Starting phenix.real_space_refine on Fri Mar 22 03:14:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jx7_9891/03_2024/6jx7_9891.pdb" } resolution = 3.31 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= -0.008 sd= 0.895 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 156 5.16 5 C 20265 2.51 5 N 4938 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "A PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1158": "OE1" <-> "OE2" Residue "A GLU 1161": "OE1" <-> "OE2" Residue "A GLU 1200": "OE1" <-> "OE2" Residue "A GLU 1204": "OE1" <-> "OE2" Residue "A PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1247": "OE1" <-> "OE2" Residue "A GLU 1316": "OE1" <-> "OE2" Residue "A GLU 1333": "OE1" <-> "OE2" Residue "B GLU 268": "OE1" <-> "OE2" Residue "B PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 876": "OE1" <-> "OE2" Residue "B PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1158": "OE1" <-> "OE2" Residue "B GLU 1161": "OE1" <-> "OE2" Residue "B GLU 1200": "OE1" <-> "OE2" Residue "B GLU 1204": "OE1" <-> "OE2" Residue "B PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1247": "OE1" <-> "OE2" Residue "B GLU 1316": "OE1" <-> "OE2" Residue "B GLU 1333": "OE1" <-> "OE2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C PHE 629": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C PHE 1111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1158": "OE1" <-> "OE2" Residue "C GLU 1161": "OE1" <-> "OE2" Residue "C GLU 1200": "OE1" <-> "OE2" Residue "C GLU 1204": "OE1" <-> "OE2" Residue "C PHE 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1247": "OE1" <-> "OE2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "C GLU 1333": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32115 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "B" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "C" Number of atoms: 9768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1245, 9768 Classifications: {'peptide': 1245} Link IDs: {'PTRANS': 36, 'TRANS': 1208} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 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: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" 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: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 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: 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: 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: 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: "a" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "b" 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 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: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "i" Number of atoms: 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: "j" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "k" 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: "l" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 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: "q" 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: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "t" 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: "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: 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: "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: 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: "z" 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: "0" 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: "1" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 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: "2" 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: "3" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "4" 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 148 Unusual residues: {'MAN': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.83, per 1000 atoms: 0.52 Number of scatterers: 32115 At special positions: 0 Unit cell: (180.96, 194.01, 180.09, 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 156 16.00 O 6756 8.00 N 4938 7.00 C 20265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 178 " distance=2.05 Simple disulfide: pdb=" SG CYS A 269 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 510 " distance=2.03 Simple disulfide: pdb=" SG CYS A 595 " - pdb=" SG CYS A 644 " distance=2.05 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 702 " - pdb=" SG CYS A 753 " distance=2.03 Simple disulfide: pdb=" SG CYS A 820 " - pdb=" SG CYS A 832 " distance=2.03 Simple disulfide: pdb=" SG CYS A 889 " - pdb=" SG CYS A 911 " distance=2.03 Simple disulfide: pdb=" SG CYS A 894 " - pdb=" SG CYS A 900 " distance=2.03 Simple disulfide: pdb=" SG CYS A1003 " - pdb=" SG CYS A1014 " distance=2.03 Simple disulfide: pdb=" SG CYS A1205 " - pdb=" SG CYS A1216 " distance=2.02 Simple disulfide: pdb=" SG CYS A1255 " - pdb=" SG CYS A1302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 178 " distance=2.05 Simple disulfide: pdb=" SG CYS B 269 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS B 510 " distance=2.03 Simple disulfide: pdb=" SG CYS B 595 " - pdb=" SG CYS B 644 " distance=2.05 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 702 " - pdb=" SG CYS B 753 " distance=2.03 Simple disulfide: pdb=" SG CYS B 820 " - pdb=" SG CYS B 832 " distance=2.03 Simple disulfide: pdb=" SG CYS B 889 " - pdb=" SG CYS B 911 " distance=2.03 Simple disulfide: pdb=" SG CYS B 894 " - pdb=" SG CYS B 900 " distance=2.03 Simple disulfide: pdb=" SG CYS B1003 " - pdb=" SG CYS B1014 " distance=2.03 Simple disulfide: pdb=" SG CYS B1205 " - pdb=" SG CYS B1216 " distance=2.02 Simple disulfide: pdb=" SG CYS B1255 " - pdb=" SG CYS B1302 " distance=2.03 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 178 " distance=2.05 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS C 510 " distance=2.03 Simple disulfide: pdb=" SG CYS C 595 " - pdb=" SG CYS C 644 " distance=2.05 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 702 " - pdb=" SG CYS C 753 " distance=2.03 Simple disulfide: pdb=" SG CYS C 820 " - pdb=" SG CYS C 832 " distance=2.03 Simple disulfide: pdb=" SG CYS C 889 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 894 " - pdb=" SG CYS C 900 " distance=2.03 Simple disulfide: pdb=" SG CYS C1003 " - pdb=" SG CYS C1014 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1216 " distance=2.02 Simple disulfide: pdb=" SG CYS C1255 " - pdb=" SG CYS C1302 " distance=2.03 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=3, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN I 4 " - " MAN I 5 " " MAN T 4 " - " MAN T 5 " " MAN a 4 " - " MAN a 5 " " MAN l 4 " - " MAN l 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 2 3 " - " MAN 2 4 " " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA I 3 " - " MAN I 4 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " MAN T 6 " - " MAN T 7 " " BMA a 3 " - " MAN a 4 " " BMA k 3 " - " MAN k 4 " " BMA l 3 " - " MAN l 4 " " MAN l 6 " - " MAN l 7 " " BMA s 3 " - " MAN s 4 " ALPHA1-6 " BMA 2 3 " - " MAN 2 5 " " BMA 3 3 " - " MAN 3 6 " " BMA I 3 " - " MAN I 6 " " MAN I 6 " - " MAN I 7 " " BMA J 3 " - " MAN J 4 " " BMA L 3 " - " MAN L 4 " " BMA O 3 " - " MAN O 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 6 " " BMA a 3 " - " MAN a 6 " " MAN a 6 " - " MAN a 7 " " BMA b 3 " - " MAN b 4 " " BMA d 3 " - " MAN d 4 " " BMA g 3 " - " MAN g 4 " " BMA h 3 " - " MAN h 4 " " BMA k 3 " - " MAN k 5 " " BMA l 3 " - " MAN l 6 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 7 " " BMA t 3 " - " MAN t 4 " " BMA v 3 " - " MAN v 4 " " BMA y 3 " - " MAN y 4 " " BMA z 3 " - " MAN z 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG D 1 " - " NAG D 2 " " 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " 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 Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " 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 " " NAG z 2 " - " BMA z 3 " BETA1-6 " NAG 1 1 " - " FUC 1 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG R 1 " - " FUC R 4 " " NAG j 1 " - " FUC j 4 " NAG-ASN " NAG 0 1 " - " ASN C 868 " " NAG 1 1 " - " ASN C 949 " " NAG 2 1 " - " ASN C1092 " " NAG 3 1 " - " ASN C1218 " " NAG 4 1 " - " ASN C1308 " " NAG A1508 " - " ASN A 260 " " NAG A1522 " - " ASN A 380 " " NAG A1523 " - " ASN A 464 " " NAG A1535 " - " ASN A 585 " " NAG A1536 " - " ASN A 590 " " NAG A1541 " - " ASN A 819 " " NAG A1568 " - " ASN A1257 " " NAG A1569 " - " ASN A1275 " " NAG A1572 " - " ASN A1325 " " NAG B1508 " - " ASN B 260 " " NAG B1522 " - " ASN B 380 " " NAG B1523 " - " ASN B 464 " " NAG B1535 " - " ASN B 585 " " NAG B1536 " - " ASN B 590 " " NAG B1541 " - " ASN B 819 " " NAG B1568 " - " ASN B1257 " " NAG B1569 " - " ASN B1275 " " NAG B1572 " - " ASN B1325 " " NAG C1509 " - " ASN C 260 " " NAG C1523 " - " ASN C 380 " " NAG C1524 " - " ASN C 464 " " NAG C1536 " - " ASN C 585 " " NAG C1537 " - " ASN C 590 " " NAG C1542 " - " ASN C 819 " " NAG C1569 " - " ASN C1257 " " NAG C1570 " - " ASN C1275 " " NAG C1573 " - " ASN C1325 " " NAG D 1 " - " ASN A 161 " " NAG E 1 " - " ASN A 246 " " NAG F 1 " - " ASN A 254 " " NAG G 1 " - " ASN A 331 " " NAG H 1 " - " ASN A 346 " " NAG I 1 " - " ASN A 357 " " NAG J 1 " - " ASN A 482 " " NAG K 1 " - " ASN A 491 " " NAG L 1 " - " ASN A 547 " " NAG M 1 " - " ASN A 774 " " NAG N 1 " - " ASN A 814 " " NAG O 1 " - " ASN A 841 " " NAG P 1 " - " ASN A 862 " " NAG Q 1 " - " ASN A 868 " " NAG R 1 " - " ASN A 949 " " NAG S 1 " - " ASN A1092 " " NAG T 1 " - " ASN A1218 " " NAG U 1 " - " ASN A1308 " " NAG V 1 " - " ASN B 161 " " NAG W 1 " - " ASN B 246 " " NAG X 1 " - " ASN B 254 " " NAG Y 1 " - " ASN B 331 " " NAG Z 1 " - " ASN B 346 " " NAG a 1 " - " ASN B 357 " " NAG b 1 " - " ASN B 482 " " NAG c 1 " - " ASN B 491 " " NAG d 1 " - " ASN B 547 " " NAG e 1 " - " ASN B 774 " " NAG f 1 " - " ASN B 814 " " NAG g 1 " - " ASN B 841 " " NAG h 1 " - " ASN B 862 " " NAG i 1 " - " ASN B 868 " " NAG j 1 " - " ASN B 949 " " NAG k 1 " - " ASN B1092 " " NAG l 1 " - " ASN B1218 " " NAG m 1 " - " ASN B1308 " " NAG n 1 " - " ASN C 161 " " NAG o 1 " - " ASN C 246 " " NAG p 1 " - " ASN C 254 " " NAG q 1 " - " ASN C 331 " " NAG r 1 " - " ASN C 346 " " NAG s 1 " - " ASN C 357 " " NAG t 1 " - " ASN C 482 " " NAG u 1 " - " ASN C 491 " " NAG v 1 " - " ASN C 547 " " NAG w 1 " - " ASN C 774 " " NAG x 1 " - " ASN C 814 " " NAG y 1 " - " ASN C 841 " " NAG z 1 " - " ASN C 862 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.18 Conformation dependent library (CDL) restraints added in 5.8 seconds 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7032 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 54 sheets defined 22.6% alpha, 24.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE A 74 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 77 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA A 572 " --> pdb=" O ALA A 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER A 573 " --> pdb=" O PRO A 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 574' Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR A 892 " --> pdb=" O ASP A 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 893 " --> pdb=" O CYS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU A 901 " --> pdb=" O ASN A 897 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASN A 902 " --> pdb=" O ARG A 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 897 through 902' Processing helix chain 'A' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN A 906 " --> pdb=" O LEU A 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 903 through 906' Processing helix chain 'A' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR A 913 " --> pdb=" O SER A 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 921 " --> pdb=" O SER A 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 925 " --> pdb=" O GLY A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER A 968 " --> pdb=" O ASP A 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 969 " --> pdb=" O GLY A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 1011 through 1019 removed outlier: 3.784A pdb=" N ASN A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY A1043 " --> pdb=" O SER A1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA A1045 " --> pdb=" O ILE A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A1067 " --> pdb=" O ALA A1063 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN A1079 " --> pdb=" O LEU A1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A1080 " --> pdb=" O GLN A1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY A1098 " --> pdb=" O THR A1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER A1116 " --> pdb=" O ASN A1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1117 " --> pdb=" O SER A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU A1132 " --> pdb=" O GLN A1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER A1133 " --> pdb=" O GLY A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1140 No H-bonds generated for 'chain 'A' and resid 1138 through 1140' Processing helix chain 'A' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE A1153 " --> pdb=" O SER A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP A1163 " --> pdb=" O LYS A1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA A1164 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG A1168 " --> pdb=" O ALA A1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A1169 " --> pdb=" O GLN A1165 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A1183 " --> pdb=" O ALA A1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN A1187 " --> pdb=" O GLN A1183 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A1200 " --> pdb=" O GLN A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1294 No H-bonds generated for 'chain 'A' and resid 1292 through 1294' Processing helix chain 'A' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU A1316 " --> pdb=" O THR A1312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A1317 " --> pdb=" O THR A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR A1327 " --> pdb=" O ASP A1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA A1329 " --> pdb=" O ASN A1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP A1330 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A1331 " --> pdb=" O THR A1327 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE B 74 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 513 removed outlier: 3.556A pdb=" N ILE B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU B 571 " --> pdb=" O GLY B 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA B 572 " --> pdb=" O ALA B 568 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 573 " --> pdb=" O PRO B 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 567 through 574' Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR B 892 " --> pdb=" O ASP B 888 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 893 " --> pdb=" O CYS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU B 901 " --> pdb=" O ASN B 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B 902 " --> pdb=" O ARG B 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 897 through 902' Processing helix chain 'B' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN B 906 " --> pdb=" O LEU B 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 903 through 906' Processing helix chain 'B' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR B 913 " --> pdb=" O SER B 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 914 " --> pdb=" O ALA B 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU B 915 " --> pdb=" O CYS B 911 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 921 " --> pdb=" O SER B 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU B 925 " --> pdb=" O GLY B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU B 941 " --> pdb=" O ASP B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 970 removed outlier: 4.193A pdb=" N SER B 968 " --> pdb=" O ASP B 964 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU B 969 " --> pdb=" O GLY B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY B1043 " --> pdb=" O SER B1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA B1045 " --> pdb=" O ILE B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1056 through 1067 removed outlier: 3.872A pdb=" N ASN B1066 " --> pdb=" O GLN B1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B1067 " --> pdb=" O ALA B1063 " (cutoff:3.500A) Processing helix chain 'B' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN B1079 " --> pdb=" O LEU B1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B1080 " --> pdb=" O GLN B1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS B1099 " --> pdb=" O LEU B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER B1116 " --> pdb=" O ASN B1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B1117 " --> pdb=" O SER B1113 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU B1132 " --> pdb=" O GLN B1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B1133 " --> pdb=" O GLY B1129 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1140 No H-bonds generated for 'chain 'B' and resid 1138 through 1140' Processing helix chain 'B' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE B1153 " --> pdb=" O SER B1149 " (cutoff:3.500A) Processing helix chain 'B' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP B1163 " --> pdb=" O LYS B1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA B1164 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B1165 " --> pdb=" O GLU B1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG B1168 " --> pdb=" O ALA B1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU B1169 " --> pdb=" O GLN B1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B1183 " --> pdb=" O ALA B1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN B1187 " --> pdb=" O GLN B1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU B1200 " --> pdb=" O GLN B1196 " (cutoff:3.500A) Processing helix chain 'B' and resid 1292 through 1294 No H-bonds generated for 'chain 'B' and resid 1292 through 1294' Processing helix chain 'B' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN B1315 " --> pdb=" O HIS B1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU B1316 " --> pdb=" O THR B1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B1317 " --> pdb=" O THR B1313 " (cutoff:3.500A) Processing helix chain 'B' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR B1327 " --> pdb=" O ASP B1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA B1329 " --> pdb=" O ASN B1325 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP B1330 " --> pdb=" O LYS B1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B1331 " --> pdb=" O THR B1327 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 removed outlier: 3.517A pdb=" N PHE C 74 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN C 77 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 513 removed outlier: 3.555A pdb=" N ILE C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 567 through 574 removed outlier: 3.542A pdb=" N LEU C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 572 " --> pdb=" O ALA C 568 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 573 " --> pdb=" O PRO C 569 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 574' Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 888 through 894 removed outlier: 3.669A pdb=" N TYR C 892 " --> pdb=" O ASP C 888 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 893 " --> pdb=" O CYS C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 902 removed outlier: 3.627A pdb=" N LEU C 901 " --> pdb=" O ASN C 897 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN C 902 " --> pdb=" O ARG C 898 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 897 through 902' Processing helix chain 'C' and resid 903 through 906 removed outlier: 3.724A pdb=" N GLN C 906 " --> pdb=" O LEU C 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 903 through 906' Processing helix chain 'C' and resid 907 through 930 removed outlier: 3.532A pdb=" N THR C 913 " --> pdb=" O SER C 909 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE C 914 " --> pdb=" O ALA C 910 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU C 915 " --> pdb=" O CYS C 911 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY C 921 " --> pdb=" O SER C 917 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 925 " --> pdb=" O GLY C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 941 removed outlier: 3.768A pdb=" N GLU C 941 " --> pdb=" O ASP C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 970 removed outlier: 4.194A pdb=" N SER C 968 " --> pdb=" O ASP C 964 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU C 969 " --> pdb=" O GLY C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 1011 through 1019 removed outlier: 3.783A pdb=" N ASN C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1046 removed outlier: 3.510A pdb=" N GLY C1043 " --> pdb=" O SER C1039 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C1045 " --> pdb=" O ILE C1041 " (cutoff:3.500A) Processing helix chain 'C' and resid 1056 through 1067 removed outlier: 3.873A pdb=" N ASN C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR C1067 " --> pdb=" O ALA C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1099 removed outlier: 3.833A pdb=" N GLN C1079 " --> pdb=" O LEU C1075 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C1080 " --> pdb=" O GLN C1076 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY C1098 " --> pdb=" O THR C1094 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS C1099 " --> pdb=" O LEU C1095 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1125 removed outlier: 3.625A pdb=" N SER C1116 " --> pdb=" O ASN C1112 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1117 " --> pdb=" O SER C1113 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1137 removed outlier: 4.257A pdb=" N LEU C1132 " --> pdb=" O GLN C1128 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER C1133 " --> pdb=" O GLY C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1140 No H-bonds generated for 'chain 'C' and resid 1138 through 1140' Processing helix chain 'C' and resid 1149 through 1154 removed outlier: 3.699A pdb=" N ILE C1153 " --> pdb=" O SER C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1158 through 1205 removed outlier: 3.746A pdb=" N ASP C1163 " --> pdb=" O LYS C1159 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA C1164 " --> pdb=" O VAL C1160 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C1168 " --> pdb=" O ALA C1164 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C1169 " --> pdb=" O GLN C1165 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN C1183 " --> pdb=" O ALA C1179 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN C1187 " --> pdb=" O GLN C1183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU C1200 " --> pdb=" O GLN C1196 " (cutoff:3.500A) Processing helix chain 'C' and resid 1292 through 1294 No H-bonds generated for 'chain 'C' and resid 1292 through 1294' Processing helix chain 'C' and resid 1310 through 1318 removed outlier: 3.731A pdb=" N GLN C1315 " --> pdb=" O HIS C1311 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU C1316 " --> pdb=" O THR C1312 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C1317 " --> pdb=" O THR C1313 " (cutoff:3.500A) Processing helix chain 'C' and resid 1323 through 1336 removed outlier: 3.853A pdb=" N THR C1327 " --> pdb=" O ASP C1323 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA C1329 " --> pdb=" O ASN C1325 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP C1330 " --> pdb=" O LYS C1326 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET C1331 " --> pdb=" O THR C1327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA A 227 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 107 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 124 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 151 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE A 180 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN A 199 " --> pdb=" O ASP A 206 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE A 447 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 324 removed outlier: 3.785A pdb=" N VAL A 312 " --> pdb=" O VAL A 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN A 482 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL A 320 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR A 480 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS A 322 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE A 478 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP A 485 " --> pdb=" O TYR A 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR A 500 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 487 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU A 498 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP A 489 " --> pdb=" O THR A 496 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA A 334 " --> pdb=" O PHE A 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 383 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR A 413 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 431 " --> pdb=" O TYR A 413 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N CYS A 415 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 427 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 809 " --> pdb=" O ALA A 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 771 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 807 " --> pdb=" O THR A 771 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY A 712 " --> pdb=" O TYR A 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU A 737 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS A 578 " --> pdb=" O HIS A 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL A 552 " --> pdb=" O LYS A 606 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU A 554 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 623 " --> pdb=" O SER A 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 659 " --> pdb=" O GLN A 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 621 " --> pdb=" O VAL A 659 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU A 601 " --> pdb=" O THR A 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 642 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 678 " --> pdb=" O PHE A 640 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 829 through 831 Processing sheet with id=AB4, first strand: chain 'A' and resid 843 through 844 removed outlier: 6.089A pdb=" N THR A 843 " --> pdb=" O VAL C 935 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 862 through 864 Processing sheet with id=AB6, first strand: chain 'A' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY A1232 " --> pdb=" O SER A1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER A1228 " --> pdb=" O GLY A1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A1234 " --> pdb=" O VAL A1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL A1226 " --> pdb=" O LEU A1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE A1236 " --> pdb=" O SER A1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER A1224 " --> pdb=" O PHE A1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR A1238 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 885 through 887 Processing sheet with id=AB8, first strand: chain 'A' and resid 934 through 935 Processing sheet with id=AB9, first strand: chain 'A' and resid 1296 through 1299 Processing sheet with id=AC1, first strand: chain 'A' and resid 1269 through 1273 Processing sheet with id=AC2, first strand: chain 'B' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA B 227 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG B 107 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 124 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 180 " --> pdb=" O ILE B 154 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN B 199 " --> pdb=" O ASP B 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 447 " --> pdb=" O TYR B 454 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL B 312 " --> pdb=" O VAL B 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN B 482 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL B 320 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR B 480 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS B 322 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 478 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP B 485 " --> pdb=" O TYR B 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR B 500 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET B 487 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU B 498 " --> pdb=" O MET B 487 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP B 489 " --> pdb=" O THR B 496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA B 334 " --> pdb=" O PHE B 465 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 383 " --> pdb=" O PHE B 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 386 through 387 removed outlier: 5.796A pdb=" N TYR B 413 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 431 " --> pdb=" O TYR B 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS B 415 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN B 427 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE B 770 " --> pdb=" O GLN B 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 809 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR B 771 " --> pdb=" O TYR B 807 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR B 807 " --> pdb=" O THR B 771 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 534 through 537 removed outlier: 3.504A pdb=" N GLY B 712 " --> pdb=" O TYR B 705 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N LEU B 737 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 588 through 591 removed outlier: 3.552A pdb=" N HIS B 578 " --> pdb=" O HIS B 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 552 " --> pdb=" O LYS B 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 554 " --> pdb=" O THR B 608 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN B 623 " --> pdb=" O SER B 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 659 " --> pdb=" O GLN B 621 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B 621 " --> pdb=" O VAL B 659 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU B 601 " --> pdb=" O THR B 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 642 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY B 678 " --> pdb=" O PHE B 640 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 829 through 831 Processing sheet with id=AD5, first strand: chain 'B' and resid 862 through 864 Processing sheet with id=AD6, first strand: chain 'B' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY B1232 " --> pdb=" O SER B1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER B1228 " --> pdb=" O GLY B1232 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1234 " --> pdb=" O VAL B1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B1226 " --> pdb=" O LEU B1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE B1236 " --> pdb=" O SER B1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1224 " --> pdb=" O PHE B1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR B1238 " --> pdb=" O LEU B1222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 885 through 887 Processing sheet with id=AD8, first strand: chain 'B' and resid 934 through 935 Processing sheet with id=AD9, first strand: chain 'B' and resid 1296 through 1299 Processing sheet with id=AE1, first strand: chain 'B' and resid 1269 through 1273 Processing sheet with id=AE2, first strand: chain 'C' and resid 105 through 108 removed outlier: 3.583A pdb=" N ALA C 227 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG C 107 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 124 " --> pdb=" O SER C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 151 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 180 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 214 through 216 removed outlier: 3.784A pdb=" N GLN C 199 " --> pdb=" O ASP C 206 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE C 447 " --> pdb=" O TYR C 454 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 309 through 324 removed outlier: 3.784A pdb=" N VAL C 312 " --> pdb=" O VAL C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASN C 482 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 320 " --> pdb=" O TYR C 480 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR C 480 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N CYS C 322 " --> pdb=" O ILE C 478 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE C 478 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ASP C 485 " --> pdb=" O TYR C 500 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TYR C 500 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET C 487 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LEU C 498 " --> pdb=" O MET C 487 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASP C 489 " --> pdb=" O THR C 496 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 334 through 337 removed outlier: 3.687A pdb=" N ALA C 334 " --> pdb=" O PHE C 465 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 383 " --> pdb=" O PHE C 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 386 through 387 removed outlier: 5.797A pdb=" N TYR C 413 " --> pdb=" O ILE C 431 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE C 431 " --> pdb=" O TYR C 413 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N CYS C 415 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN C 427 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 520 through 524 removed outlier: 3.585A pdb=" N ILE C 770 " --> pdb=" O GLN C 758 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 809 " --> pdb=" O ALA C 769 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 771 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 807 " --> pdb=" O THR C 771 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 534 through 537 removed outlier: 3.503A pdb=" N GLY C 712 " --> pdb=" O TYR C 705 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 737 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 588 through 591 removed outlier: 3.553A pdb=" N HIS C 578 " --> pdb=" O HIS C 551 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 552 " --> pdb=" O LYS C 606 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 554 " --> pdb=" O THR C 608 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C 623 " --> pdb=" O SER C 657 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 659 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 621 " --> pdb=" O VAL C 659 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 600 through 601 removed outlier: 3.754A pdb=" N LEU C 601 " --> pdb=" O THR C 682 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR C 642 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 678 " --> pdb=" O PHE C 640 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 829 through 831 Processing sheet with id=AF5, first strand: chain 'C' and resid 862 through 864 Processing sheet with id=AF6, first strand: chain 'C' and resid 869 through 878 removed outlier: 7.196A pdb=" N GLY C1232 " --> pdb=" O SER C1228 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N SER C1228 " --> pdb=" O GLY C1232 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU C1234 " --> pdb=" O VAL C1226 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL C1226 " --> pdb=" O LEU C1234 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE C1236 " --> pdb=" O SER C1224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER C1224 " --> pdb=" O PHE C1236 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C1238 " --> pdb=" O LEU C1222 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 885 through 887 Processing sheet with id=AF8, first strand: chain 'C' and resid 1296 through 1299 Processing sheet with id=AF9, first strand: chain 'C' and resid 1269 through 1273 875 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.55 Time building geometry restraints manager: 17.19 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: 9685 1.34 - 1.47: 9241 1.47 - 1.60: 13642 1.60 - 1.73: 0 1.73 - 1.86: 222 Bond restraints: 32790 Sorted by residual: bond pdb=" C3 NAG 3 1 " pdb=" C4 NAG 3 1 " ideal model delta sigma weight residual 1.524 1.455 0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG l 1 " pdb=" C4 NAG l 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " ideal model delta sigma weight residual 1.524 1.456 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" N LYS B 85 " pdb=" CA LYS B 85 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.13e+00 bond pdb=" N TYR B 253 " pdb=" CA TYR B 253 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.31e-02 5.83e+03 9.08e+00 ... (remaining 32785 not shown) Histogram of bond angle deviations from ideal: 94.43 - 102.38: 126 102.38 - 110.32: 10180 110.32 - 118.27: 16119 118.27 - 126.21: 17855 126.21 - 134.16: 423 Bond angle restraints: 44703 Sorted by residual: angle pdb=" C GLN C 775 " pdb=" N THR C 776 " pdb=" CA THR C 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.49e+01 angle pdb=" C GLN A 775 " pdb=" N THR A 776 " pdb=" CA THR A 776 " ideal model delta sigma weight residual 120.87 110.35 10.52 1.42e+00 4.96e-01 5.48e+01 angle pdb=" C GLN B 775 " pdb=" N THR B 776 " pdb=" CA THR B 776 " ideal model delta sigma weight residual 120.87 110.37 10.50 1.42e+00 4.96e-01 5.47e+01 angle pdb=" C ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta sigma weight residual 110.42 95.72 14.70 1.99e+00 2.53e-01 5.45e+01 angle pdb=" C ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta sigma weight residual 110.42 95.73 14.69 1.99e+00 2.53e-01 5.45e+01 ... (remaining 44698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 20360 23.84 - 47.67: 1138 47.67 - 71.51: 237 71.51 - 95.34: 198 95.34 - 119.18: 105 Dihedral angle restraints: 22038 sinusoidal: 11079 harmonic: 10959 Sorted by residual: dihedral pdb=" C ASN A 774 " pdb=" N ASN A 774 " pdb=" CA ASN A 774 " pdb=" CB ASN A 774 " ideal model delta harmonic sigma weight residual -122.60 -99.83 -22.77 0 2.50e+00 1.60e-01 8.30e+01 dihedral pdb=" C ASN C 774 " pdb=" N ASN C 774 " pdb=" CA ASN C 774 " pdb=" CB ASN C 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 dihedral pdb=" C ASN B 774 " pdb=" N ASN B 774 " pdb=" CA ASN B 774 " pdb=" CB ASN B 774 " ideal model delta harmonic sigma weight residual -122.60 -99.84 -22.76 0 2.50e+00 1.60e-01 8.29e+01 ... (remaining 22035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 5703 0.310 - 0.619: 56 0.619 - 0.929: 13 0.929 - 1.239: 3 1.239 - 1.548: 3 Chirality restraints: 5778 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN l 6 " pdb=" O6 BMA l 3 " pdb=" C2 MAN l 6 " pdb=" O5 MAN l 6 " both_signs ideal model delta sigma weight residual False 2.40 0.85 1.55 2.00e-02 2.50e+03 5.99e+03 chirality pdb=" C1 MAN 3 6 " pdb=" O6 BMA 3 3 " pdb=" C2 MAN 3 6 " pdb=" O5 MAN 3 6 " both_signs ideal model delta sigma weight residual False 2.40 0.86 1.54 2.00e-02 2.50e+03 5.95e+03 ... (remaining 5775 not shown) Planarity restraints: 5457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG M 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG e 2 " -0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG e 2 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG e 2 " -0.161 2.00e-02 2.50e+03 pdb=" N2 NAG e 2 " 0.529 2.00e-02 2.50e+03 pdb=" O7 NAG e 2 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG w 2 " 0.352 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" C7 NAG w 2 " -0.087 2.00e-02 2.50e+03 pdb=" C8 NAG w 2 " 0.161 2.00e-02 2.50e+03 pdb=" N2 NAG w 2 " -0.529 2.00e-02 2.50e+03 pdb=" O7 NAG w 2 " 0.104 2.00e-02 2.50e+03 ... (remaining 5454 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 847 2.65 - 3.21: 29237 3.21 - 3.78: 49006 3.78 - 4.34: 62037 4.34 - 4.90: 100985 Nonbonded interactions: 242112 Sorted by model distance: nonbonded pdb=" O3 NAG M 1 " pdb=" O7 NAG M 1 " model vdw 2.092 2.440 nonbonded pdb=" O3 NAG w 1 " pdb=" O7 NAG w 1 " model vdw 2.092 2.440 nonbonded pdb=" O3 NAG e 1 " pdb=" O7 NAG e 1 " model vdw 2.092 2.440 nonbonded pdb=" OD1 ASN B 254 " pdb=" OG1 THR B 256 " model vdw 2.172 2.440 nonbonded pdb=" OD1 ASN C 254 " pdb=" OG1 THR C 256 " model vdw 2.173 2.440 ... (remaining 242107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain 'D' selection = chain 'F' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'u' selection = chain 'w' selection = chain 'x' } ncs_group { reference = (chain '1' and resid 1 through 3) selection = (chain 'J' and resid 1 through 3) selection = (chain 'L' and resid 1 through 3) selection = (chain 'O' and resid 1 through 3) selection = (chain 'P' and resid 1 through 3) selection = (chain 'R' and resid 1 through 3) selection = (chain 'b' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) selection = (chain 'h' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) selection = (chain 'v' and resid 1 through 3) selection = (chain 'y' and resid 1 through 3) selection = (chain 'z' and resid 1 through 3) } ncs_group { reference = chain '2' selection = chain 'S' selection = chain 'k' } ncs_group { reference = chain '3' selection = chain 'I' selection = chain 'T' selection = chain 'a' selection = chain 'l' selection = chain 's' } ncs_group { reference = (chain 'A' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'B' and (resid 62 through 1337 or resid 1522 through 1523 or resid 1536 t \ hrough 1572)) selection = (chain 'C' and (resid 62 through 1337 or resid 1509 through 1523 or resid 1536 t \ hrough 1570)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'o' selection = chain 'q' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 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: 0.020 Extract box with map and model: 20.810 Check model and map are aligned: 0.600 Set scattering table: 0.300 Process input model: 89.230 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.650 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: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 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 : 0.010 0.072 32790 Z= 0.607 Angle : 1.263 16.774 44703 Z= 0.604 Chirality : 0.098 1.548 5778 Planarity : 0.020 0.299 5376 Dihedral : 19.253 119.180 14880 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 12.32 % Favored : 87.36 % Rotamer: Outliers : 0.82 % Allowed : 9.10 % Favored : 90.07 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -5.20 (0.10), residues: 3717 helix: -3.94 (0.08), residues: 729 sheet: -2.68 (0.16), residues: 906 loop : -3.75 (0.10), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 200 HIS 0.010 0.002 HIS B 374 PHE 0.016 0.002 PHE C 629 TYR 0.035 0.002 TYR B 826 ARG 0.005 0.001 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 782 time to evaluate : 3.604 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: A 158 ASN cc_start: 0.2529 (OUTLIER) cc_final: 0.2141 (m-40) REVERT: A 309 GLN cc_start: 0.8763 (mt0) cc_final: 0.8439 (tt0) REVERT: A 341 ASP cc_start: 0.8068 (p0) cc_final: 0.6874 (p0) REVERT: A 444 ASP cc_start: 0.7505 (p0) cc_final: 0.7256 (p0) REVERT: A 461 LYS cc_start: 0.8293 (tttt) cc_final: 0.8088 (tttm) REVERT: A 477 THR cc_start: 0.7415 (p) cc_final: 0.7141 (p) REVERT: A 592 THR cc_start: 0.8005 (p) cc_final: 0.7754 (t) REVERT: A 597 GLN cc_start: 0.8432 (mt0) cc_final: 0.8203 (mt0) REVERT: A 611 GLN cc_start: 0.8094 (pt0) cc_final: 0.7736 (pt0) REVERT: A 641 GLU cc_start: 0.7851 (tp30) cc_final: 0.7553 (tp30) REVERT: A 680 MET cc_start: 0.7596 (mmt) cc_final: 0.7081 (mtp) REVERT: A 701 GLU cc_start: 0.7856 (pt0) cc_final: 0.7290 (pm20) REVERT: A 702 CYS cc_start: 0.6646 (m) cc_final: 0.6374 (m) REVERT: A 803 MET cc_start: 0.8738 (mmm) cc_final: 0.8416 (mmm) REVERT: A 812 TRP cc_start: 0.7001 (p-90) cc_final: 0.6465 (p-90) REVERT: A 824 ILE cc_start: 0.8488 (mm) cc_final: 0.8214 (tp) REVERT: A 898 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7527 (ttp80) REVERT: A 928 MET cc_start: 0.7900 (tpp) cc_final: 0.7539 (tpp) REVERT: A 973 ARG cc_start: 0.6400 (mtt180) cc_final: 0.6131 (mtp85) REVERT: A 1059 MET cc_start: 0.8265 (ttm) cc_final: 0.7887 (ttm) REVERT: A 1067 TYR cc_start: 0.8552 (m-80) cc_final: 0.8339 (m-10) REVERT: A 1076 GLN cc_start: 0.7390 (mm-40) cc_final: 0.6770 (tp40) REVERT: A 1141 LYS cc_start: 0.8210 (mttt) cc_final: 0.7915 (mtpt) REVERT: A 1152 GLU cc_start: 0.7675 (tp30) cc_final: 0.7269 (tp30) REVERT: A 1155 ASN cc_start: 0.8715 (m-40) cc_final: 0.8213 (m-40) REVERT: A 1159 LYS cc_start: 0.8380 (tttt) cc_final: 0.8097 (ttmt) REVERT: A 1260 TYR cc_start: 0.7422 (m-80) cc_final: 0.7068 (m-10) REVERT: A 1279 MET cc_start: 0.7451 (mmm) cc_final: 0.7236 (mmt) REVERT: A 1315 GLN cc_start: 0.7542 (mp10) cc_final: 0.7175 (tm-30) REVERT: A 1331 MET cc_start: 0.6853 (mpp) cc_final: 0.6578 (tmm) REVERT: B 158 ASN cc_start: 0.2839 (OUTLIER) cc_final: 0.2425 (m-40) REVERT: B 293 PHE cc_start: 0.8759 (t80) cc_final: 0.8264 (t80) REVERT: B 309 GLN cc_start: 0.8728 (mt0) cc_final: 0.8528 (tt0) REVERT: B 592 THR cc_start: 0.8093 (p) cc_final: 0.7829 (t) REVERT: B 611 GLN cc_start: 0.8083 (pt0) cc_final: 0.7700 (pt0) REVERT: B 633 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7982 (mm-40) REVERT: B 680 MET cc_start: 0.7803 (mmt) cc_final: 0.7285 (mtp) REVERT: B 701 GLU cc_start: 0.7783 (pt0) cc_final: 0.7215 (pm20) REVERT: B 702 CYS cc_start: 0.6816 (m) cc_final: 0.6448 (m) REVERT: B 803 MET cc_start: 0.8706 (mmm) cc_final: 0.8296 (mmm) REVERT: B 824 ILE cc_start: 0.8461 (mm) cc_final: 0.8088 (tp) REVERT: B 883 LYS cc_start: 0.8646 (mttm) cc_final: 0.8343 (mttm) REVERT: B 928 MET cc_start: 0.7869 (tpp) cc_final: 0.7572 (tpp) REVERT: B 973 ARG cc_start: 0.6383 (mtt180) cc_final: 0.6060 (mtp85) REVERT: B 1011 ASP cc_start: 0.6372 (t0) cc_final: 0.6049 (t0) REVERT: B 1059 MET cc_start: 0.8184 (ttm) cc_final: 0.7757 (ttm) REVERT: B 1076 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6633 (tp-100) REVERT: B 1155 ASN cc_start: 0.8718 (m-40) cc_final: 0.8149 (m-40) REVERT: B 1159 LYS cc_start: 0.8310 (tttt) cc_final: 0.8108 (mttt) REVERT: B 1161 GLU cc_start: 0.6639 (pm20) cc_final: 0.6404 (pm20) REVERT: B 1283 ARG cc_start: 0.8152 (mtt90) cc_final: 0.7366 (mtm-85) REVERT: B 1307 LEU cc_start: 0.8270 (tp) cc_final: 0.8051 (tt) REVERT: B 1315 GLN cc_start: 0.7678 (mp10) cc_final: 0.7205 (tm-30) REVERT: B 1319 ILE cc_start: 0.7309 (tt) cc_final: 0.7093 (pt) REVERT: C 158 ASN cc_start: 0.2821 (OUTLIER) cc_final: 0.2430 (m110) REVERT: C 364 TYR cc_start: 0.8266 (m-10) cc_final: 0.7894 (m-80) REVERT: C 444 ASP cc_start: 0.7428 (p0) cc_final: 0.7159 (p0) REVERT: C 455 PHE cc_start: 0.8290 (p90) cc_final: 0.8079 (p90) REVERT: C 571 LEU cc_start: 0.7110 (mp) cc_final: 0.6868 (mp) REVERT: C 592 THR cc_start: 0.8001 (p) cc_final: 0.7757 (t) REVERT: C 611 GLN cc_start: 0.8069 (pt0) cc_final: 0.7689 (pt0) REVERT: C 623 GLN cc_start: 0.7844 (mt0) cc_final: 0.7420 (mt0) REVERT: C 641 GLU cc_start: 0.7724 (tp30) cc_final: 0.7497 (tp30) REVERT: C 668 PHE cc_start: 0.8064 (m-10) cc_final: 0.7851 (m-10) REVERT: C 680 MET cc_start: 0.7682 (mmt) cc_final: 0.7092 (mtp) REVERT: C 701 GLU cc_start: 0.7746 (pt0) cc_final: 0.7253 (pm20) REVERT: C 702 CYS cc_start: 0.6689 (m) cc_final: 0.6211 (m) REVERT: C 803 MET cc_start: 0.8612 (mmm) cc_final: 0.8118 (mmm) REVERT: C 883 LYS cc_start: 0.8569 (mttm) cc_final: 0.8248 (mttm) REVERT: C 898 ARG cc_start: 0.7739 (ttp80) cc_final: 0.6941 (tpp80) REVERT: C 902 ASN cc_start: 0.8529 (m-40) cc_final: 0.8312 (m-40) REVERT: C 928 MET cc_start: 0.7867 (tpp) cc_final: 0.7597 (tpp) REVERT: C 973 ARG cc_start: 0.6274 (mtt180) cc_final: 0.6033 (mtp85) REVERT: C 1059 MET cc_start: 0.8118 (ttm) cc_final: 0.7787 (ttm) REVERT: C 1076 GLN cc_start: 0.7237 (mm-40) cc_final: 0.6628 (tp40) REVERT: C 1084 ASN cc_start: 0.8592 (m-40) cc_final: 0.8372 (m-40) REVERT: C 1141 LYS cc_start: 0.8132 (mttt) cc_final: 0.7908 (mtmt) REVERT: C 1155 ASN cc_start: 0.8664 (m-40) cc_final: 0.7419 (t0) REVERT: C 1159 LYS cc_start: 0.8312 (tttt) cc_final: 0.7922 (tttt) REVERT: C 1283 ARG cc_start: 0.8214 (mtt90) cc_final: 0.7049 (mtm-85) REVERT: C 1293 MET cc_start: 0.8211 (pmm) cc_final: 0.7989 (tpp) REVERT: C 1307 LEU cc_start: 0.8390 (tp) cc_final: 0.8176 (tt) REVERT: C 1315 GLN cc_start: 0.7586 (mp10) cc_final: 0.7178 (tm-30) REVERT: C 1331 MET cc_start: 0.6848 (mpp) cc_final: 0.6423 (tpt) outliers start: 27 outliers final: 9 residues processed: 807 average time/residue: 0.4323 time to fit residues: 568.3372 Evaluate side-chains 558 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 546 time to evaluate : 3.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 537 VAL Chi-restraints excluded: chain A residue 595 CYS Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 595 CYS Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 595 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 0.9980 chunk 281 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 190 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 291 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 217 optimal weight: 0.8980 chunk 337 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 92 GLN A 93 ASN A 95 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN A 220 ASN A 372 GLN A 411 ASN A 418 ASN ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 660 HIS A 667 GLN A 763 ASN A 906 GLN A1066 ASN A1122 GLN A1126 ASN A1311 HIS B 83 ASN B 92 GLN B 93 ASN B 95 ASN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 HIS B 177 GLN B 220 ASN B 372 GLN B 411 ASN B 418 ASN B 450 ASN B 458 GLN B 551 HIS ** B 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 660 HIS B 667 GLN B 763 ASN B1066 ASN B1122 GLN B1126 ASN ** B1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN C 83 ASN C 92 GLN C 93 ASN C 95 ASN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 156 HIS C 177 GLN C 220 ASN C 372 GLN C 411 ASN C 418 ASN ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 623 GLN C 624 ASN C 660 HIS C 667 GLN C 758 GLN C 763 ASN C 986 ASN C1066 ASN C1122 GLN C1126 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32790 Z= 0.209 Angle : 0.808 10.464 44703 Z= 0.383 Chirality : 0.053 0.450 5778 Planarity : 0.004 0.051 5376 Dihedral : 15.540 101.184 8457 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.49 % Favored : 88.43 % Rotamer: Outliers : 3.02 % Allowed : 15.28 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.33 % 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: -4.01 (0.12), residues: 3717 helix: -1.41 (0.16), residues: 759 sheet: -2.34 (0.16), residues: 864 loop : -3.42 (0.11), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 812 HIS 0.007 0.001 HIS C 156 PHE 0.027 0.001 PHE C 428 TYR 0.025 0.001 TYR A 204 ARG 0.005 0.000 ARG A1283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 664 time to evaluate : 3.550 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: A 115 TRP cc_start: 0.6855 (p-90) cc_final: 0.6487 (p-90) REVERT: A 286 ASP cc_start: 0.8582 (t0) cc_final: 0.8378 (t0) REVERT: A 309 GLN cc_start: 0.8693 (mt0) cc_final: 0.8405 (tt0) REVERT: A 461 LYS cc_start: 0.8336 (tttt) cc_final: 0.7993 (tttm) REVERT: A 471 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6944 (tp30) REVERT: A 592 THR cc_start: 0.7846 (p) cc_final: 0.7572 (t) REVERT: A 595 CYS cc_start: 0.5852 (t) cc_final: 0.5579 (t) REVERT: A 641 GLU cc_start: 0.7741 (tp30) cc_final: 0.7256 (tp30) REVERT: A 680 MET cc_start: 0.7545 (mmt) cc_final: 0.6989 (mtp) REVERT: A 702 CYS cc_start: 0.6473 (m) cc_final: 0.6220 (m) REVERT: A 803 MET cc_start: 0.8492 (mmm) cc_final: 0.8047 (mmm) REVERT: A 824 ILE cc_start: 0.8417 (mm) cc_final: 0.8128 (tp) REVERT: A 829 PHE cc_start: 0.7082 (m-80) cc_final: 0.6468 (p90) REVERT: A 883 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8527 (mmtp) REVERT: A 898 ARG cc_start: 0.7676 (ttp80) cc_final: 0.7020 (tpp80) REVERT: A 973 ARG cc_start: 0.6424 (mtt180) cc_final: 0.6072 (mtp85) REVERT: A 1033 MET cc_start: 0.8331 (tpp) cc_final: 0.8117 (mmm) REVERT: A 1059 MET cc_start: 0.8168 (ttm) cc_final: 0.7860 (ttm) REVERT: A 1141 LYS cc_start: 0.8349 (mttt) cc_final: 0.7947 (mtpt) REVERT: A 1155 ASN cc_start: 0.8552 (m-40) cc_final: 0.7254 (t0) REVERT: A 1279 MET cc_start: 0.7321 (mmm) cc_final: 0.7069 (mmt) REVERT: B 286 ASP cc_start: 0.8654 (t0) cc_final: 0.8395 (t0) REVERT: B 293 PHE cc_start: 0.8776 (t80) cc_final: 0.8403 (t80) REVERT: B 455 PHE cc_start: 0.8047 (p90) cc_final: 0.7719 (p90) REVERT: B 595 CYS cc_start: 0.5699 (t) cc_final: 0.5406 (t) REVERT: B 633 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7593 (mm-40) REVERT: B 641 GLU cc_start: 0.7757 (tp30) cc_final: 0.6846 (tp30) REVERT: B 680 MET cc_start: 0.7684 (mmt) cc_final: 0.7063 (mtp) REVERT: B 701 GLU cc_start: 0.7630 (pt0) cc_final: 0.7121 (pm20) REVERT: B 702 CYS cc_start: 0.6547 (m) cc_final: 0.6158 (m) REVERT: B 775 GLN cc_start: 0.8378 (pm20) cc_final: 0.8143 (pm20) REVERT: B 797 THR cc_start: 0.7608 (p) cc_final: 0.7383 (t) REVERT: B 803 MET cc_start: 0.8479 (mmm) cc_final: 0.7845 (mmm) REVERT: B 805 GLN cc_start: 0.7828 (mt0) cc_final: 0.7621 (mp10) REVERT: B 824 ILE cc_start: 0.8478 (mm) cc_final: 0.8053 (tp) REVERT: B 829 PHE cc_start: 0.7090 (m-80) cc_final: 0.6557 (p90) REVERT: B 883 LYS cc_start: 0.8747 (mttm) cc_final: 0.8502 (mmtp) REVERT: B 898 ARG cc_start: 0.7626 (ttp80) cc_final: 0.6850 (tpp80) REVERT: B 928 MET cc_start: 0.7926 (tpp) cc_final: 0.7377 (tpp) REVERT: B 973 ARG cc_start: 0.6481 (mtt180) cc_final: 0.6152 (mtp85) REVERT: B 1029 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: B 1059 MET cc_start: 0.8029 (ttm) cc_final: 0.7670 (ttm) REVERT: B 1066 ASN cc_start: 0.8519 (m110) cc_final: 0.8042 (m110) REVERT: B 1155 ASN cc_start: 0.8366 (m-40) cc_final: 0.7279 (t0) REVERT: B 1283 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7462 (mtm-85) REVERT: B 1307 LEU cc_start: 0.7785 (tp) cc_final: 0.7575 (tt) REVERT: B 1321 TYR cc_start: 0.8182 (t80) cc_final: 0.7894 (t80) REVERT: C 198 PHE cc_start: 0.8031 (m-10) cc_final: 0.7679 (m-10) REVERT: C 286 ASP cc_start: 0.8538 (t0) cc_final: 0.8259 (t0) REVERT: C 455 PHE cc_start: 0.8000 (p90) cc_final: 0.7764 (p90) REVERT: C 571 LEU cc_start: 0.7151 (mp) cc_final: 0.6944 (mp) REVERT: C 595 CYS cc_start: 0.5796 (t) cc_final: 0.5545 (t) REVERT: C 623 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7442 (mt0) REVERT: C 680 MET cc_start: 0.7647 (mmt) cc_final: 0.7069 (mtp) REVERT: C 702 CYS cc_start: 0.6474 (m) cc_final: 0.6023 (m) REVERT: C 803 MET cc_start: 0.8450 (mmm) cc_final: 0.7813 (mmm) REVERT: C 805 GLN cc_start: 0.7922 (mt0) cc_final: 0.7503 (mp10) REVERT: C 829 PHE cc_start: 0.7148 (m-80) cc_final: 0.6445 (p90) REVERT: C 883 LYS cc_start: 0.8850 (mttm) cc_final: 0.8519 (mmtp) REVERT: C 898 ARG cc_start: 0.7718 (ttp80) cc_final: 0.6891 (tpp80) REVERT: C 928 MET cc_start: 0.7925 (tpp) cc_final: 0.7392 (tpp) REVERT: C 973 ARG cc_start: 0.6401 (mtt180) cc_final: 0.6059 (mtp85) REVERT: C 1000 TYR cc_start: 0.7927 (m-80) cc_final: 0.7495 (m-80) REVERT: C 1059 MET cc_start: 0.8086 (ttm) cc_final: 0.7855 (ttm) REVERT: C 1066 ASN cc_start: 0.8453 (m110) cc_final: 0.7840 (m110) REVERT: C 1076 GLN cc_start: 0.7106 (mm-40) cc_final: 0.6464 (tp40) REVERT: C 1130 GLU cc_start: 0.7531 (mp0) cc_final: 0.7186 (mp0) REVERT: C 1141 LYS cc_start: 0.8243 (mttt) cc_final: 0.7911 (mtmt) REVERT: C 1152 GLU cc_start: 0.7681 (tp30) cc_final: 0.6888 (tp30) REVERT: C 1155 ASN cc_start: 0.8479 (m-40) cc_final: 0.7293 (t0) REVERT: C 1279 MET cc_start: 0.7428 (mmt) cc_final: 0.7178 (mmt) REVERT: C 1307 LEU cc_start: 0.7819 (tp) cc_final: 0.7542 (tt) REVERT: C 1331 MET cc_start: 0.6511 (mpp) cc_final: 0.5974 (tpt) outliers start: 99 outliers final: 55 residues processed: 732 average time/residue: 0.4153 time to fit residues: 509.1960 Evaluate side-chains 621 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 564 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 346 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 964 ASP Chi-restraints excluded: chain A residue 974 VAL Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1167 ASP Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1238 THR Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 346 ASN Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 450 ASN Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1238 THR Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 346 ASN Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 0.0010 chunk 281 optimal weight: 7.9990 chunk 230 optimal weight: 0.3980 chunk 93 optimal weight: 7.9990 chunk 338 optimal weight: 4.9990 chunk 365 optimal weight: 5.9990 chunk 301 optimal weight: 0.5980 chunk 335 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN A1078 ASN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 623 GLN B 758 GLN B 906 GLN B1078 ASN B1227 ASN C 83 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 583 GLN C 623 GLN C 906 GLN C 986 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32790 Z= 0.250 Angle : 0.747 9.700 44703 Z= 0.357 Chirality : 0.051 0.367 5778 Planarity : 0.004 0.042 5376 Dihedral : 12.711 94.064 8452 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.64 % Favored : 87.27 % Rotamer: Outliers : 4.77 % Allowed : 17.26 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.17 % 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: -3.47 (0.12), residues: 3717 helix: -0.27 (0.18), residues: 762 sheet: -2.12 (0.16), residues: 921 loop : -3.34 (0.11), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 812 HIS 0.005 0.001 HIS A 156 PHE 0.039 0.001 PHE A 104 TYR 0.023 0.001 TYR A 204 ARG 0.009 0.000 ARG B 977 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 582 time to evaluate : 3.814 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: A 115 TRP cc_start: 0.6798 (p-90) cc_final: 0.6564 (p-90) REVERT: A 286 ASP cc_start: 0.8605 (t70) cc_final: 0.8153 (t0) REVERT: A 309 GLN cc_start: 0.8806 (mt0) cc_final: 0.8549 (tt0) REVERT: A 372 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: A 461 LYS cc_start: 0.8458 (tttt) cc_final: 0.8116 (tttm) REVERT: A 477 THR cc_start: 0.7265 (OUTLIER) cc_final: 0.6907 (p) REVERT: A 592 THR cc_start: 0.7826 (p) cc_final: 0.7533 (t) REVERT: A 597 GLN cc_start: 0.8416 (mt0) cc_final: 0.8133 (mt0) REVERT: A 641 GLU cc_start: 0.7740 (tp30) cc_final: 0.7145 (tp30) REVERT: A 680 MET cc_start: 0.7570 (mmt) cc_final: 0.6955 (mtp) REVERT: A 701 GLU cc_start: 0.7719 (pt0) cc_final: 0.7192 (pm20) REVERT: A 702 CYS cc_start: 0.6449 (m) cc_final: 0.6223 (m) REVERT: A 824 ILE cc_start: 0.8360 (mm) cc_final: 0.8076 (tp) REVERT: A 829 PHE cc_start: 0.7284 (m-80) cc_final: 0.6626 (p90) REVERT: A 883 LYS cc_start: 0.8765 (mmtp) cc_final: 0.8508 (mmtp) REVERT: A 898 ARG cc_start: 0.7732 (ttp80) cc_final: 0.6969 (tpp80) REVERT: A 925 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8033 (tt0) REVERT: A 928 MET cc_start: 0.8126 (tpt) cc_final: 0.7723 (tpt) REVERT: A 973 ARG cc_start: 0.6310 (mtt180) cc_final: 0.6044 (mtp85) REVERT: A 1033 MET cc_start: 0.8263 (tpp) cc_final: 0.8018 (mmm) REVERT: A 1059 MET cc_start: 0.8155 (ttm) cc_final: 0.7841 (ttm) REVERT: A 1076 GLN cc_start: 0.7778 (mp10) cc_final: 0.6781 (tp40) REVERT: A 1141 LYS cc_start: 0.8413 (mttt) cc_final: 0.7907 (mtpt) REVERT: A 1155 ASN cc_start: 0.8523 (m-40) cc_final: 0.7055 (t0) REVERT: A 1279 MET cc_start: 0.7204 (mmm) cc_final: 0.6996 (mmt) REVERT: B 286 ASP cc_start: 0.8702 (t70) cc_final: 0.8142 (t0) REVERT: B 293 PHE cc_start: 0.8798 (t80) cc_final: 0.8456 (t80) REVERT: B 597 GLN cc_start: 0.8282 (mt0) cc_final: 0.7669 (tp40) REVERT: B 603 LEU cc_start: 0.8507 (tp) cc_final: 0.8204 (tp) REVERT: B 633 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7576 (mm-40) REVERT: B 680 MET cc_start: 0.7772 (mmt) cc_final: 0.7213 (mtp) REVERT: B 701 GLU cc_start: 0.7667 (pt0) cc_final: 0.7148 (pm20) REVERT: B 702 CYS cc_start: 0.6562 (m) cc_final: 0.6176 (m) REVERT: B 797 THR cc_start: 0.7525 (p) cc_final: 0.7305 (t) REVERT: B 824 ILE cc_start: 0.8358 (mm) cc_final: 0.8091 (tp) REVERT: B 829 PHE cc_start: 0.7180 (m-80) cc_final: 0.6678 (p90) REVERT: B 883 LYS cc_start: 0.8743 (mttm) cc_final: 0.8506 (mmtp) REVERT: B 898 ARG cc_start: 0.7646 (ttp80) cc_final: 0.6880 (tpp80) REVERT: B 928 MET cc_start: 0.7925 (tpp) cc_final: 0.7352 (tpp) REVERT: B 973 ARG cc_start: 0.6476 (mtt180) cc_final: 0.6210 (mtp85) REVERT: B 1059 MET cc_start: 0.7980 (ttm) cc_final: 0.7603 (ttm) REVERT: B 1066 ASN cc_start: 0.8548 (m110) cc_final: 0.8047 (m110) REVERT: B 1076 GLN cc_start: 0.7860 (mp10) cc_final: 0.6902 (tp-100) REVERT: B 1155 ASN cc_start: 0.8344 (m-40) cc_final: 0.7249 (t0) REVERT: B 1283 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7413 (mtm-85) REVERT: C 286 ASP cc_start: 0.8669 (t70) cc_final: 0.8030 (t0) REVERT: C 372 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: C 455 PHE cc_start: 0.7958 (p90) cc_final: 0.7728 (p90) REVERT: C 570 GLU cc_start: 0.7175 (mp0) cc_final: 0.6952 (mp0) REVERT: C 664 TRP cc_start: 0.6548 (m-10) cc_final: 0.6187 (m100) REVERT: C 680 MET cc_start: 0.7594 (mmt) cc_final: 0.7060 (mtp) REVERT: C 702 CYS cc_start: 0.6399 (m) cc_final: 0.5963 (m) REVERT: C 803 MET cc_start: 0.8383 (mmm) cc_final: 0.7679 (mmm) REVERT: C 805 GLN cc_start: 0.7977 (mt0) cc_final: 0.7553 (mp10) REVERT: C 829 PHE cc_start: 0.7221 (m-80) cc_final: 0.6491 (p90) REVERT: C 883 LYS cc_start: 0.8839 (mttm) cc_final: 0.8494 (mmtp) REVERT: C 898 ARG cc_start: 0.7632 (ttp80) cc_final: 0.6912 (tpp80) REVERT: C 928 MET cc_start: 0.7954 (tpp) cc_final: 0.7384 (tpp) REVERT: C 938 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7634 (tpm-80) REVERT: C 973 ARG cc_start: 0.6378 (mtt180) cc_final: 0.6078 (mtp85) REVERT: C 1000 TYR cc_start: 0.7993 (m-80) cc_final: 0.7660 (m-80) REVERT: C 1059 MET cc_start: 0.8065 (ttm) cc_final: 0.7854 (ttm) REVERT: C 1130 GLU cc_start: 0.7625 (mp0) cc_final: 0.7338 (mp0) REVERT: C 1141 LYS cc_start: 0.8263 (mttt) cc_final: 0.7793 (mtmt) REVERT: C 1152 GLU cc_start: 0.7668 (tp30) cc_final: 0.6790 (tp30) REVERT: C 1155 ASN cc_start: 0.8488 (m-40) cc_final: 0.7276 (t0) REVERT: C 1279 MET cc_start: 0.7390 (mmt) cc_final: 0.7165 (mmt) REVERT: C 1283 ARG cc_start: 0.8052 (mtt90) cc_final: 0.6844 (mtm-85) outliers start: 156 outliers final: 112 residues processed: 682 average time/residue: 0.3813 time to fit residues: 435.0959 Evaluate side-chains 667 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 551 time to evaluate : 3.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1078 ASN Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 593 SER Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 476 TRP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 938 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1029 ASP Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 8.9990 chunk 254 optimal weight: 9.9990 chunk 175 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 161 optimal weight: 0.8980 chunk 227 optimal weight: 7.9990 chunk 339 optimal weight: 0.9990 chunk 359 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 321 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 109 HIS ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 623 GLN A 906 GLN A1078 ASN B 109 HIS ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 906 GLN C 109 HIS ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS C 986 ASN ** C1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 32790 Z= 0.177 Angle : 0.697 9.609 44703 Z= 0.335 Chirality : 0.050 0.376 5778 Planarity : 0.003 0.039 5376 Dihedral : 10.958 87.761 8445 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.27 % Favored : 88.65 % Rotamer: Outliers : 4.22 % Allowed : 18.61 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.11 (0.13), residues: 3717 helix: 0.27 (0.19), residues: 756 sheet: -1.94 (0.17), residues: 906 loop : -3.18 (0.12), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 222 HIS 0.005 0.001 HIS A 156 PHE 0.041 0.001 PHE B 104 TYR 0.020 0.001 TYR A 204 ARG 0.004 0.000 ARG B 977 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 599 time to evaluate : 3.606 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: A 115 TRP cc_start: 0.6775 (p-90) cc_final: 0.6481 (p-90) REVERT: A 286 ASP cc_start: 0.8557 (t70) cc_final: 0.8106 (t0) REVERT: A 309 GLN cc_start: 0.8870 (mt0) cc_final: 0.8627 (tt0) REVERT: A 372 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: A 461 LYS cc_start: 0.8456 (tttt) cc_final: 0.8124 (tttm) REVERT: A 680 MET cc_start: 0.7623 (mmt) cc_final: 0.7088 (mtp) REVERT: A 702 CYS cc_start: 0.6417 (m) cc_final: 0.6131 (m) REVERT: A 824 ILE cc_start: 0.8310 (mm) cc_final: 0.8030 (tp) REVERT: A 829 PHE cc_start: 0.7250 (m-80) cc_final: 0.6534 (p90) REVERT: A 850 ASP cc_start: 0.8402 (t70) cc_final: 0.7993 (t70) REVERT: A 883 LYS cc_start: 0.8771 (mmtp) cc_final: 0.8527 (mmtp) REVERT: A 898 ARG cc_start: 0.7709 (ttp80) cc_final: 0.6902 (tpp80) REVERT: A 925 GLU cc_start: 0.8853 (mt-10) cc_final: 0.7990 (tt0) REVERT: A 928 MET cc_start: 0.8130 (tpt) cc_final: 0.7719 (tpt) REVERT: A 973 ARG cc_start: 0.6042 (mtt180) cc_final: 0.5811 (mtp85) REVERT: A 1000 TYR cc_start: 0.8109 (m-80) cc_final: 0.7702 (m-80) REVERT: A 1033 MET cc_start: 0.8239 (tpp) cc_final: 0.7998 (mmm) REVERT: A 1059 MET cc_start: 0.8164 (ttm) cc_final: 0.7850 (ttm) REVERT: A 1076 GLN cc_start: 0.7785 (mp10) cc_final: 0.6812 (tp40) REVERT: A 1130 GLU cc_start: 0.7474 (mp0) cc_final: 0.7214 (mp0) REVERT: A 1141 LYS cc_start: 0.8409 (mttt) cc_final: 0.7895 (mtpt) REVERT: A 1152 GLU cc_start: 0.7628 (tp30) cc_final: 0.6871 (tp30) REVERT: A 1155 ASN cc_start: 0.8394 (m-40) cc_final: 0.6985 (t0) REVERT: A 1279 MET cc_start: 0.7196 (mmm) cc_final: 0.6974 (mmt) REVERT: B 198 PHE cc_start: 0.7942 (m-80) cc_final: 0.7398 (m-10) REVERT: B 247 ARG cc_start: 0.7148 (mtt180) cc_final: 0.6573 (mtt180) REVERT: B 286 ASP cc_start: 0.8669 (t70) cc_final: 0.8221 (t0) REVERT: B 293 PHE cc_start: 0.8769 (t80) cc_final: 0.8468 (t80) REVERT: B 597 GLN cc_start: 0.8277 (mt0) cc_final: 0.7780 (tp-100) REVERT: B 633 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7327 (mm-40) REVERT: B 680 MET cc_start: 0.7770 (mmt) cc_final: 0.7209 (mtp) REVERT: B 701 GLU cc_start: 0.7621 (pt0) cc_final: 0.7100 (pm20) REVERT: B 702 CYS cc_start: 0.6460 (m) cc_final: 0.6080 (m) REVERT: B 797 THR cc_start: 0.7549 (p) cc_final: 0.7314 (t) REVERT: B 805 GLN cc_start: 0.7896 (mt0) cc_final: 0.7609 (mp10) REVERT: B 824 ILE cc_start: 0.8358 (mm) cc_final: 0.8069 (tp) REVERT: B 829 PHE cc_start: 0.7131 (m-80) cc_final: 0.6594 (p90) REVERT: B 883 LYS cc_start: 0.8732 (mttm) cc_final: 0.8483 (mmtp) REVERT: B 898 ARG cc_start: 0.7640 (ttp80) cc_final: 0.6870 (tpp80) REVERT: B 928 MET cc_start: 0.7946 (tpp) cc_final: 0.7424 (tpp) REVERT: B 973 ARG cc_start: 0.6420 (mtt180) cc_final: 0.6143 (mtp85) REVERT: B 1059 MET cc_start: 0.7977 (ttm) cc_final: 0.7577 (ttm) REVERT: B 1066 ASN cc_start: 0.8413 (m110) cc_final: 0.7927 (m110) REVERT: B 1076 GLN cc_start: 0.7899 (mp10) cc_final: 0.6949 (tp-100) REVERT: B 1152 GLU cc_start: 0.7706 (tp30) cc_final: 0.6872 (tp30) REVERT: B 1155 ASN cc_start: 0.8328 (m-40) cc_final: 0.7235 (t0) REVERT: B 1283 ARG cc_start: 0.8035 (mtt90) cc_final: 0.7538 (mtm-85) REVERT: C 247 ARG cc_start: 0.7117 (mtt180) cc_final: 0.6490 (mtm180) REVERT: C 286 ASP cc_start: 0.8605 (t70) cc_final: 0.8026 (t0) REVERT: C 309 GLN cc_start: 0.8504 (tt0) cc_final: 0.8291 (tt0) REVERT: C 372 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: C 623 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7494 (mt0) REVERT: C 664 TRP cc_start: 0.6531 (m-10) cc_final: 0.6185 (m100) REVERT: C 680 MET cc_start: 0.7636 (mmt) cc_final: 0.7141 (mtp) REVERT: C 701 GLU cc_start: 0.7607 (pt0) cc_final: 0.7108 (pm20) REVERT: C 702 CYS cc_start: 0.6352 (m) cc_final: 0.5962 (m) REVERT: C 805 GLN cc_start: 0.7898 (mt0) cc_final: 0.7525 (mp10) REVERT: C 829 PHE cc_start: 0.7216 (m-80) cc_final: 0.6534 (p90) REVERT: C 883 LYS cc_start: 0.8845 (mttm) cc_final: 0.8497 (mmtp) REVERT: C 898 ARG cc_start: 0.7626 (ttp80) cc_final: 0.6839 (tpp80) REVERT: C 925 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8217 (tt0) REVERT: C 928 MET cc_start: 0.7917 (tpp) cc_final: 0.7301 (tpp) REVERT: C 973 ARG cc_start: 0.6321 (mtt180) cc_final: 0.6079 (mtp85) REVERT: C 1059 MET cc_start: 0.8028 (ttm) cc_final: 0.7818 (ttm) REVERT: C 1066 ASN cc_start: 0.8260 (m110) cc_final: 0.7826 (m110) REVERT: C 1076 GLN cc_start: 0.7745 (mp10) cc_final: 0.6861 (tp40) REVERT: C 1130 GLU cc_start: 0.7596 (mp0) cc_final: 0.7320 (mp0) REVERT: C 1141 LYS cc_start: 0.8280 (mttt) cc_final: 0.7808 (mtpt) REVERT: C 1152 GLU cc_start: 0.7624 (tp30) cc_final: 0.6775 (tp30) REVERT: C 1155 ASN cc_start: 0.8407 (m-40) cc_final: 0.7263 (t0) REVERT: C 1279 MET cc_start: 0.7322 (mmt) cc_final: 0.7108 (mmt) REVERT: C 1283 ARG cc_start: 0.8033 (mtt90) cc_final: 0.6814 (mtm-85) outliers start: 138 outliers final: 101 residues processed: 692 average time/residue: 0.3958 time to fit residues: 457.2525 Evaluate side-chains 657 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 553 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 670 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1310 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 812 TRP Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1029 ASP Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 306 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 322 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 758 GLN ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B 611 GLN B1227 ASN B1269 HIS C 92 GLN ** C 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 HIS ** C 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 906 GLN C1311 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 32790 Z= 0.188 Angle : 0.673 9.597 44703 Z= 0.324 Chirality : 0.049 0.341 5778 Planarity : 0.003 0.040 5376 Dihedral : 9.899 82.607 8445 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 4.92 % Allowed : 19.28 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.88 (0.13), residues: 3717 helix: 0.64 (0.20), residues: 756 sheet: -1.84 (0.17), residues: 864 loop : -3.08 (0.12), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 200 HIS 0.008 0.001 HIS C 156 PHE 0.032 0.001 PHE B 104 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG B 977 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 584 time to evaluate : 3.622 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: A 286 ASP cc_start: 0.8599 (t70) cc_final: 0.8082 (t0) REVERT: A 309 GLN cc_start: 0.8833 (mt0) cc_final: 0.8612 (tt0) REVERT: A 382 THR cc_start: 0.7882 (m) cc_final: 0.7567 (t) REVERT: A 461 LYS cc_start: 0.8390 (tttt) cc_final: 0.8053 (tttm) REVERT: A 477 THR cc_start: 0.7309 (OUTLIER) cc_final: 0.6933 (p) REVERT: A 680 MET cc_start: 0.7598 (mmt) cc_final: 0.7097 (mtp) REVERT: A 702 CYS cc_start: 0.6411 (m) cc_final: 0.6135 (m) REVERT: A 824 ILE cc_start: 0.8288 (mm) cc_final: 0.7966 (tp) REVERT: A 829 PHE cc_start: 0.7194 (m-80) cc_final: 0.6630 (p90) REVERT: A 850 ASP cc_start: 0.8365 (t70) cc_final: 0.7888 (t70) REVERT: A 883 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8541 (mmtp) REVERT: A 898 ARG cc_start: 0.7676 (ttp80) cc_final: 0.6824 (tpp80) REVERT: A 925 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8010 (tt0) REVERT: A 928 MET cc_start: 0.8161 (tpt) cc_final: 0.7875 (tpt) REVERT: A 1000 TYR cc_start: 0.8147 (m-80) cc_final: 0.7843 (m-80) REVERT: A 1059 MET cc_start: 0.8180 (ttm) cc_final: 0.7859 (ttm) REVERT: A 1141 LYS cc_start: 0.8398 (mttt) cc_final: 0.7876 (mtpt) REVERT: A 1152 GLU cc_start: 0.7664 (tp30) cc_final: 0.6834 (tp30) REVERT: A 1155 ASN cc_start: 0.8360 (m-40) cc_final: 0.6994 (t0) REVERT: A 1279 MET cc_start: 0.7180 (mmm) cc_final: 0.6959 (mmt) REVERT: B 247 ARG cc_start: 0.7231 (mtt180) cc_final: 0.6598 (mtt180) REVERT: B 286 ASP cc_start: 0.8700 (t70) cc_final: 0.8146 (t0) REVERT: B 293 PHE cc_start: 0.8717 (t80) cc_final: 0.8464 (t80) REVERT: B 382 THR cc_start: 0.7997 (m) cc_final: 0.7700 (t) REVERT: B 597 GLN cc_start: 0.8299 (mt0) cc_final: 0.7801 (tp-100) REVERT: B 603 LEU cc_start: 0.8548 (tp) cc_final: 0.8181 (tp) REVERT: B 633 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7268 (mm-40) REVERT: B 680 MET cc_start: 0.7770 (mmt) cc_final: 0.7209 (mtp) REVERT: B 701 GLU cc_start: 0.7662 (pt0) cc_final: 0.7100 (pm20) REVERT: B 702 CYS cc_start: 0.6355 (m) cc_final: 0.5940 (m) REVERT: B 797 THR cc_start: 0.7537 (p) cc_final: 0.7298 (t) REVERT: B 805 GLN cc_start: 0.7913 (mt0) cc_final: 0.7613 (mp10) REVERT: B 824 ILE cc_start: 0.8294 (mm) cc_final: 0.8012 (tp) REVERT: B 829 PHE cc_start: 0.7123 (m-80) cc_final: 0.6678 (p90) REVERT: B 876 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7145 (mt-10) REVERT: B 883 LYS cc_start: 0.8749 (mttm) cc_final: 0.8507 (mmtp) REVERT: B 925 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8005 (tt0) REVERT: B 928 MET cc_start: 0.7982 (tpp) cc_final: 0.7333 (tpp) REVERT: B 973 ARG cc_start: 0.6362 (mtt180) cc_final: 0.6106 (mtp85) REVERT: B 1000 TYR cc_start: 0.7953 (m-80) cc_final: 0.7716 (m-80) REVERT: B 1059 MET cc_start: 0.7992 (ttm) cc_final: 0.7591 (ttm) REVERT: B 1066 ASN cc_start: 0.8388 (m110) cc_final: 0.7926 (m110) REVERT: B 1152 GLU cc_start: 0.7757 (tp30) cc_final: 0.7318 (tt0) REVERT: B 1155 ASN cc_start: 0.8387 (m-40) cc_final: 0.7346 (t0) REVERT: B 1293 MET cc_start: 0.7880 (tpt) cc_final: 0.7624 (tpt) REVERT: C 215 LYS cc_start: 0.8309 (mttt) cc_final: 0.8102 (mttt) REVERT: C 247 ARG cc_start: 0.7181 (mtt180) cc_final: 0.6441 (mtm-85) REVERT: C 286 ASP cc_start: 0.8576 (t70) cc_final: 0.7988 (t70) REVERT: C 293 PHE cc_start: 0.8740 (t80) cc_final: 0.8018 (t80) REVERT: C 372 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8400 (tt0) REVERT: C 623 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7457 (mt0) REVERT: C 664 TRP cc_start: 0.6527 (m-10) cc_final: 0.6174 (m100) REVERT: C 680 MET cc_start: 0.7712 (mmt) cc_final: 0.7173 (mtp) REVERT: C 701 GLU cc_start: 0.7616 (pt0) cc_final: 0.7170 (pm20) REVERT: C 805 GLN cc_start: 0.7902 (mt0) cc_final: 0.7523 (mp10) REVERT: C 829 PHE cc_start: 0.7258 (m-80) cc_final: 0.6574 (p90) REVERT: C 883 LYS cc_start: 0.8851 (mttm) cc_final: 0.8516 (mmtp) REVERT: C 898 ARG cc_start: 0.7684 (ttp80) cc_final: 0.6929 (tpp80) REVERT: C 925 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8064 (tt0) REVERT: C 928 MET cc_start: 0.7927 (tpp) cc_final: 0.7295 (tpp) REVERT: C 973 ARG cc_start: 0.6150 (mtt180) cc_final: 0.5913 (mtp85) REVERT: C 1059 MET cc_start: 0.8045 (ttm) cc_final: 0.7835 (ttm) REVERT: C 1066 ASN cc_start: 0.8245 (m110) cc_final: 0.7774 (m110) REVERT: C 1075 LEU cc_start: 0.8394 (mm) cc_final: 0.7982 (mm) REVERT: C 1076 GLN cc_start: 0.7737 (mp10) cc_final: 0.6777 (tp40) REVERT: C 1130 GLU cc_start: 0.7592 (mp0) cc_final: 0.7335 (mp0) REVERT: C 1141 LYS cc_start: 0.8297 (mttt) cc_final: 0.7809 (mtpt) REVERT: C 1152 GLU cc_start: 0.7729 (tp30) cc_final: 0.7330 (tt0) REVERT: C 1155 ASN cc_start: 0.8459 (m-40) cc_final: 0.7334 (t0) REVERT: C 1161 GLU cc_start: 0.6619 (pm20) cc_final: 0.6417 (pm20) outliers start: 161 outliers final: 118 residues processed: 689 average time/residue: 0.4053 time to fit residues: 466.7143 Evaluate side-chains 682 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 561 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 467 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1227 ASN Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1310 THR Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1029 ASP Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 3.9990 chunk 323 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 359 optimal weight: 3.9990 chunk 298 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 188 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 HIS ** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN A1112 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN B1112 ASN C 374 HIS C 624 ASN C1062 GLN C1066 ASN C1078 ASN C1112 ASN C1269 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32790 Z= 0.320 Angle : 0.727 9.668 44703 Z= 0.354 Chirality : 0.050 0.347 5778 Planarity : 0.003 0.038 5376 Dihedral : 9.605 78.572 8445 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.62 % Favored : 87.30 % Rotamer: Outliers : 5.16 % Allowed : 19.83 % Favored : 75.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.83 (0.13), residues: 3717 helix: 0.68 (0.20), residues: 759 sheet: -1.94 (0.17), residues: 906 loop : -2.99 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 222 HIS 0.007 0.001 HIS B 156 PHE 0.026 0.001 PHE B 104 TYR 0.032 0.002 TYR C1067 ARG 0.004 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 574 time to evaluate : 3.610 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: A 286 ASP cc_start: 0.8638 (t70) cc_final: 0.8262 (t0) REVERT: A 309 GLN cc_start: 0.8829 (mt0) cc_final: 0.8605 (tt0) REVERT: A 382 THR cc_start: 0.8024 (m) cc_final: 0.7678 (t) REVERT: A 461 LYS cc_start: 0.8429 (tttt) cc_final: 0.8075 (tttm) REVERT: A 477 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.7120 (p) REVERT: A 641 GLU cc_start: 0.8034 (tp30) cc_final: 0.7022 (tp30) REVERT: A 680 MET cc_start: 0.7615 (mmt) cc_final: 0.6911 (mtp) REVERT: A 702 CYS cc_start: 0.6309 (m) cc_final: 0.5954 (m) REVERT: A 824 ILE cc_start: 0.8314 (mm) cc_final: 0.8002 (tp) REVERT: A 829 PHE cc_start: 0.7210 (m-80) cc_final: 0.6634 (p90) REVERT: A 850 ASP cc_start: 0.8386 (t70) cc_final: 0.7862 (t70) REVERT: A 883 LYS cc_start: 0.8800 (mmtp) cc_final: 0.8534 (mmtp) REVERT: A 898 ARG cc_start: 0.7759 (ttp80) cc_final: 0.6970 (tpp80) REVERT: A 925 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8086 (tt0) REVERT: A 1059 MET cc_start: 0.8171 (ttm) cc_final: 0.7843 (ttm) REVERT: A 1141 LYS cc_start: 0.8355 (mttt) cc_final: 0.7802 (mtpt) REVERT: A 1152 GLU cc_start: 0.7749 (tp30) cc_final: 0.6877 (tp30) REVERT: A 1155 ASN cc_start: 0.8481 (m-40) cc_final: 0.7175 (t0) REVERT: A 1279 MET cc_start: 0.7165 (mmm) cc_final: 0.6956 (mmt) REVERT: B 286 ASP cc_start: 0.8714 (t70) cc_final: 0.8314 (t0) REVERT: B 293 PHE cc_start: 0.8739 (t80) cc_final: 0.8527 (t80) REVERT: B 382 THR cc_start: 0.8062 (m) cc_final: 0.7712 (t) REVERT: B 597 GLN cc_start: 0.8332 (mt0) cc_final: 0.7726 (tp40) REVERT: B 603 LEU cc_start: 0.8557 (tp) cc_final: 0.8198 (tp) REVERT: B 623 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: B 633 GLN cc_start: 0.8001 (mm-40) cc_final: 0.7515 (mm-40) REVERT: B 701 GLU cc_start: 0.7788 (pt0) cc_final: 0.7583 (pt0) REVERT: B 702 CYS cc_start: 0.6361 (m) cc_final: 0.5876 (m) REVERT: B 797 THR cc_start: 0.7526 (p) cc_final: 0.7287 (t) REVERT: B 824 ILE cc_start: 0.8261 (mm) cc_final: 0.7998 (tp) REVERT: B 829 PHE cc_start: 0.7160 (m-80) cc_final: 0.6685 (p90) REVERT: B 883 LYS cc_start: 0.8759 (mttm) cc_final: 0.8550 (mmtp) REVERT: B 898 ARG cc_start: 0.7610 (ttp80) cc_final: 0.6908 (tpp80) REVERT: B 925 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8183 (tt0) REVERT: B 973 ARG cc_start: 0.6287 (mtt180) cc_final: 0.6064 (mtp85) REVERT: B 1059 MET cc_start: 0.8010 (ttm) cc_final: 0.7632 (ttm) REVERT: B 1066 ASN cc_start: 0.8482 (m110) cc_final: 0.8023 (m110) REVERT: B 1152 GLU cc_start: 0.7743 (tp30) cc_final: 0.6874 (tp30) REVERT: B 1155 ASN cc_start: 0.8435 (m-40) cc_final: 0.7463 (t0) REVERT: B 1268 ASP cc_start: 0.8378 (m-30) cc_final: 0.8043 (m-30) REVERT: B 1293 MET cc_start: 0.7900 (tpt) cc_final: 0.7511 (tpt) REVERT: C 215 LYS cc_start: 0.8276 (mttt) cc_final: 0.8017 (mttt) REVERT: C 247 ARG cc_start: 0.7246 (mtt180) cc_final: 0.6620 (mtm180) REVERT: C 286 ASP cc_start: 0.8638 (t70) cc_final: 0.8138 (t0) REVERT: C 293 PHE cc_start: 0.8714 (t80) cc_final: 0.8137 (t80) REVERT: C 372 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8456 (tt0) REVERT: C 531 ASP cc_start: 0.8268 (t0) cc_final: 0.8049 (t0) REVERT: C 570 GLU cc_start: 0.7199 (mp0) cc_final: 0.6981 (mp0) REVERT: C 623 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: C 635 ASN cc_start: 0.8426 (m-40) cc_final: 0.7996 (m-40) REVERT: C 664 TRP cc_start: 0.6596 (m-10) cc_final: 0.6074 (m100) REVERT: C 680 MET cc_start: 0.7728 (mmt) cc_final: 0.7110 (mtp) REVERT: C 694 ILE cc_start: 0.4886 (OUTLIER) cc_final: 0.4285 (tp) REVERT: C 701 GLU cc_start: 0.7578 (pt0) cc_final: 0.7116 (pm20) REVERT: C 805 GLN cc_start: 0.7967 (mt0) cc_final: 0.7596 (mp10) REVERT: C 829 PHE cc_start: 0.7308 (m-80) cc_final: 0.6584 (p90) REVERT: C 883 LYS cc_start: 0.8863 (mttm) cc_final: 0.8494 (mmtp) REVERT: C 898 ARG cc_start: 0.7748 (ttp80) cc_final: 0.6983 (tpp80) REVERT: C 925 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8173 (tt0) REVERT: C 928 MET cc_start: 0.7879 (tpp) cc_final: 0.7251 (tpp) REVERT: C 973 ARG cc_start: 0.6128 (mtt180) cc_final: 0.5914 (mtp85) REVERT: C 1059 MET cc_start: 0.8067 (ttm) cc_final: 0.7748 (ttm) REVERT: C 1130 GLU cc_start: 0.7638 (mp0) cc_final: 0.7409 (mp0) REVERT: C 1141 LYS cc_start: 0.8287 (mttt) cc_final: 0.7719 (mtpt) REVERT: C 1152 GLU cc_start: 0.7762 (tp30) cc_final: 0.6887 (tp30) REVERT: C 1155 ASN cc_start: 0.8550 (m-40) cc_final: 0.7336 (t0) REVERT: C 1266 ASP cc_start: 0.7919 (t0) cc_final: 0.7681 (t0) REVERT: C 1268 ASP cc_start: 0.8364 (m-30) cc_final: 0.7821 (m-30) REVERT: C 1283 ARG cc_start: 0.8047 (mtt90) cc_final: 0.6873 (mtm-85) outliers start: 169 outliers final: 138 residues processed: 684 average time/residue: 0.4167 time to fit residues: 480.2750 Evaluate side-chains 689 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 546 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 674 SER Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1046 LEU Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1124 VAL Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain A residue 1318 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 476 TRP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 623 GLN Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 668 PHE Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 816 THR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 964 ASP Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain B residue 1318 VAL Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 242 ILE Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 476 TRP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 621 GLN Chi-restraints excluded: chain C residue 623 GLN Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 854 VAL Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1124 VAL Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1318 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 203 optimal weight: 0.0040 chunk 302 optimal weight: 0.6980 chunk 200 optimal weight: 0.0870 chunk 358 optimal weight: 0.8980 chunk 224 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS A1269 HIS B 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32790 Z= 0.161 Angle : 0.663 9.701 44703 Z= 0.320 Chirality : 0.048 0.344 5778 Planarity : 0.003 0.038 5376 Dihedral : 9.014 73.164 8445 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.33 % Allowed : 22.36 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.13), residues: 3717 helix: 0.93 (0.20), residues: 780 sheet: -1.67 (0.18), residues: 849 loop : -2.86 (0.12), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 222 HIS 0.002 0.000 HIS A 132 PHE 0.022 0.001 PHE B 104 TYR 0.023 0.001 TYR C1067 ARG 0.004 0.000 ARG B1283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 577 time to evaluate : 3.310 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: A 208 TYR cc_start: 0.6976 (m-80) cc_final: 0.6388 (m-80) REVERT: A 215 LYS cc_start: 0.8138 (mttt) cc_final: 0.7801 (mttt) REVERT: A 247 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6993 (mtm180) REVERT: A 286 ASP cc_start: 0.8653 (t70) cc_final: 0.8215 (t0) REVERT: A 293 PHE cc_start: 0.8636 (t80) cc_final: 0.7533 (t80) REVERT: A 309 GLN cc_start: 0.8768 (mt0) cc_final: 0.8522 (tt0) REVERT: A 311 ARG cc_start: 0.8480 (mtt90) cc_final: 0.8254 (ttm-80) REVERT: A 461 LYS cc_start: 0.8407 (tttt) cc_final: 0.7945 (tmtt) REVERT: A 680 MET cc_start: 0.7574 (mmt) cc_final: 0.7086 (mtp) REVERT: A 702 CYS cc_start: 0.6330 (m) cc_final: 0.6046 (m) REVERT: A 805 GLN cc_start: 0.7974 (mt0) cc_final: 0.7632 (mp10) REVERT: A 824 ILE cc_start: 0.8246 (mm) cc_final: 0.7899 (tp) REVERT: A 829 PHE cc_start: 0.7212 (m-80) cc_final: 0.6625 (p90) REVERT: A 850 ASP cc_start: 0.8288 (t70) cc_final: 0.7717 (t70) REVERT: A 883 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8543 (mmtp) REVERT: A 898 ARG cc_start: 0.7673 (ttp80) cc_final: 0.6870 (tpp80) REVERT: A 925 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8215 (tt0) REVERT: A 928 MET cc_start: 0.8176 (tpt) cc_final: 0.7947 (tpt) REVERT: A 1059 MET cc_start: 0.8148 (ttm) cc_final: 0.7824 (ttm) REVERT: A 1141 LYS cc_start: 0.8309 (mttt) cc_final: 0.7744 (mtpt) REVERT: A 1152 GLU cc_start: 0.7716 (tp30) cc_final: 0.6851 (tp30) REVERT: A 1155 ASN cc_start: 0.8349 (m-40) cc_final: 0.6983 (t0) REVERT: A 1279 MET cc_start: 0.7108 (mmm) cc_final: 0.6865 (mmt) REVERT: A 1290 LYS cc_start: 0.8378 (mttt) cc_final: 0.8097 (mttp) REVERT: B 247 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6720 (mtt90) REVERT: B 286 ASP cc_start: 0.8687 (t70) cc_final: 0.8263 (t0) REVERT: B 597 GLN cc_start: 0.8321 (mt0) cc_final: 0.7738 (tp40) REVERT: B 603 LEU cc_start: 0.8539 (tp) cc_final: 0.8134 (tp) REVERT: B 633 GLN cc_start: 0.7862 (mm-40) cc_final: 0.7226 (mm-40) REVERT: B 680 MET cc_start: 0.8021 (mmm) cc_final: 0.7386 (mtp) REVERT: B 702 CYS cc_start: 0.6199 (m) cc_final: 0.5717 (m) REVERT: B 797 THR cc_start: 0.7530 (p) cc_final: 0.7288 (t) REVERT: B 805 GLN cc_start: 0.7921 (mt0) cc_final: 0.7614 (mp10) REVERT: B 824 ILE cc_start: 0.8313 (mm) cc_final: 0.7986 (tp) REVERT: B 829 PHE cc_start: 0.7161 (m-80) cc_final: 0.6664 (p90) REVERT: B 876 GLU cc_start: 0.7477 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 883 LYS cc_start: 0.8761 (mttm) cc_final: 0.8530 (mmtp) REVERT: B 925 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8269 (tt0) REVERT: B 928 MET cc_start: 0.8150 (tpt) cc_final: 0.7802 (tpt) REVERT: B 973 ARG cc_start: 0.6199 (mtt180) cc_final: 0.5954 (mtp85) REVERT: B 1059 MET cc_start: 0.7976 (ttm) cc_final: 0.7576 (ttm) REVERT: B 1066 ASN cc_start: 0.8332 (m110) cc_final: 0.7907 (m110) REVERT: B 1152 GLU cc_start: 0.7739 (tp30) cc_final: 0.6824 (tp30) REVERT: B 1155 ASN cc_start: 0.8391 (m-40) cc_final: 0.7372 (t0) REVERT: C 215 LYS cc_start: 0.8277 (mttt) cc_final: 0.8073 (mttt) REVERT: C 247 ARG cc_start: 0.7311 (mtt180) cc_final: 0.6713 (mtm180) REVERT: C 286 ASP cc_start: 0.8699 (t70) cc_final: 0.8129 (t0) REVERT: C 293 PHE cc_start: 0.8668 (t80) cc_final: 0.8016 (t80) REVERT: C 372 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: C 664 TRP cc_start: 0.6372 (m-10) cc_final: 0.6028 (m100) REVERT: C 805 GLN cc_start: 0.7946 (mt0) cc_final: 0.7592 (mp10) REVERT: C 829 PHE cc_start: 0.7305 (m-80) cc_final: 0.6586 (p90) REVERT: C 883 LYS cc_start: 0.8842 (mttm) cc_final: 0.8501 (mmtp) REVERT: C 898 ARG cc_start: 0.7714 (ttp80) cc_final: 0.6902 (tpp80) REVERT: C 925 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8210 (tt0) REVERT: C 928 MET cc_start: 0.7877 (tpp) cc_final: 0.7295 (tpp) REVERT: C 973 ARG cc_start: 0.6010 (mtt180) cc_final: 0.5726 (mtp85) REVERT: C 1059 MET cc_start: 0.7985 (ttm) cc_final: 0.7677 (ttm) REVERT: C 1066 ASN cc_start: 0.8156 (m110) cc_final: 0.7822 (m110) REVERT: C 1076 GLN cc_start: 0.7664 (mp10) cc_final: 0.6735 (tp40) REVERT: C 1130 GLU cc_start: 0.7607 (mp0) cc_final: 0.7340 (mp0) REVERT: C 1141 LYS cc_start: 0.8249 (mttt) cc_final: 0.7705 (mtpt) REVERT: C 1152 GLU cc_start: 0.7741 (tp30) cc_final: 0.6840 (tp30) REVERT: C 1155 ASN cc_start: 0.8442 (m-40) cc_final: 0.7266 (t0) REVERT: C 1266 ASP cc_start: 0.7847 (t0) cc_final: 0.7644 (t0) REVERT: C 1321 TYR cc_start: 0.8105 (t80) cc_final: 0.7897 (t80) outliers start: 109 outliers final: 89 residues processed: 643 average time/residue: 0.3855 time to fit residues: 411.3410 Evaluate side-chains 642 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 552 time to evaluate : 3.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 677 ASP Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 70 optimal weight: 0.0970 chunk 69 optimal weight: 4.9990 chunk 227 optimal weight: 0.9990 chunk 244 optimal weight: 4.9990 chunk 177 optimal weight: 0.0050 chunk 33 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 overall best weight: 1.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 611 GLN C 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 32790 Z= 0.228 Angle : 0.682 9.683 44703 Z= 0.330 Chirality : 0.048 0.345 5778 Planarity : 0.003 0.039 5376 Dihedral : 8.838 70.094 8445 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 3.94 % Allowed : 22.15 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 3717 helix: 0.99 (0.20), residues: 783 sheet: -1.78 (0.17), residues: 915 loop : -2.84 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 222 HIS 0.004 0.001 HIS A 156 PHE 0.021 0.001 PHE B 104 TYR 0.023 0.001 TYR C1067 ARG 0.004 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 558 time to evaluate : 3.436 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: A 286 ASP cc_start: 0.8677 (t70) cc_final: 0.8189 (t0) REVERT: A 293 PHE cc_start: 0.8641 (t80) cc_final: 0.7570 (t80) REVERT: A 461 LYS cc_start: 0.8451 (tttt) cc_final: 0.7962 (tmtt) REVERT: A 477 THR cc_start: 0.7571 (OUTLIER) cc_final: 0.7186 (p) REVERT: A 527 LEU cc_start: 0.8545 (pt) cc_final: 0.8138 (mp) REVERT: A 570 GLU cc_start: 0.7236 (mp0) cc_final: 0.6971 (mp0) REVERT: A 680 MET cc_start: 0.7579 (mmt) cc_final: 0.7086 (mtp) REVERT: A 702 CYS cc_start: 0.6244 (m) cc_final: 0.5940 (m) REVERT: A 805 GLN cc_start: 0.8000 (mt0) cc_final: 0.7614 (mp10) REVERT: A 824 ILE cc_start: 0.8255 (mm) cc_final: 0.7973 (tp) REVERT: A 829 PHE cc_start: 0.7293 (m-80) cc_final: 0.6705 (p90) REVERT: A 883 LYS cc_start: 0.8797 (mmtp) cc_final: 0.8528 (mmtp) REVERT: A 898 ARG cc_start: 0.7752 (ttp80) cc_final: 0.6945 (tpp80) REVERT: A 925 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8241 (tt0) REVERT: A 1059 MET cc_start: 0.8179 (ttm) cc_final: 0.7838 (ttm) REVERT: A 1067 TYR cc_start: 0.8448 (m-80) cc_final: 0.8243 (m-80) REVERT: A 1152 GLU cc_start: 0.7730 (tp30) cc_final: 0.6812 (tp30) REVERT: A 1155 ASN cc_start: 0.8408 (m-40) cc_final: 0.7220 (t0) REVERT: A 1279 MET cc_start: 0.7082 (mmm) cc_final: 0.6854 (mmt) REVERT: A 1290 LYS cc_start: 0.8440 (mttt) cc_final: 0.8143 (mttp) REVERT: B 247 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6848 (mtm180) REVERT: B 286 ASP cc_start: 0.8678 (t70) cc_final: 0.8243 (t0) REVERT: B 597 GLN cc_start: 0.8313 (mt0) cc_final: 0.7731 (tp-100) REVERT: B 603 LEU cc_start: 0.8494 (tp) cc_final: 0.8138 (tp) REVERT: B 633 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7380 (mm-40) REVERT: B 680 MET cc_start: 0.8062 (mmm) cc_final: 0.7431 (mtp) REVERT: B 702 CYS cc_start: 0.6292 (m) cc_final: 0.5802 (m) REVERT: B 797 THR cc_start: 0.7509 (p) cc_final: 0.7264 (t) REVERT: B 824 ILE cc_start: 0.8243 (mm) cc_final: 0.7936 (tp) REVERT: B 829 PHE cc_start: 0.7166 (m-80) cc_final: 0.6674 (p90) REVERT: B 883 LYS cc_start: 0.8764 (mttm) cc_final: 0.8540 (mmtp) REVERT: B 925 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8270 (tt0) REVERT: B 1059 MET cc_start: 0.7982 (ttm) cc_final: 0.7600 (ttm) REVERT: B 1066 ASN cc_start: 0.8374 (m110) cc_final: 0.7940 (m110) REVERT: B 1152 GLU cc_start: 0.7731 (tp30) cc_final: 0.6798 (tp30) REVERT: B 1155 ASN cc_start: 0.8361 (m-40) cc_final: 0.7450 (t0) REVERT: B 1293 MET cc_start: 0.8008 (tpt) cc_final: 0.7630 (tpt) REVERT: C 247 ARG cc_start: 0.7378 (mtt180) cc_final: 0.6780 (mtm180) REVERT: C 286 ASP cc_start: 0.8664 (t70) cc_final: 0.8391 (t0) REVERT: C 293 PHE cc_start: 0.8670 (t80) cc_final: 0.8061 (t80) REVERT: C 372 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 531 ASP cc_start: 0.8279 (t0) cc_final: 0.8061 (t0) REVERT: C 635 ASN cc_start: 0.8411 (m-40) cc_final: 0.8038 (m-40) REVERT: C 664 TRP cc_start: 0.6401 (m-10) cc_final: 0.5948 (m100) REVERT: C 680 MET cc_start: 0.8028 (mmm) cc_final: 0.7352 (mtp) REVERT: C 701 GLU cc_start: 0.7341 (pt0) cc_final: 0.6971 (pm20) REVERT: C 805 GLN cc_start: 0.7916 (mt0) cc_final: 0.7547 (mp10) REVERT: C 829 PHE cc_start: 0.7318 (m-80) cc_final: 0.6585 (p90) REVERT: C 883 LYS cc_start: 0.8855 (mttm) cc_final: 0.8501 (mmtp) REVERT: C 898 ARG cc_start: 0.7716 (ttp80) cc_final: 0.6913 (tpp80) REVERT: C 925 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8165 (tt0) REVERT: C 928 MET cc_start: 0.7968 (tpp) cc_final: 0.7314 (tpp) REVERT: C 973 ARG cc_start: 0.6074 (mtt180) cc_final: 0.5810 (mtp85) REVERT: C 1059 MET cc_start: 0.8079 (ttm) cc_final: 0.7771 (ttm) REVERT: C 1130 GLU cc_start: 0.7626 (mp0) cc_final: 0.7378 (mp0) REVERT: C 1141 LYS cc_start: 0.8259 (mttt) cc_final: 0.7692 (mtpt) REVERT: C 1152 GLU cc_start: 0.7757 (tp30) cc_final: 0.6872 (tp30) REVERT: C 1155 ASN cc_start: 0.8464 (m-40) cc_final: 0.7331 (t0) REVERT: C 1266 ASP cc_start: 0.7910 (t0) cc_final: 0.7602 (t0) REVERT: C 1283 ARG cc_start: 0.8047 (mtt90) cc_final: 0.6684 (mtm-85) REVERT: C 1293 MET cc_start: 0.7924 (tpt) cc_final: 0.7624 (tpt) REVERT: C 1321 TYR cc_start: 0.8133 (t80) cc_final: 0.7897 (t80) outliers start: 129 outliers final: 109 residues processed: 639 average time/residue: 0.4093 time to fit residues: 438.2245 Evaluate side-chains 653 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 542 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 668 PHE Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1270 SER Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1294 SER Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 674 SER Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1124 VAL Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1280 VAL Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 95 ASN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 201 THR Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 592 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 666 THR Chi-restraints excluded: chain C residue 668 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 855 ILE Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 997 ASP Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1231 ASP Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1280 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.5980 chunk 343 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 334 optimal weight: 0.3980 chunk 201 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 262 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 301 optimal weight: 0.0030 chunk 316 optimal weight: 0.9980 chunk 332 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS B1088 ASN C 515 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 32790 Z= 0.153 Angle : 0.650 9.712 44703 Z= 0.313 Chirality : 0.047 0.341 5778 Planarity : 0.003 0.037 5376 Dihedral : 8.395 64.915 8445 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 3.21 % Allowed : 23.40 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.14), residues: 3717 helix: 1.19 (0.20), residues: 762 sheet: -1.56 (0.17), residues: 891 loop : -2.73 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 222 HIS 0.003 0.000 HIS A 156 PHE 0.022 0.001 PHE C1272 TYR 0.025 0.001 TYR C1067 ARG 0.005 0.000 ARG B 898 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 579 time to evaluate : 3.438 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: A 247 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6942 (mtm180) REVERT: A 286 ASP cc_start: 0.8651 (t70) cc_final: 0.8139 (t0) REVERT: A 293 PHE cc_start: 0.8582 (t80) cc_final: 0.7449 (t80) REVERT: A 461 LYS cc_start: 0.8408 (tttt) cc_final: 0.8026 (tttt) REVERT: A 570 GLU cc_start: 0.7241 (mp0) cc_final: 0.6978 (mp0) REVERT: A 623 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7361 (mt0) REVERT: A 641 GLU cc_start: 0.7916 (tp30) cc_final: 0.7119 (tp30) REVERT: A 680 MET cc_start: 0.7586 (mmt) cc_final: 0.7103 (mtp) REVERT: A 702 CYS cc_start: 0.6330 (m) cc_final: 0.6061 (m) REVERT: A 711 GLN cc_start: 0.8480 (tt0) cc_final: 0.7922 (mt0) REVERT: A 803 MET cc_start: 0.7989 (mmm) cc_final: 0.7588 (mmp) REVERT: A 805 GLN cc_start: 0.7988 (mt0) cc_final: 0.7653 (mp10) REVERT: A 824 ILE cc_start: 0.8233 (mm) cc_final: 0.7929 (tp) REVERT: A 829 PHE cc_start: 0.7255 (m-80) cc_final: 0.6662 (p90) REVERT: A 850 ASP cc_start: 0.8228 (t70) cc_final: 0.7593 (t70) REVERT: A 883 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8549 (mmtp) REVERT: A 898 ARG cc_start: 0.7665 (ttp80) cc_final: 0.6811 (tpp80) REVERT: A 925 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8252 (tt0) REVERT: A 1059 MET cc_start: 0.8155 (ttm) cc_final: 0.7828 (ttm) REVERT: A 1114 MET cc_start: 0.7775 (tpp) cc_final: 0.7566 (mmt) REVERT: A 1130 GLU cc_start: 0.7489 (mp0) cc_final: 0.7132 (mp0) REVERT: A 1152 GLU cc_start: 0.7729 (tp30) cc_final: 0.6854 (tp30) REVERT: A 1155 ASN cc_start: 0.8287 (m-40) cc_final: 0.7115 (t0) REVERT: A 1290 LYS cc_start: 0.8359 (mttt) cc_final: 0.8085 (mttp) REVERT: B 93 ASN cc_start: 0.7861 (m110) cc_final: 0.7611 (t0) REVERT: B 286 ASP cc_start: 0.8624 (t70) cc_final: 0.8139 (t0) REVERT: B 371 ASP cc_start: 0.6817 (p0) cc_final: 0.6087 (m-30) REVERT: B 597 GLN cc_start: 0.8301 (mt0) cc_final: 0.7709 (tp-100) REVERT: B 599 ARG cc_start: 0.8127 (mmt180) cc_final: 0.7926 (mmm-85) REVERT: B 603 LEU cc_start: 0.8456 (tp) cc_final: 0.8094 (tp) REVERT: B 633 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7364 (mm-40) REVERT: B 664 TRP cc_start: 0.6531 (m-10) cc_final: 0.6246 (m100) REVERT: B 680 MET cc_start: 0.7982 (mmm) cc_final: 0.7179 (mtp) REVERT: B 702 CYS cc_start: 0.6133 (m) cc_final: 0.5666 (m) REVERT: B 711 GLN cc_start: 0.8418 (tt0) cc_final: 0.7689 (mt0) REVERT: B 797 THR cc_start: 0.7514 (p) cc_final: 0.7273 (t) REVERT: B 803 MET cc_start: 0.7798 (mmm) cc_final: 0.7584 (mmp) REVERT: B 805 GLN cc_start: 0.7986 (mt0) cc_final: 0.7664 (mp10) REVERT: B 824 ILE cc_start: 0.8224 (mm) cc_final: 0.7908 (tp) REVERT: B 829 PHE cc_start: 0.7204 (m-80) cc_final: 0.6670 (p90) REVERT: B 883 LYS cc_start: 0.8753 (mttm) cc_final: 0.8511 (mmtp) REVERT: B 925 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8320 (tt0) REVERT: B 1059 MET cc_start: 0.7973 (ttm) cc_final: 0.7574 (ttm) REVERT: B 1066 ASN cc_start: 0.8292 (m110) cc_final: 0.7863 (m110) REVERT: B 1152 GLU cc_start: 0.7702 (tp30) cc_final: 0.6727 (tp30) REVERT: B 1155 ASN cc_start: 0.8328 (m-40) cc_final: 0.7404 (t0) REVERT: B 1161 GLU cc_start: 0.6399 (pm20) cc_final: 0.6175 (pm20) REVERT: B 1293 MET cc_start: 0.8084 (tpt) cc_final: 0.7687 (tpt) REVERT: C 247 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7074 (mtt-85) REVERT: C 286 ASP cc_start: 0.8635 (t70) cc_final: 0.8349 (t0) REVERT: C 293 PHE cc_start: 0.8590 (t80) cc_final: 0.7841 (t80) REVERT: C 371 ASP cc_start: 0.6659 (p0) cc_final: 0.5922 (m-30) REVERT: C 372 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: C 529 LYS cc_start: 0.8153 (mmmm) cc_final: 0.7688 (mmmm) REVERT: C 635 ASN cc_start: 0.8293 (m-40) cc_final: 0.7952 (m-40) REVERT: C 657 SER cc_start: 0.8066 (OUTLIER) cc_final: 0.7479 (p) REVERT: C 663 LYS cc_start: 0.8674 (tttt) cc_final: 0.8299 (tppp) REVERT: C 680 MET cc_start: 0.7974 (mmm) cc_final: 0.7386 (mtp) REVERT: C 701 GLU cc_start: 0.7168 (pt0) cc_final: 0.6793 (pm20) REVERT: C 805 GLN cc_start: 0.7984 (mt0) cc_final: 0.7650 (mp10) REVERT: C 829 PHE cc_start: 0.7335 (m-80) cc_final: 0.6600 (p90) REVERT: C 883 LYS cc_start: 0.8829 (mttm) cc_final: 0.8515 (mmtp) REVERT: C 898 ARG cc_start: 0.7687 (ttp80) cc_final: 0.6914 (tpp80) REVERT: C 925 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8263 (tt0) REVERT: C 928 MET cc_start: 0.7968 (tpp) cc_final: 0.7280 (tpp) REVERT: C 1016 GLN cc_start: 0.8424 (mt0) cc_final: 0.8219 (mt0) REVERT: C 1059 MET cc_start: 0.8034 (ttm) cc_final: 0.7736 (ttm) REVERT: C 1066 ASN cc_start: 0.8074 (m110) cc_final: 0.7811 (m110) REVERT: C 1076 GLN cc_start: 0.7661 (mp10) cc_final: 0.6719 (tp40) REVERT: C 1130 GLU cc_start: 0.7647 (mp0) cc_final: 0.7353 (mp0) REVERT: C 1141 LYS cc_start: 0.8236 (mttt) cc_final: 0.7694 (mtpt) REVERT: C 1155 ASN cc_start: 0.8373 (m-40) cc_final: 0.7344 (t0) REVERT: C 1244 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7536 (mp0) REVERT: C 1266 ASP cc_start: 0.7853 (t0) cc_final: 0.7569 (t0) REVERT: C 1321 TYR cc_start: 0.8067 (t80) cc_final: 0.7850 (t80) outliers start: 105 outliers final: 89 residues processed: 641 average time/residue: 0.3859 time to fit residues: 411.0324 Evaluate side-chains 650 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 557 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1231 ASP Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain A residue 1317 ILE Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1231 ASP Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 674 SER Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 895 ASN Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1294 SER Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 9.9990 chunk 353 optimal weight: 0.3980 chunk 215 optimal weight: 0.9980 chunk 167 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 7.9990 chunk 341 optimal weight: 0.5980 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 227 optimal weight: 0.0470 chunk 180 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS B1298 GLN C 515 HIS C 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32790 Z= 0.159 Angle : 0.646 9.692 44703 Z= 0.312 Chirality : 0.047 0.352 5778 Planarity : 0.003 0.039 5376 Dihedral : 8.179 62.156 8445 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.57 % Favored : 88.43 % Rotamer: Outliers : 2.87 % Allowed : 23.65 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.14), residues: 3717 helix: 1.25 (0.20), residues: 762 sheet: -1.53 (0.18), residues: 855 loop : -2.67 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 222 HIS 0.003 0.000 HIS A 156 PHE 0.019 0.001 PHE B 104 TYR 0.029 0.001 TYR C1067 ARG 0.004 0.000 ARG B 898 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7434 Ramachandran restraints generated. 3717 Oldfield, 0 Emsley, 3717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 555 time to evaluate : 3.618 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: A 247 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.6987 (mtm180) REVERT: A 286 ASP cc_start: 0.8667 (t70) cc_final: 0.8141 (t0) REVERT: A 293 PHE cc_start: 0.8564 (t80) cc_final: 0.7458 (t80) REVERT: A 461 LYS cc_start: 0.8438 (tttt) cc_final: 0.8056 (tttt) REVERT: A 477 THR cc_start: 0.7582 (OUTLIER) cc_final: 0.7147 (p) REVERT: A 570 GLU cc_start: 0.7252 (mp0) cc_final: 0.6987 (mp0) REVERT: A 623 GLN cc_start: 0.7852 (OUTLIER) cc_final: 0.7359 (mt0) REVERT: A 641 GLU cc_start: 0.7938 (tp30) cc_final: 0.7112 (tp30) REVERT: A 680 MET cc_start: 0.7592 (mmt) cc_final: 0.6949 (mtp) REVERT: A 702 CYS cc_start: 0.6320 (m) cc_final: 0.6000 (m) REVERT: A 711 GLN cc_start: 0.8365 (tt0) cc_final: 0.7920 (mt0) REVERT: A 803 MET cc_start: 0.7968 (mmm) cc_final: 0.7569 (mmp) REVERT: A 805 GLN cc_start: 0.7979 (mt0) cc_final: 0.7669 (mp10) REVERT: A 829 PHE cc_start: 0.7265 (m-80) cc_final: 0.6707 (p90) REVERT: A 883 LYS cc_start: 0.8810 (mmtp) cc_final: 0.8558 (mmtp) REVERT: A 898 ARG cc_start: 0.7673 (ttp80) cc_final: 0.6808 (tpp80) REVERT: A 923 ARG cc_start: 0.7776 (ttp80) cc_final: 0.7553 (ttp80) REVERT: A 925 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8267 (tt0) REVERT: A 1059 MET cc_start: 0.8163 (ttm) cc_final: 0.7816 (ttm) REVERT: A 1130 GLU cc_start: 0.7509 (mp0) cc_final: 0.7213 (mp0) REVERT: A 1152 GLU cc_start: 0.7674 (tp30) cc_final: 0.6804 (tp30) REVERT: A 1155 ASN cc_start: 0.8254 (m-40) cc_final: 0.7105 (t0) REVERT: A 1279 MET cc_start: 0.7247 (mmt) cc_final: 0.6931 (mmt) REVERT: A 1290 LYS cc_start: 0.8254 (mttt) cc_final: 0.8053 (mttp) REVERT: B 184 PHE cc_start: 0.6493 (m-80) cc_final: 0.6221 (m-80) REVERT: B 286 ASP cc_start: 0.8695 (t70) cc_final: 0.8167 (t0) REVERT: B 371 ASP cc_start: 0.6807 (p0) cc_final: 0.6071 (m-30) REVERT: B 597 GLN cc_start: 0.8291 (mt0) cc_final: 0.7722 (tp-100) REVERT: B 603 LEU cc_start: 0.8463 (tp) cc_final: 0.8097 (tp) REVERT: B 633 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7316 (mm-40) REVERT: B 664 TRP cc_start: 0.6560 (m-10) cc_final: 0.6150 (m100) REVERT: B 680 MET cc_start: 0.7984 (mmm) cc_final: 0.7184 (mtp) REVERT: B 702 CYS cc_start: 0.6146 (m) cc_final: 0.5689 (m) REVERT: B 711 GLN cc_start: 0.8409 (tt0) cc_final: 0.7686 (mt0) REVERT: B 797 THR cc_start: 0.7504 (p) cc_final: 0.7263 (t) REVERT: B 803 MET cc_start: 0.7801 (mmm) cc_final: 0.7582 (mmp) REVERT: B 805 GLN cc_start: 0.8011 (mt0) cc_final: 0.7676 (mp10) REVERT: B 829 PHE cc_start: 0.7195 (m-80) cc_final: 0.6670 (p90) REVERT: B 883 LYS cc_start: 0.8787 (mttm) cc_final: 0.8547 (mmtp) REVERT: B 925 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8293 (tt0) REVERT: B 1059 MET cc_start: 0.7964 (ttm) cc_final: 0.7563 (ttm) REVERT: B 1066 ASN cc_start: 0.8303 (m110) cc_final: 0.7879 (m110) REVERT: B 1152 GLU cc_start: 0.7653 (tp30) cc_final: 0.6677 (tp30) REVERT: B 1155 ASN cc_start: 0.8300 (m-40) cc_final: 0.7414 (t0) REVERT: B 1161 GLU cc_start: 0.6408 (pm20) cc_final: 0.6177 (pm20) REVERT: B 1260 TYR cc_start: 0.6966 (m-10) cc_final: 0.6657 (m-10) REVERT: C 247 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7105 (mtt-85) REVERT: C 286 ASP cc_start: 0.8683 (t70) cc_final: 0.8370 (t0) REVERT: C 293 PHE cc_start: 0.8567 (t80) cc_final: 0.7819 (t80) REVERT: C 371 ASP cc_start: 0.6678 (p0) cc_final: 0.5916 (m-30) REVERT: C 372 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8380 (tt0) REVERT: C 489 ASP cc_start: 0.8140 (m-30) cc_final: 0.6900 (m-30) REVERT: C 529 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7673 (mmmm) REVERT: C 657 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7467 (p) REVERT: C 663 LYS cc_start: 0.8672 (tttt) cc_final: 0.8295 (tppp) REVERT: C 680 MET cc_start: 0.8015 (mmm) cc_final: 0.7377 (mtp) REVERT: C 701 GLU cc_start: 0.7197 (pt0) cc_final: 0.6809 (pm20) REVERT: C 805 GLN cc_start: 0.7954 (mt0) cc_final: 0.7640 (mp10) REVERT: C 829 PHE cc_start: 0.7326 (m-80) cc_final: 0.6623 (p90) REVERT: C 883 LYS cc_start: 0.8808 (mttm) cc_final: 0.8504 (mmtp) REVERT: C 898 ARG cc_start: 0.7701 (ttp80) cc_final: 0.6883 (tpp80) REVERT: C 925 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8174 (tt0) REVERT: C 928 MET cc_start: 0.7974 (tpp) cc_final: 0.7270 (tpp) REVERT: C 1016 GLN cc_start: 0.8393 (mt0) cc_final: 0.8181 (mt0) REVERT: C 1059 MET cc_start: 0.8041 (ttm) cc_final: 0.7737 (ttm) REVERT: C 1066 ASN cc_start: 0.8048 (m110) cc_final: 0.7780 (m110) REVERT: C 1075 LEU cc_start: 0.8400 (mm) cc_final: 0.7824 (tp) REVERT: C 1130 GLU cc_start: 0.7644 (mp0) cc_final: 0.7334 (mp0) REVERT: C 1141 LYS cc_start: 0.8235 (mttt) cc_final: 0.7691 (mtpt) REVERT: C 1155 ASN cc_start: 0.8281 (m-40) cc_final: 0.7299 (t0) REVERT: C 1266 ASP cc_start: 0.7852 (t0) cc_final: 0.7575 (t0) REVERT: C 1278 TYR cc_start: 0.8383 (m-80) cc_final: 0.8136 (m-10) REVERT: C 1321 TYR cc_start: 0.8051 (t80) cc_final: 0.7833 (t80) outliers start: 94 outliers final: 83 residues processed: 612 average time/residue: 0.3982 time to fit residues: 407.2519 Evaluate side-chains 629 residues out of total 3273 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 541 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 TYR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 476 TRP Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 623 GLN Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 657 SER Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 756 THR Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 773 THR Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 894 CYS Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 1044 MET Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1249 THR Chi-restraints excluded: chain A residue 1256 VAL Chi-restraints excluded: chain A residue 1295 ASP Chi-restraints excluded: chain A residue 1312 THR Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 592 THR Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 657 SER Chi-restraints excluded: chain B residue 666 THR Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 756 THR Chi-restraints excluded: chain B residue 761 VAL Chi-restraints excluded: chain B residue 895 ASN Chi-restraints excluded: chain B residue 1116 SER Chi-restraints excluded: chain B residue 1249 THR Chi-restraints excluded: chain B residue 1294 SER Chi-restraints excluded: chain B residue 1295 ASP Chi-restraints excluded: chain B residue 1311 HIS Chi-restraints excluded: chain B residue 1312 THR Chi-restraints excluded: chain B residue 1317 ILE Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 158 ASN Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 385 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 503 SER Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 657 SER Chi-restraints excluded: chain C residue 662 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 703 THR Chi-restraints excluded: chain C residue 816 THR Chi-restraints excluded: chain C residue 894 CYS Chi-restraints excluded: chain C residue 977 ARG Chi-restraints excluded: chain C residue 998 ASP Chi-restraints excluded: chain C residue 1097 LEU Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1140 GLN Chi-restraints excluded: chain C residue 1249 THR Chi-restraints excluded: chain C residue 1256 VAL Chi-restraints excluded: chain C residue 1295 ASP Chi-restraints excluded: chain C residue 1312 THR Chi-restraints excluded: chain C residue 1317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 272 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 295 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 303 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 515 HIS C 515 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.171003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.126616 restraints weight = 52116.983| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.97 r_work: 0.3452 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32790 Z= 0.229 Angle : 0.672 9.696 44703 Z= 0.325 Chirality : 0.048 0.341 5778 Planarity : 0.003 0.039 5376 Dihedral : 8.168 59.816 8445 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 3.27 % Allowed : 23.43 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3717 helix: 1.18 (0.20), residues: 768 sheet: -1.58 (0.18), residues: 849 loop : -2.69 (0.13), residues: 2100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 222 HIS 0.004 0.001 HIS C1237 PHE 0.019 0.001 PHE B 104 TYR 0.034 0.001 TYR C1067 ARG 0.008 0.000 ARG C 923 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9101.51 seconds wall clock time: 164 minutes 27.37 seconds (9867.37 seconds total)