0.9425 (pttp) cc_final: 0.8695 (tptt) REVERT: M 81 ARG cc_start: 0.8895 (ttp-110) cc_final: 0.8533 (ptp90) REVERT: M 100 MET cc_start: 0.9371 (mpp) cc_final: 0.8876 (mmm) REVERT: N 87 TYR cc_start: 0.8040 (m-80) cc_final: 0.7559 (m-80) REVERT: Q 97 ASP cc_start: 0.8803 (m-30) cc_final: 0.8341 (t0) REVERT: Q 110 ASP cc_start: 0.8255 (p0) cc_final: 0.8016 (p0) REVERT: Q 122 GLN cc_start: 0.8650 (pm20) cc_final: 0.8398 (pm20) REVERT: R 37 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8180 (tm-30) REVERT: h 81 MET cc_start: 0.6807 (mmm) cc_final: 0.5579 (tpp) REVERT: m 31 ASP cc_start: 0.8879 (t0) cc_final: 0.8404 (t0) REVERT: m 32 ASN cc_start: 0.8053 (t0) cc_final: 0.7193 (p0) REVERT: m 86 ASP cc_start: 0.7058 (t0) cc_final: 0.6705 (m-30) REVERT: m 94 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.6605 (p) REVERT: m 100 MET cc_start: 0.9509 (mpp) cc_final: 0.8612 (mmm) REVERT: n 52 ASN cc_start: 0.9399 (t0) cc_final: 0.9121 (t0) REVERT: n 95 ARG cc_start: 0.8812 (mmm-85) cc_final: 0.8573 (mmm-85) REVERT: q 97 ASP cc_start: 0.8782 (m-30) cc_final: 0.8337 (m-30) REVERT: r 56 SER cc_start: 0.8996 (m) cc_final: 0.8752 (p) outliers start: 110 outliers final: 77 residues processed: 372 average time/residue: 0.4010 time to fit residues: 244.5639 Evaluate side-chains 357 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 267 time to evaluate : 3.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain l residue 93 CYS Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 46 GLU Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 212 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 362 optimal weight: 6.9990 chunk 301 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS Q 3 GLN l 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 42 GLN q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32403 Z= 0.249 Angle : 0.661 11.794 44025 Z= 0.325 Chirality : 0.045 0.219 5199 Planarity : 0.004 0.045 5448 Dihedral : 8.083 55.387 6496 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.66 % Allowed : 12.70 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.67 (0.14), residues: 3783 helix: 0.47 (0.27), residues: 396 sheet: -0.87 (0.14), residues: 1356 loop : -1.59 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP 3 47 HIS 0.004 0.001 HIS N 89 PHE 0.016 0.001 PHE Q 102 TYR 0.027 0.001 TYR 6 87 ARG 0.007 0.000 ARG M 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 286 time to evaluate : 3.950 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: c 34 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7870 (mm) REVERT: c 125 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9264 (tt) REVERT: 2 104 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8076 (tmm) REVERT: 2 125 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9186 (tt) REVERT: 2 255 VAL cc_start: 0.9324 (OUTLIER) cc_final: 0.9067 (p) REVERT: C 34 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8019 (mm) REVERT: C 100 MET cc_start: 0.8921 (ptm) cc_final: 0.8615 (ppp) REVERT: C 416 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8782 (pp) REVERT: 3 39 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7320 (tp40) REVERT: 3 47 TRP cc_start: 0.5521 (OUTLIER) cc_final: 0.5206 (t60) REVERT: 3 65 LYS cc_start: 0.8963 (tttt) cc_final: 0.8401 (pttt) REVERT: 4 29 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7369 (tp) REVERT: 4 50 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7662 (mmtp) REVERT: 5 86 ASP cc_start: 0.7236 (m-30) cc_final: 0.6937 (m-30) REVERT: 5 100 MET cc_start: 0.9549 (mpp) cc_final: 0.9254 (mmm) REVERT: 5 103 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8727 (mptt) REVERT: 6 20 ARG cc_start: 0.6218 (mmm-85) cc_final: 0.5859 (mmm-85) REVERT: 6 52 ASN cc_start: 0.9450 (t0) cc_final: 0.9135 (m-40) REVERT: 6 104 LEU cc_start: 0.7261 (tp) cc_final: 0.6777 (tt) REVERT: 7 97 ASP cc_start: 0.8857 (m-30) cc_final: 0.8424 (m-30) REVERT: D 530 MET cc_start: 0.8897 (mmt) cc_final: 0.8267 (mmp) REVERT: D 657 GLU cc_start: 0.8974 (tp30) cc_final: 0.8468 (mt-10) REVERT: L 4 MET cc_start: 0.5555 (tpp) cc_final: 0.5179 (tpp) REVERT: L 29 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7646 (tp) REVERT: L 50 LYS cc_start: 0.7320 (mttt) cc_final: 0.7065 (tptp) REVERT: M 5 GLN cc_start: 0.9199 (tp40) cc_final: 0.8198 (mp10) REVERT: M 13 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8587 (mmmm) REVERT: M 75 LYS cc_start: 0.9377 (pttp) cc_final: 0.8683 (tptt) REVERT: M 81 ARG cc_start: 0.8930 (ttp-110) cc_final: 0.8559 (ptp90) REVERT: M 100 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9177 (mmmt) REVERT: M 100 MET cc_start: 0.9409 (mpp) cc_final: 0.8896 (mmm) REVERT: N 25 GLU cc_start: 0.8045 (tp30) cc_final: 0.7748 (mm-30) REVERT: N 90 ILE cc_start: 0.9509 (pt) cc_final: 0.9210 (tp) REVERT: Q 80 ASP cc_start: 0.8680 (t0) cc_final: 0.7784 (p0) REVERT: Q 97 ASP cc_start: 0.8824 (m-30) cc_final: 0.8347 (t0) REVERT: R 37 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: d 535 MET cc_start: 0.8412 (mpt) cc_final: 0.8011 (mpt) REVERT: h 81 MET cc_start: 0.6878 (mmm) cc_final: 0.5592 (tpp) REVERT: m 31 ASP cc_start: 0.8905 (t0) cc_final: 0.8466 (t0) REVERT: m 32 ASN cc_start: 0.7949 (t0) cc_final: 0.7270 (p0) REVERT: m 86 ASP cc_start: 0.6986 (t0) cc_final: 0.6581 (m-30) REVERT: m 94 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.6650 (p) REVERT: m 100 MET cc_start: 0.9469 (mpp) cc_final: 0.8503 (mmm) REVERT: n 52 ASN cc_start: 0.9348 (t0) cc_final: 0.9043 (t0) REVERT: q 97 ASP cc_start: 0.8785 (m-30) cc_final: 0.8549 (m-30) REVERT: r 33 MET cc_start: 0.8041 (ppp) cc_final: 0.7518 (ppp) outliers start: 122 outliers final: 88 residues processed: 382 average time/residue: 0.4744 time to fit residues: 299.2969 Evaluate side-chains 365 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 264 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 242 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 424 ILE Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 31 ASP Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain Q residue 3 GLN Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 573 ILE Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 67 LYS Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain l residue 93 CYS Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 42 GLN Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Chi-restraints excluded: chain r residue 104 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 264 optimal weight: 7.9990 chunk 205 optimal weight: 0.9980 chunk 305 optimal weight: 0.0060 chunk 202 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 220 optimal weight: 0.6980 chunk 166 optimal weight: 9.9990 overall best weight: 2.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 ASN 5 68 HIS D 625 ASN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32403 Z= 0.291 Angle : 0.682 12.126 44025 Z= 0.335 Chirality : 0.045 0.331 5199 Planarity : 0.004 0.044 5448 Dihedral : 7.912 54.991 6496 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.69 % Allowed : 13.00 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.69 (0.14), residues: 3783 helix: 0.31 (0.26), residues: 414 sheet: -0.95 (0.14), residues: 1344 loop : -1.53 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP 3 47 HIS 0.003 0.001 HIS 5 97 PHE 0.027 0.002 PHE l 76 TYR 0.014 0.001 TYR 4 92 ARG 0.006 0.000 ARG c 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 272 time to evaluate : 3.539 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: c 34 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7825 (mm) REVERT: c 103 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8059 (pp30) REVERT: c 125 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9267 (tt) REVERT: 2 104 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8166 (tmm) REVERT: 2 125 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9177 (tt) REVERT: 2 259 LEU cc_start: 0.8908 (mp) cc_final: 0.8669 (pp) REVERT: C 34 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7947 (mm) REVERT: C 416 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8804 (pp) REVERT: 3 39 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7303 (tp40) REVERT: 3 47 TRP cc_start: 0.5686 (OUTLIER) cc_final: 0.5404 (t60) REVERT: 3 65 LYS cc_start: 0.9022 (tttt) cc_final: 0.8450 (pttt) REVERT: 3 81 MET cc_start: 0.7095 (mmm) cc_final: 0.6581 (mmm) REVERT: 4 29 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7434 (tp) REVERT: 4 50 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.7680 (mmtp) REVERT: 5 86 ASP cc_start: 0.7275 (m-30) cc_final: 0.6984 (m-30) REVERT: 5 100 MET cc_start: 0.9537 (mpp) cc_final: 0.9249 (mmm) REVERT: 5 103 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8739 (mptt) REVERT: 6 52 ASN cc_start: 0.9455 (t0) cc_final: 0.9187 (m-40) REVERT: 6 104 LEU cc_start: 0.7393 (tp) cc_final: 0.6925 (tt) REVERT: 7 89 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8201 (mm-30) REVERT: 7 97 ASP cc_start: 0.8866 (m-30) cc_final: 0.8389 (m-30) REVERT: 8 36 TYR cc_start: 0.9044 (m-10) cc_final: 0.8734 (m-10) REVERT: D 530 MET cc_start: 0.8936 (mmt) cc_final: 0.8367 (mmp) REVERT: D 657 GLU cc_start: 0.8942 (tp30) cc_final: 0.8427 (mt-10) REVERT: H 81 MET cc_start: 0.6222 (mmm) cc_final: 0.5569 (mmm) REVERT: L 4 MET cc_start: 0.5491 (tpp) cc_final: 0.5213 (tpp) REVERT: L 29 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7695 (tp) REVERT: M 5 GLN cc_start: 0.9197 (tp40) cc_final: 0.8197 (mp10) REVERT: M 75 LYS cc_start: 0.9379 (pttp) cc_final: 0.8699 (tptt) REVERT: M 81 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8554 (ptp90) REVERT: M 100 MET cc_start: 0.9419 (mpp) cc_final: 0.8911 (mmm) REVERT: N 25 GLU cc_start: 0.8105 (tp30) cc_final: 0.7829 (mm-30) REVERT: N 87 TYR cc_start: 0.7911 (m-80) cc_final: 0.7623 (m-10) REVERT: N 90 ILE cc_start: 0.9533 (pt) cc_final: 0.9210 (tp) REVERT: Q 80 ASP cc_start: 0.8721 (t0) cc_final: 0.7688 (p0) REVERT: Q 97 ASP cc_start: 0.8807 (m-30) cc_final: 0.8565 (m-30) REVERT: R 37 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8289 (tm-30) REVERT: d 535 MET cc_start: 0.8436 (mpt) cc_final: 0.8002 (mpt) REVERT: d 638 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.5085 (p90) REVERT: h 81 MET cc_start: 0.6885 (mmm) cc_final: 0.5605 (tpp) REVERT: m 31 ASP cc_start: 0.8911 (t0) cc_final: 0.8510 (t0) REVERT: m 32 ASN cc_start: 0.8005 (t0) cc_final: 0.7378 (p0) REVERT: m 86 ASP cc_start: 0.6954 (t0) cc_final: 0.6579 (m-30) REVERT: m 94 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.6894 (p) REVERT: m 100 MET cc_start: 0.9453 (mpp) cc_final: 0.8478 (mmm) REVERT: n 52 ASN cc_start: 0.9327 (t0) cc_final: 0.9040 (t0) REVERT: q 97 ASP cc_start: 0.8786 (m-30) cc_final: 0.8540 (m-30) REVERT: r 33 MET cc_start: 0.8059 (ppp) cc_final: 0.7482 (ppp) outliers start: 123 outliers final: 93 residues processed: 367 average time/residue: 0.3959 time to fit residues: 238.2020 Evaluate side-chains 363 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 256 time to evaluate : 3.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 103 GLN Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 245 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 108 ILE Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain 2 residue 496 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 573 ILE Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 105 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 573 ILE Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 593 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 616 ASN Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 67 LYS Chi-restraints excluded: chain h residue 87 THR Chi-restraints excluded: chain l residue 93 CYS Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 72 ASP Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 58 VAL Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 chunk 215 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 246 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 284 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 425 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 89 HIS Q 3 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32403 Z= 0.204 Angle : 0.653 14.313 44025 Z= 0.321 Chirality : 0.045 0.223 5199 Planarity : 0.004 0.048 5448 Dihedral : 7.562 56.170 6496 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 3.72 % Allowed : 13.21 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.52 (0.14), residues: 3783 helix: 0.46 (0.26), residues: 414 sheet: -0.67 (0.15), residues: 1305 loop : -1.55 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 3 47 HIS 0.003 0.001 HIS H 35 PHE 0.049 0.001 PHE R 83 TYR 0.017 0.001 TYR 4 92 ARG 0.006 0.000 ARG c 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 275 time to evaluate : 3.554 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: c 34 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7836 (mm) REVERT: c 103 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (pp30) REVERT: c 125 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9258 (tt) REVERT: 2 103 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8238 (pp30) REVERT: 2 104 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8242 (tmm) REVERT: 2 125 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9210 (tt) REVERT: 2 255 VAL cc_start: 0.9181 (OUTLIER) cc_final: 0.8932 (p) REVERT: C 34 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7895 (mm) REVERT: C 161 MET cc_start: 0.9012 (tpp) cc_final: 0.8759 (tpt) REVERT: C 416 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8832 (pp) REVERT: C 426 MET cc_start: 0.8689 (tmm) cc_final: 0.8487 (tmm) REVERT: 3 39 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7254 (tp40) REVERT: 3 47 TRP cc_start: 0.5804 (OUTLIER) cc_final: 0.5587 (t60) REVERT: 3 65 LYS cc_start: 0.9005 (tttt) cc_final: 0.8440 (pttt) REVERT: 3 103 TRP cc_start: 0.8955 (m100) cc_final: 0.8718 (m100) REVERT: 4 29 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7444 (tp) REVERT: 4 50 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7811 (mmtp) REVERT: 5 86 ASP cc_start: 0.7312 (m-30) cc_final: 0.6982 (m-30) REVERT: 5 100 MET cc_start: 0.9549 (mpp) cc_final: 0.9275 (mmm) REVERT: 5 103 LYS cc_start: 0.8985 (mtpt) cc_final: 0.8728 (mptt) REVERT: 6 25 GLU cc_start: 0.8562 (tp30) cc_final: 0.8099 (mm-30) REVERT: 6 52 ASN cc_start: 0.9486 (t0) cc_final: 0.9151 (m-40) REVERT: 6 104 LEU cc_start: 0.7525 (tp) cc_final: 0.7047 (tt) REVERT: 7 89 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8323 (mm-30) REVERT: 7 97 ASP cc_start: 0.8856 (m-30) cc_final: 0.8386 (m-30) REVERT: 8 36 TYR cc_start: 0.8960 (m-10) cc_final: 0.8738 (m-10) REVERT: D 530 MET cc_start: 0.8867 (mmt) cc_final: 0.8385 (mmp) REVERT: D 657 GLU cc_start: 0.8939 (tp30) cc_final: 0.8432 (mt-10) REVERT: H 81 MET cc_start: 0.6410 (mmm) cc_final: 0.5943 (mmm) REVERT: L 4 MET cc_start: 0.5530 (tpp) cc_final: 0.5079 (tpp) REVERT: L 29 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7688 (tp) REVERT: M 5 GLN cc_start: 0.9196 (tp40) cc_final: 0.8241 (mp10) REVERT: M 75 LYS cc_start: 0.9387 (pttp) cc_final: 0.8722 (tptt) REVERT: M 81 ARG cc_start: 0.8947 (ttp-110) cc_final: 0.8578 (ptp90) REVERT: M 100 LYS cc_start: 0.9422 (mmmt) cc_final: 0.8708 (tmtt) REVERT: M 100 MET cc_start: 0.9432 (mpp) cc_final: 0.8938 (mmm) REVERT: N 25 GLU cc_start: 0.8050 (tp30) cc_final: 0.7753 (mm-30) REVERT: N 87 TYR cc_start: 0.7876 (m-80) cc_final: 0.7607 (m-10) REVERT: N 90 ILE cc_start: 0.9495 (pt) cc_final: 0.9166 (tp) REVERT: Q 80 ASP cc_start: 0.8741 (t0) cc_final: 0.7650 (p0) REVERT: Q 97 ASP cc_start: 0.8833 (m-30) cc_final: 0.8572 (m-30) REVERT: R 37 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: d 535 MET cc_start: 0.8461 (mpt) cc_final: 0.7996 (mpt) REVERT: d 626 MET cc_start: 0.7738 (mmm) cc_final: 0.7403 (mmm) REVERT: d 638 TYR cc_start: 0.7054 (OUTLIER) cc_final: 0.5226 (p90) REVERT: h 67 LYS cc_start: 0.2227 (OUTLIER) cc_final: 0.0844 (mtpt) REVERT: h 81 MET cc_start: 0.6850 (mmm) cc_final: 0.5552 (tpp) REVERT: l 43 GLN cc_start: 0.4267 (tp40) cc_final: 0.3905 (tp40) REVERT: m 31 ASP cc_start: 0.8969 (t0) cc_final: 0.8578 (t0) REVERT: m 32 ASN cc_start: 0.8146 (t0) cc_final: 0.7567 (p0) REVERT: m 77 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (tp) REVERT: m 86 ASP cc_start: 0.6958 (t0) cc_final: 0.6544 (m-30) REVERT: m 94 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.6798 (p) REVERT: m 100 MET cc_start: 0.9450 (mpp) cc_final: 0.8463 (mmm) REVERT: n 52 ASN cc_start: 0.9363 (t0) cc_final: 0.9074 (t0) REVERT: q 97 ASP cc_start: 0.8765 (m-30) cc_final: 0.8505 (m-30) REVERT: r 33 MET cc_start: 0.7807 (ppp) cc_final: 0.7299 (ppp) outliers start: 124 outliers final: 83 residues processed: 376 average time/residue: 0.3984 time to fit residues: 245.5195 Evaluate side-chains 361 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 260 time to evaluate : 3.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 103 GLN Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 245 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 108 ILE Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 374 HIS Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 518 VAL Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 47 TRP Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 4 residue 90 VAL Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain N residue 47 ILE Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 67 LYS Chi-restraints excluded: chain l residue 93 CYS Chi-restraints excluded: chain m residue 16 GLU Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 315 optimal weight: 0.0970 chunk 336 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 304 optimal weight: 0.6980 chunk 318 optimal weight: 9.9990 chunk 335 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 425 ASN c 478 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 35 HIS 4 35 ASN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 89 GLN l 27 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 32403 Z= 0.320 Angle : 0.714 16.831 44025 Z= 0.347 Chirality : 0.046 0.219 5199 Planarity : 0.004 0.046 5448 Dihedral : 7.599 54.197 6496 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.72 % Allowed : 13.39 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.57 (0.14), residues: 3783 helix: 0.57 (0.26), residues: 396 sheet: -0.77 (0.14), residues: 1335 loop : -1.55 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP 3 47 HIS 0.005 0.001 HIS 2 374 PHE 0.053 0.002 PHE R 83 TYR 0.019 0.001 TYR 6 87 ARG 0.005 0.001 ARG c 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7566 Ramachandran restraints generated. 3783 Oldfield, 0 Emsley, 3783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 268 time to evaluate : 3.532 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: c 34 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7833 (mm) REVERT: c 103 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8081 (pp30) REVERT: c 125 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9282 (tt) REVERT: 2 103 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8132 (pp30) REVERT: 2 104 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: 2 125 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9178 (tt) REVERT: 2 255 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8978 (p) REVERT: C 34 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 161 MET cc_start: 0.9023 (tpp) cc_final: 0.8793 (tpt) REVERT: C 416 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (pp) REVERT: 3 39 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7399 (tp40) REVERT: 3 65 LYS cc_start: 0.9052 (tttt) cc_final: 0.8488 (pttt) REVERT: 3 81 MET cc_start: 0.6949 (mmt) cc_final: 0.6674 (mmm) REVERT: 4 29 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7506 (tp) REVERT: 4 50 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7833 (mmtp) REVERT: 5 86 ASP cc_start: 0.7375 (m-30) cc_final: 0.7030 (m-30) REVERT: 5 100 MET cc_start: 0.9537 (mpp) cc_final: 0.9266 (mmm) REVERT: 5 103 LYS cc_start: 0.8984 (mtpt) cc_final: 0.8722 (mptt) REVERT: 6 104 LEU cc_start: 0.7586 (tp) cc_final: 0.7094 (tt) REVERT: 7 89 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8307 (mm-30) REVERT: 8 36 TYR cc_start: 0.8998 (m-10) cc_final: 0.8683 (m-10) REVERT: D 530 MET cc_start: 0.8926 (mmt) cc_final: 0.8398 (mmp) REVERT: D 657 GLU cc_start: 0.8942 (tp30) cc_final: 0.8487 (mt-10) REVERT: H 81 MET cc_start: 0.6537 (mmm) cc_final: 0.6058 (mmm) REVERT: L 4 MET cc_start: 0.5619 (tpp) cc_final: 0.5322 (tpp) REVERT: L 29 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7771 (tp) REVERT: M 5 GLN cc_start: 0.9171 (tp40) cc_final: 0.8302 (mp10) REVERT: M 13 LYS cc_start: 0.8848 (mmtm) cc_final: 0.8590 (mmmm) REVERT: M 75 LYS cc_start: 0.9370 (pttp) cc_final: 0.8660 (tptt) REVERT: M 81 ARG cc_start: 0.8997 (ttp-110) cc_final: 0.8607 (ptp90) REVERT: M 100 LYS cc_start: 0.9429 (mmmt) cc_final: 0.8625 (tmtt) REVERT: M 100 MET cc_start: 0.9446 (mpp) cc_final: 0.8958 (mmm) REVERT: N 25 GLU cc_start: 0.7967 (tp30) cc_final: 0.7662 (mm-30) REVERT: N 90 ILE cc_start: 0.9487 (pt) cc_final: 0.9166 (tp) REVERT: Q 80 ASP cc_start: 0.8760 (t0) cc_final: 0.8491 (t0) REVERT: Q 97 ASP cc_start: 0.8835 (m-30) cc_final: 0.8563 (m-30) REVERT: R 37 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8278 (tm-30) REVERT: d 535 MET cc_start: 0.8489 (mpt) cc_final: 0.8073 (mpt) REVERT: d 626 MET cc_start: 0.7763 (mmm) cc_final: 0.7345 (mmm) REVERT: d 638 TYR cc_start: 0.7349 (OUTLIER) cc_final: 0.5687 (p90) REVERT: h 81 MET cc_start: 0.6864 (mmm) cc_final: 0.5503 (tpp) REVERT: h 83 LEU cc_start: 0.5010 (mt) cc_final: 0.3980 (mt) REVERT: l 38 LEU cc_start: 0.5777 (tp) cc_final: 0.5538 (mt) REVERT: m 31 ASP cc_start: 0.9020 (t0) cc_final: 0.8681 (t0) REVERT: m 32 ASN cc_start: 0.8245 (t0) cc_final: 0.7517 (p0) REVERT: m 77 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8180 (tt) REVERT: m 94 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7063 (p) REVERT: m 100 MET cc_start: 0.9453 (mpp) cc_final: 0.8493 (mmm) REVERT: n 52 ASN cc_start: 0.9369 (t0) cc_final: 0.9099 (t0) REVERT: q 97 ASP cc_start: 0.8788 (m-30) cc_final: 0.8509 (m-30) REVERT: r 33 MET cc_start: 0.7963 (ppp) cc_final: 0.7223 (ppp) outliers start: 124 outliers final: 91 residues processed: 363 average time/residue: 0.4096 time to fit residues: 245.8200 Evaluate side-chains 360 residues out of total 3333 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 253 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain c residue 34 LEU Chi-restraints excluded: chain c residue 36 VAL Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 103 GLN Chi-restraints excluded: chain c residue 123 THR Chi-restraints excluded: chain c residue 125 LEU Chi-restraints excluded: chain c residue 201 CYS Chi-restraints excluded: chain c residue 245 VAL Chi-restraints excluded: chain c residue 255 VAL Chi-restraints excluded: chain c residue 374 HIS Chi-restraints excluded: chain c residue 416 LEU Chi-restraints excluded: chain c residue 488 VAL Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 2 residue 42 VAL Chi-restraints excluded: chain 2 residue 47 ASP Chi-restraints excluded: chain 2 residue 89 VAL Chi-restraints excluded: chain 2 residue 103 GLN Chi-restraints excluded: chain 2 residue 104 MET Chi-restraints excluded: chain 2 residue 108 ILE Chi-restraints excluded: chain 2 residue 123 THR Chi-restraints excluded: chain 2 residue 125 LEU Chi-restraints excluded: chain 2 residue 201 CYS Chi-restraints excluded: chain 2 residue 207 LYS Chi-restraints excluded: chain 2 residue 245 VAL Chi-restraints excluded: chain 2 residue 255 VAL Chi-restraints excluded: chain 2 residue 260 LEU Chi-restraints excluded: chain 2 residue 373 THR Chi-restraints excluded: chain 2 residue 416 LEU Chi-restraints excluded: chain 2 residue 488 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 207 LYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 374 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain 1 residue 538 THR Chi-restraints excluded: chain 1 residue 587 LEU Chi-restraints excluded: chain 1 residue 598 CYS Chi-restraints excluded: chain 1 residue 615 SER Chi-restraints excluded: chain 1 residue 626 MET Chi-restraints excluded: chain 1 residue 635 ILE Chi-restraints excluded: chain 1 residue 638 TYR Chi-restraints excluded: chain 1 residue 651 ASN Chi-restraints excluded: chain 3 residue 100 ARG Chi-restraints excluded: chain 4 residue 2 VAL Chi-restraints excluded: chain 4 residue 29 ILE Chi-restraints excluded: chain 4 residue 35 ASN Chi-restraints excluded: chain 4 residue 50 LYS Chi-restraints excluded: chain 5 residue 21 THR Chi-restraints excluded: chain 7 residue 109 CYS Chi-restraints excluded: chain 8 residue 4 LEU Chi-restraints excluded: chain 8 residue 48 ILE Chi-restraints excluded: chain 8 residue 104 LEU Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 573 ILE Chi-restraints excluded: chain D residue 608 VAL Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 27 TYR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 97 HIS Chi-restraints excluded: chain Q residue 11 ILE Chi-restraints excluded: chain Q residue 40 ILE Chi-restraints excluded: chain Q residue 42 ASP Chi-restraints excluded: chain Q residue 48 ILE Chi-restraints excluded: chain Q residue 112 CYS Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 61 ARG Chi-restraints excluded: chain R residue 81 GLU Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain d residue 518 VAL Chi-restraints excluded: chain d residue 573 ILE Chi-restraints excluded: chain d residue 587 LEU Chi-restraints excluded: chain d residue 608 VAL Chi-restraints excluded: chain d residue 635 ILE Chi-restraints excluded: chain d residue 638 TYR Chi-restraints excluded: chain d residue 642 ILE Chi-restraints excluded: chain d residue 664 ASP Chi-restraints excluded: chain h residue 67 LYS Chi-restraints excluded: chain l residue 93 CYS Chi-restraints excluded: chain m residue 21 THR Chi-restraints excluded: chain m residue 77 LEU Chi-restraints excluded: chain m residue 94 THR Chi-restraints excluded: chain n residue 75 ILE Chi-restraints excluded: chain q residue 11 ILE Chi-restraints excluded: chain q residue 40 ILE Chi-restraints excluded: chain q residue 42 ASP Chi-restraints excluded: chain q residue 108 SER Chi-restraints excluded: chain q residue 109 CYS Chi-restraints excluded: chain r residue 23 CYS Chi-restraints excluded: chain r residue 48 ILE Chi-restraints excluded: chain r residue 79 ASP Chi-restraints excluded: chain r residue 81 GLU Chi-restraints excluded: chain r residue 83 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 0.8980 chunk 356 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 247 optimal weight: 8.9990 chunk 373 optimal weight: 3.9990 chunk 343 optimal weight: 10.0000 chunk 297 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 229 optimal weight: 0.4980 chunk 182 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 307, in __init__ self.caller(self.nqh_flips) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 710, in nqh_flips phenix.refinement.nqh_flips.ncs_aware(model = self.model, log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/nqh_flips.py", line 12, in __init__ self.model.flip_nqh() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/model/model.py", line 698, in flip_nqh mon_lib_srv = self.get_mon_lib_srv()) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 218, in flip pdb_hierarchy = tmp_pdb_hierarchy) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 82, in get_nqh_flips output = run_reduce(pdb_string=pdb_string, remove_hydrogens=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/rotamer/nqh.py", line 143, in run_reduce check_and_report_reduce_failure(clean, pdb_string, "reduce_failure.pdb") File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/validation/clashscore.py", line 647, in check_and_report_reduce_failure f.write(input_lines) IOError: [Errno 28] No space left on device