Starting phenix.real_space_refine on Sun Feb 18 04:38:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxn_23572/02_2024/7lxn_23572.pdb" } resolution = 3.85 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= 0.002 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 12987 2.51 5 N 3351 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 92": "OD1" <-> "OD2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "C" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "I" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "M" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "E" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3450 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 22, 'TRANS': 411} Chain breaks: 3 Chain: "F" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 950 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1041 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 5, 'TRANS': 125} Chain: "N" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 823 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 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: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "k" 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: "l" 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: "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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "s" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "u" Number of atoms: 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "x" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 11.27, per 1000 atoms: 0.54 Number of scatterers: 20820 At special positions: 0 Unit cell: (146.718, 155.952, 148.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 114 16.00 O 4368 8.00 N 3351 7.00 C 12987 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.27 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.02 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.12 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.04 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.27 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.02 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.13 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.01 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.27 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.02 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.12 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.01 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.06 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 7 " - " MAN G 8 " " MAN S 4 " - " MAN S 5 " " MAN V 4 " - " MAN V 5 " " MAN V 5 " - " MAN V 6 " " MAN a 7 " - " MAN a 8 " " MAN g 4 " - " MAN g 5 " " MAN j 4 " - " MAN j 5 " " MAN j 5 " - " MAN j 6 " " MAN o 7 " - " MAN o 8 " " MAN u 4 " - " MAN u 5 " " MAN x 4 " - " MAN x 5 " " MAN x 5 " - " MAN x 6 " ALPHA1-3 " BMA G 3 " - " MAN G 7 " " MAN G 4 " - " MAN G 5 " " BMA S 3 " - " MAN S 4 " " BMA V 3 " - " MAN V 4 " " MAN V 7 " - " MAN V 8 " " BMA a 3 " - " MAN a 7 " " MAN a 4 " - " MAN a 5 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " MAN j 7 " - " MAN j 8 " " BMA o 3 " - " MAN o 7 " " MAN o 4 " - " MAN o 5 " " BMA u 3 " - " MAN u 4 " " BMA x 3 " - " MAN x 4 " " MAN x 7 " - " MAN x 8 " ALPHA1-6 " BMA G 3 " - " MAN G 4 " " MAN G 5 " - " MAN G 6 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 7 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 7 " " MAN V 7 " - " MAN V 9 " " BMA a 3 " - " MAN a 4 " " MAN a 5 " - " MAN a 6 " " BMA g 3 " - " MAN g 6 " " MAN g 6 " - " MAN g 7 " " BMA i 3 " - " MAN i 4 " " BMA j 3 " - " MAN j 7 " " MAN j 7 " - " MAN j 9 " " BMA o 3 " - " MAN o 4 " " MAN o 5 " - " MAN o 6 " " BMA u 3 " - " MAN u 6 " " MAN u 6 " - " MAN u 7 " " BMA w 3 " - " MAN w 4 " " BMA x 3 " - " MAN x 7 " " MAN x 7 " - " MAN x 9 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 1 1 " - " NAG 1 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG 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 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 r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG u 2 " - " BMA u 3 " " NAG v 1 " - " NAG v 2 " " NAG w 1 " - " NAG w 2 " " NAG w 2 " - " BMA w 3 " " NAG x 1 " - " NAG x 2 " " NAG x 2 " - " BMA x 3 " " NAG y 1 " - " NAG y 2 " " NAG y 2 " - " BMA y 3 " " NAG z 1 " - " NAG z 2 " " NAG z 2 " - " BMA z 3 " NAG-ASN " NAG 0 1 " - " ASN E 197 " " NAG 1 1 " - " ASN E 276 " " NAG A 601 " - " ASN A 289 " " NAG A 602 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG C 601 " - " ASN C 289 " " NAG C 602 " - " ASN C 392 " " NAG D 701 " - " ASN D 611 " " NAG E 601 " - " ASN E 289 " " NAG E 602 " - " ASN E 392 " " NAG F 701 " - " ASN F 611 " " NAG G 1 " - " ASN A 138 " " NAG K 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 130 " " NAG P 1 " - " ASN A 160 " " NAG Q 1 " - " ASN A 234 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 262 " " NAG T 1 " - " ASN A 295 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " " NAG W 1 " - " ASN A 386 " " NAG X 1 " - " ASN A 448 " " NAG Y 1 " - " ASN A 197 " " NAG Z 1 " - " ASN A 276 " " NAG a 1 " - " ASN C 138 " " NAG b 1 " - " ASN C 88 " " NAG c 1 " - " ASN C 130 " " NAG d 1 " - " ASN C 160 " " NAG e 1 " - " ASN C 234 " " NAG f 1 " - " ASN C 241 " " NAG g 1 " - " ASN C 262 " " NAG h 1 " - " ASN C 295 " " NAG i 1 " - " ASN C 301 " " NAG j 1 " - " ASN C 332 " " NAG k 1 " - " ASN C 386 " " NAG l 1 " - " ASN C 448 " " NAG m 1 " - " ASN C 197 " " NAG n 1 " - " ASN C 276 " " NAG o 1 " - " ASN E 138 " " NAG p 1 " - " ASN E 88 " " NAG q 1 " - " ASN E 130 " " NAG r 1 " - " ASN E 160 " " NAG s 1 " - " ASN E 234 " " NAG t 1 " - " ASN E 241 " " NAG u 1 " - " ASN E 262 " " NAG v 1 " - " ASN E 295 " " NAG w 1 " - " ASN E 301 " " NAG x 1 " - " ASN E 332 " " NAG y 1 " - " ASN E 386 " " NAG z 1 " - " ASN E 448 " Time building additional restraints: 11.08 Conformation dependent library (CDL) restraints added in 3.3 seconds 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4446 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 22.0% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.791A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N HIS A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.710A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.908A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 removed outlier: 3.792A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.160A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.790A pdb=" N GLY H 55 " --> pdb=" O HIS H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100D through 100H Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.172A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.873A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N HIS C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.700A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.772A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 660 removed outlier: 3.512A pdb=" N SER D 649 " --> pdb=" O LEU D 645 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLU D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 4.127A pdb=" N ASN I 32 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.810A pdb=" N GLY I 55 " --> pdb=" O HIS I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 65 No H-bonds generated for 'chain 'I' and resid 63 through 65' Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'I' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.306A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.788A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N HIS E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.980A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.901A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 660 removed outlier: 4.567A pdb=" N SER F 644 " --> pdb=" O ASP F 640 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER F 649 " --> pdb=" O LEU F 645 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN F 651 " --> pdb=" O GLU F 647 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLU F 654 " --> pdb=" O GLN F 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 removed outlier: 3.978A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 56 removed outlier: 3.875A pdb=" N GLY J 55 " --> pdb=" O HIS J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'J' and resid 100D through 100H Processing helix chain 'N' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.349A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.016A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.002A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.721A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 302 current: chain 'A' and resid 357 through 361 Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.702A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.949A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.764A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.768A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.229A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 441 through 456 current: chain 'A' and resid 413 through 420 Processing sheet with id=AB1, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.162A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.727A pdb=" N TYR H 33 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.155A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR H 94 " --> pdb=" O ASP H 100Q" (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 8 through 13 removed outlier: 6.394A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 19 through 23 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.284A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.000A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.686A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.549A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 302 current: chain 'C' and resid 357 through 361 Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.951A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N VAL C 292 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 9.718A pdb=" N THR C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.252A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N CYS C 296 " --> pdb=" O LYS C 442 " (cutoff:3.500A) removed outlier: 10.415A pdb=" N LYS C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 441 through 456 current: chain 'C' and resid 413 through 420 Processing sheet with id=AC7, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.146A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.824A pdb=" N TYR I 33 " --> pdb=" O THR I 95 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR I 50 " --> pdb=" O TRP I 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.658A pdb=" N LYS I 96 " --> pdb=" O MET I 100P" (cutoff:3.500A) removed outlier: 5.159A pdb=" N MET I 100P" --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLY I 98 " --> pdb=" O PHE I 100N" (cutoff:3.500A) removed outlier: 5.390A pdb=" N PHE I 100N" --> pdb=" O GLY I 98 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG I 100 " --> pdb=" O THR I 100L" (cutoff:3.500A) removed outlier: 5.581A pdb=" N THR I 100L" --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.460A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLU M 100 " --> pdb=" O CYS M 88 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N CYS M 88 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP M 35 " --> pdb=" O ILE M 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 19 through 23 Processing sheet with id=AD4, first strand: chain 'E' and resid 494 through 499 removed outlier: 4.364A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.002A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 75 through 76 removed outlier: 3.982A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.651A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AD9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.667A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.547A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 284 through 302 current: chain 'E' and resid 357 through 361 Processing sheet with id=AE2, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.697A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.940A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.753A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.226A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 441 through 456 current: chain 'E' and resid 413 through 420 Processing sheet with id=AE3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.121A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.746A pdb=" N TYR J 33 " --> pdb=" O THR J 95 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP J 34 " --> pdb=" O TYR J 50 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N TYR J 50 " --> pdb=" O TRP J 34 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N TRP J 36 " --> pdb=" O ILE J 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 11 through 12 removed outlier: 7.190A pdb=" N CYS J 92 " --> pdb=" O TRP J 101 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP J 101 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N THR J 94 " --> pdb=" O ASP J 100Q" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 8 through 13 removed outlier: 6.390A pdb=" N THR N 8 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE N 105 " --> pdb=" O THR N 8 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL N 11 " --> pdb=" O ILE N 105 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N TRP N 35 " --> pdb=" O ILE N 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 19 through 23 738 hydrogen bonds defined for protein. 1890 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: 7.72 Time building geometry restraints manager: 11.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5147 1.32 - 1.46: 6949 1.46 - 1.60: 8990 1.60 - 1.74: 16 1.74 - 1.88: 132 Bond restraints: 21234 Sorted by residual: bond pdb=" CB HIS J 97 " pdb=" CG HIS J 97 " ideal model delta sigma weight residual 1.497 1.409 0.088 1.40e-02 5.10e+03 3.91e+01 bond pdb=" CB THR E 37 " pdb=" OG1 THR E 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.70e+01 bond pdb=" CB THR C 37 " pdb=" OG1 THR C 37 " ideal model delta sigma weight residual 1.433 1.336 0.097 1.60e-02 3.91e+03 3.64e+01 bond pdb=" CB HIS I 97 " pdb=" CG HIS I 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.61e+01 bond pdb=" CB HIS H 97 " pdb=" CG HIS H 97 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.60e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 96.24 - 103.83: 281 103.83 - 111.42: 9880 111.42 - 119.02: 8379 119.02 - 126.61: 10010 126.61 - 134.20: 316 Bond angle restraints: 28866 Sorted by residual: angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 120.03 128.04 -8.01 9.90e-01 1.02e+00 6.55e+01 angle pdb=" N CYS E 73 " pdb=" CA CYS E 73 " pdb=" C CYS E 73 " ideal model delta sigma weight residual 114.56 104.56 10.00 1.27e+00 6.20e-01 6.20e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.11 -7.55 1.01e+00 9.80e-01 5.59e+01 angle pdb=" C VAL F 608 " pdb=" N PRO F 609 " pdb=" CA PRO F 609 " ideal model delta sigma weight residual 120.31 127.61 -7.30 9.80e-01 1.04e+00 5.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.05 -7.49 1.01e+00 9.80e-01 5.51e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.15: 14087 22.15 - 44.31: 378 44.31 - 66.46: 122 66.46 - 88.62: 107 88.62 - 110.77: 72 Dihedral angle restraints: 14766 sinusoidal: 7890 harmonic: 6876 Sorted by residual: dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual -86.00 -2.51 -83.49 1 1.00e+01 1.00e-02 8.51e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.45 63.55 1 1.00e+01 1.00e-02 5.32e+01 dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 29.50 63.50 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 14763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2556 0.108 - 0.216: 964 0.216 - 0.324: 168 0.324 - 0.431: 20 0.431 - 0.539: 15 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 MAN o 7 " pdb=" O3 BMA o 3 " pdb=" C2 MAN o 7 " pdb=" O5 MAN o 7 " both_signs ideal model delta sigma weight residual False 2.40 2.11 0.29 2.00e-02 2.50e+03 2.09e+02 chirality pdb=" C1 MAN G 7 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.14 0.26 2.00e-02 2.50e+03 1.66e+02 chirality pdb=" C1 MAN a 7 " pdb=" O3 BMA a 3 " pdb=" C2 MAN a 7 " pdb=" O5 MAN a 7 " both_signs ideal model delta sigma weight residual False 2.40 2.15 0.25 2.00e-02 2.50e+03 1.62e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 138 " 0.126 2.00e-02 2.50e+03 1.30e-01 2.12e+02 pdb=" CG ASN C 138 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN C 138 " -0.023 2.00e-02 2.50e+03 pdb=" ND2 ASN C 138 " -0.205 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 138 " 0.121 2.00e-02 2.50e+03 1.21e-01 1.84e+02 pdb=" CG ASN E 138 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN E 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN E 138 " -0.184 2.00e-02 2.50e+03 pdb=" C1 NAG o 1 " 0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.118 2.00e-02 2.50e+03 1.18e-01 1.75e+02 pdb=" CG ASN A 138 " -0.050 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG G 1 " 0.142 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4975 2.79 - 3.31: 18639 3.31 - 3.84: 35363 3.84 - 4.37: 41379 4.37 - 4.90: 66457 Nonbonded interactions: 166813 Sorted by model distance: nonbonded pdb=" O4 NAG m 2 " pdb=" O6 NAG m 2 " model vdw 2.257 2.440 nonbonded pdb=" O4 NAG Y 2 " pdb=" O6 NAG Y 2 " model vdw 2.258 2.440 nonbonded pdb=" O4 NAG 0 2 " pdb=" O6 NAG 0 2 " model vdw 2.259 2.440 nonbonded pdb=" O4 NAG B 701 " pdb=" O6 NAG B 701 " model vdw 2.262 2.440 nonbonded pdb=" O4 MAN S 7 " pdb=" O6 MAN S 7 " model vdw 2.272 2.440 ... (remaining 166808 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 '1' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'm' selection = chain 'n' selection = chain 'p' selection = chain 'q' selection = chain 'r' selection = chain 's' selection = chain 't' selection = chain 'v' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 5 through 8) selection = (chain 'S' and resid 4 through 7) selection = (chain 'V' and resid 6 through 9) selection = (chain 'a' and resid 5 through 8) selection = (chain 'g' and resid 4 through 7) selection = (chain 'j' and resid 6 through 9) selection = (chain 'o' and resid 5 through 8) selection = (chain 'u' and resid 4 through 7) selection = (chain 'x' and resid 6 through 9) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'U' selection = chain 'i' selection = chain 'w' } ncs_group { reference = chain 'W' selection = chain 'X' selection = chain 'k' selection = chain 'l' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 3.710 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 59.580 Find NCS groups from input model: 1.500 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.020 0.184 21234 Z= 1.314 Angle : 1.794 11.339 28866 Z= 1.118 Chirality : 0.112 0.539 3723 Planarity : 0.009 0.059 3429 Dihedral : 15.735 110.770 10203 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.29 % Favored : 98.58 % Rotamer: Outliers : 0.52 % Allowed : 0.43 % Favored : 99.05 % Cbeta Deviations : 0.13 % 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: 0.84 (0.17), residues: 2325 helix: -0.69 (0.23), residues: 420 sheet: 1.20 (0.19), residues: 624 loop : 0.85 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.010 TRP E 112 HIS 0.011 0.002 HIS E 216 PHE 0.037 0.007 PHE M 67C TYR 0.076 0.009 TYR C 40 ARG 0.005 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 545 time to evaluate : 2.382 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: A 69 TRP cc_start: 0.8750 (m-90) cc_final: 0.8456 (m-90) REVERT: A 100 MET cc_start: 0.7993 (mtp) cc_final: 0.7716 (mtm) REVERT: B 584 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8407 (mt-10) REVERT: B 648 GLU cc_start: 0.8877 (tt0) cc_final: 0.8658 (tm-30) REVERT: H 100 MET cc_start: 0.8863 (mpp) cc_final: 0.8634 (mpp) REVERT: L 36 TYR cc_start: 0.8021 (m-80) cc_final: 0.7348 (m-80) REVERT: C 104 MET cc_start: 0.8807 (ttm) cc_final: 0.8468 (ttm) REVERT: C 202 THR cc_start: 0.9607 (m) cc_final: 0.9145 (p) REVERT: C 217 TYR cc_start: 0.8096 (m-80) cc_final: 0.7737 (m-10) REVERT: C 326 ILE cc_start: 0.9038 (mt) cc_final: 0.8750 (tt) REVERT: C 475 MET cc_start: 0.8339 (mmm) cc_final: 0.8030 (mmm) REVERT: D 624 ASP cc_start: 0.8440 (t70) cc_final: 0.8213 (m-30) REVERT: D 629 MET cc_start: 0.8300 (mmm) cc_final: 0.8052 (mmm) REVERT: D 648 GLU cc_start: 0.9042 (tt0) cc_final: 0.8725 (tm-30) REVERT: I 100 MET cc_start: 0.8871 (mpp) cc_final: 0.8649 (mpp) REVERT: M 21 ILE cc_start: 0.9167 (mt) cc_final: 0.8966 (mt) REVERT: E 104 MET cc_start: 0.8883 (ttm) cc_final: 0.8392 (ttm) REVERT: E 112 TRP cc_start: 0.8586 (m100) cc_final: 0.7986 (m100) REVERT: E 283 THR cc_start: 0.8606 (m) cc_final: 0.8313 (p) REVERT: E 326 ILE cc_start: 0.9034 (mt) cc_final: 0.8807 (tt) REVERT: E 434 MET cc_start: 0.9124 (ttp) cc_final: 0.8591 (ttp) REVERT: F 584 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8594 (mt-10) REVERT: F 648 GLU cc_start: 0.8811 (tt0) cc_final: 0.8092 (tm-30) outliers start: 11 outliers final: 9 residues processed: 556 average time/residue: 0.3541 time to fit residues: 289.8102 Evaluate side-chains 283 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 3.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 181 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 209 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 ASN A 362 ASN B 653 GLN H 39 GLN C 229 ASN C 362 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 650 GLN I 39 GLN I 68 HIS E 362 ASN F 591 GLN J 68 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21234 Z= 0.279 Angle : 0.805 9.696 28866 Z= 0.400 Chirality : 0.053 0.514 3723 Planarity : 0.005 0.037 3429 Dihedral : 13.237 88.083 5763 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.33 % Allowed : 8.69 % Favored : 88.98 % 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: 0.84 (0.17), residues: 2325 helix: 0.55 (0.26), residues: 405 sheet: 0.86 (0.19), residues: 636 loop : 0.56 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 112 HIS 0.005 0.001 HIS A 330 PHE 0.028 0.002 PHE C 233 TYR 0.016 0.002 TYR A 39 ARG 0.009 0.001 ARG D 579 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 326 time to evaluate : 2.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8633 (m-90) cc_final: 0.8368 (m-90) REVERT: A 475 MET cc_start: 0.7929 (mmm) cc_final: 0.7464 (tpp) REVERT: B 577 GLN cc_start: 0.8734 (tm-30) cc_final: 0.8500 (tm-30) REVERT: B 623 TRP cc_start: 0.7071 (m100) cc_final: 0.6763 (m-10) REVERT: B 648 GLU cc_start: 0.8821 (tt0) cc_final: 0.8595 (tm-30) REVERT: H 16 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6733 (tm-30) REVERT: L 36 TYR cc_start: 0.8178 (m-80) cc_final: 0.7773 (m-80) REVERT: L 78 VAL cc_start: 0.9151 (t) cc_final: 0.8877 (m) REVERT: C 202 THR cc_start: 0.9591 (m) cc_final: 0.9349 (p) REVERT: C 260 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8639 (mm) REVERT: C 326 ILE cc_start: 0.8968 (mt) cc_final: 0.8761 (tt) REVERT: D 630 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 648 GLU cc_start: 0.8961 (tt0) cc_final: 0.8720 (tm-30) REVERT: I 100 MET cc_start: 0.8703 (mpp) cc_final: 0.8441 (mmt) REVERT: M 36 TYR cc_start: 0.8350 (m-80) cc_final: 0.8043 (m-80) REVERT: M 104 LEU cc_start: 0.7475 (tp) cc_final: 0.7168 (tp) REVERT: E 195 ASN cc_start: 0.8398 (m-40) cc_final: 0.8078 (t0) REVERT: E 283 THR cc_start: 0.8573 (m) cc_final: 0.8224 (p) REVERT: E 475 MET cc_start: 0.8032 (tpp) cc_final: 0.7674 (tpp) REVERT: F 626 MET cc_start: 0.7681 (ttt) cc_final: 0.7448 (ttt) REVERT: F 648 GLU cc_start: 0.8536 (tt0) cc_final: 0.8323 (tm-30) REVERT: F 652 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8122 (mm-40) REVERT: N 28 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8252 (mm) outliers start: 49 outliers final: 31 residues processed: 360 average time/residue: 0.3305 time to fit residues: 182.1090 Evaluate side-chains 284 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 251 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 21 THR Chi-restraints excluded: chain J residue 68 HIS Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain N residue 28 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.0070 chunk 65 optimal weight: 5.9990 chunk 174 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN H 3 HIS H 97 HIS L 52 ASN C 72 HIS ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN E 229 ASN F 625 ASN J 68 HIS N 52 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21234 Z= 0.251 Angle : 0.717 9.024 28866 Z= 0.352 Chirality : 0.051 0.520 3723 Planarity : 0.005 0.141 3429 Dihedral : 11.258 83.501 5763 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.28 % Allowed : 9.64 % Favored : 87.08 % 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: 0.59 (0.17), residues: 2325 helix: 0.39 (0.26), residues: 408 sheet: 0.74 (0.19), residues: 678 loop : 0.33 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 631 HIS 0.013 0.001 HIS J 68 PHE 0.022 0.002 PHE C 233 TYR 0.016 0.002 TYR H 33 ARG 0.009 0.001 ARG I 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 259 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8584 (m-90) cc_final: 0.8301 (m-90) REVERT: A 202 THR cc_start: 0.9539 (m) cc_final: 0.9310 (p) REVERT: A 260 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8238 (mm) REVERT: B 575 GLN cc_start: 0.8923 (tp40) cc_final: 0.8675 (tp40) REVERT: B 584 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8222 (mp0) REVERT: B 623 TRP cc_start: 0.7090 (m-10) cc_final: 0.6795 (m-10) REVERT: H 16 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6772 (tm-30) REVERT: H 22 CYS cc_start: 0.3927 (t) cc_final: 0.1804 (t) REVERT: H 30 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7291 (tpp-160) REVERT: L 73 LEU cc_start: 0.9150 (tp) cc_final: 0.8912 (tt) REVERT: C 91 GLU cc_start: 0.7303 (mp0) cc_final: 0.7076 (mp0) REVERT: C 202 THR cc_start: 0.9586 (m) cc_final: 0.9357 (p) REVERT: C 326 ILE cc_start: 0.9051 (mt) cc_final: 0.8842 (tt) REVERT: C 475 MET cc_start: 0.7848 (mmm) cc_final: 0.7517 (tpp) REVERT: D 584 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8592 (mt-10) REVERT: D 630 GLU cc_start: 0.8776 (mm-30) cc_final: 0.8484 (mm-30) REVERT: D 648 GLU cc_start: 0.8886 (tt0) cc_final: 0.8672 (tm-30) REVERT: M 83 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7687 (tm-30) REVERT: E 195 ASN cc_start: 0.8309 (m-40) cc_final: 0.8017 (t0) REVERT: F 584 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8423 (mp0) REVERT: J 69 LEU cc_start: 0.8419 (mp) cc_final: 0.8168 (mt) REVERT: J 73 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8419 (mtmm) REVERT: N 28 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8286 (mm) outliers start: 69 outliers final: 43 residues processed: 306 average time/residue: 0.3149 time to fit residues: 148.4662 Evaluate side-chains 278 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 231 time to evaluate : 2.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 3 HIS Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 619 GLN Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 640 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 73 LYS Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain N residue 28 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 210 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 199 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS E 72 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN J 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 21234 Z= 0.344 Angle : 0.741 9.448 28866 Z= 0.362 Chirality : 0.051 0.510 3723 Planarity : 0.005 0.072 3429 Dihedral : 10.443 84.476 5763 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.32 % Allowed : 11.25 % Favored : 85.42 % 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: 0.51 (0.17), residues: 2325 helix: 0.44 (0.27), residues: 408 sheet: 0.95 (0.20), residues: 624 loop : 0.09 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 91 HIS 0.026 0.002 HIS H 3 PHE 0.014 0.002 PHE C 233 TYR 0.023 0.002 TYR H 33 ARG 0.007 0.001 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 233 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8667 (m-90) cc_final: 0.8397 (m-10) REVERT: A 202 THR cc_start: 0.9558 (m) cc_final: 0.9344 (p) REVERT: A 260 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8473 (mm) REVERT: B 584 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8393 (mt-10) REVERT: B 623 TRP cc_start: 0.7150 (m-10) cc_final: 0.6831 (m-10) REVERT: H 16 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7058 (tt0) REVERT: H 30 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7973 (mmp80) REVERT: C 91 GLU cc_start: 0.7360 (mp0) cc_final: 0.7102 (mp0) REVERT: C 202 THR cc_start: 0.9536 (m) cc_final: 0.9334 (p) REVERT: C 475 MET cc_start: 0.8049 (mmm) cc_final: 0.7756 (tpp) REVERT: D 584 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8564 (mt-10) REVERT: M 79 GLU cc_start: 0.8625 (mp0) cc_final: 0.8322 (mp0) REVERT: E 116 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9090 (tt) REVERT: E 195 ASN cc_start: 0.8364 (m-40) cc_final: 0.8075 (t0) REVERT: F 584 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8546 (mt-10) REVERT: F 629 MET cc_start: 0.8974 (mmm) cc_final: 0.8565 (mmt) REVERT: J 30 ARG cc_start: 0.8660 (ttp-110) cc_final: 0.8395 (ttp-110) outliers start: 70 outliers final: 47 residues processed: 282 average time/residue: 0.3236 time to fit residues: 140.7126 Evaluate side-chains 255 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 204 time to evaluate : 2.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 92 CYS Chi-restraints excluded: chain M residue 85 ASP Chi-restraints excluded: chain E residue 88 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 322 ILE Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 449 ILE Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 105 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 56 optimal weight: 20.0000 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 HIS D 591 GLN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21234 Z= 0.286 Angle : 0.700 9.590 28866 Z= 0.339 Chirality : 0.050 0.491 3723 Planarity : 0.004 0.049 3429 Dihedral : 10.009 82.265 5763 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.28 % Allowed : 11.59 % Favored : 85.14 % 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: 0.44 (0.17), residues: 2325 helix: 0.86 (0.28), residues: 372 sheet: 0.78 (0.19), residues: 657 loop : -0.06 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 91 HIS 0.018 0.001 HIS H 97 PHE 0.016 0.002 PHE C 233 TYR 0.035 0.002 TYR F 643 ARG 0.007 0.001 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 208 time to evaluate : 2.482 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: A 69 TRP cc_start: 0.8684 (m-90) cc_final: 0.8411 (m-90) REVERT: A 202 THR cc_start: 0.9577 (m) cc_final: 0.9348 (p) REVERT: A 260 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8466 (mm) REVERT: A 475 MET cc_start: 0.8377 (tpp) cc_final: 0.8079 (tpp) REVERT: B 584 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8347 (mt-10) REVERT: B 623 TRP cc_start: 0.7176 (m-10) cc_final: 0.6867 (m-10) REVERT: H 16 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7024 (tt0) REVERT: H 30 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7351 (tpp-160) REVERT: H 43 LYS cc_start: 0.8284 (mmmt) cc_final: 0.8077 (mmmt) REVERT: L 79 GLU cc_start: 0.8482 (mp0) cc_final: 0.8215 (mp0) REVERT: C 91 GLU cc_start: 0.7341 (mp0) cc_final: 0.7134 (mp0) REVERT: C 475 MET cc_start: 0.8083 (mmm) cc_final: 0.7606 (tpp) REVERT: D 542 ARG cc_start: 0.6666 (tpt170) cc_final: 0.6350 (tpm170) REVERT: D 584 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8509 (mt-10) REVERT: M 79 GLU cc_start: 0.8630 (mp0) cc_final: 0.8297 (mp0) REVERT: E 195 ASN cc_start: 0.8339 (m-40) cc_final: 0.8052 (t0) REVERT: E 283 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8437 (p) REVERT: F 584 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8572 (mt-10) REVERT: F 629 MET cc_start: 0.9010 (mmm) cc_final: 0.8703 (mmt) outliers start: 69 outliers final: 49 residues processed: 263 average time/residue: 0.3262 time to fit residues: 132.9127 Evaluate side-chains 250 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 55 optimal weight: 20.0000 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21234 Z= 0.295 Angle : 0.699 9.921 28866 Z= 0.339 Chirality : 0.049 0.474 3723 Planarity : 0.005 0.062 3429 Dihedral : 9.857 81.777 5763 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.13 % Allowed : 10.97 % Favored : 84.90 % 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: 0.34 (0.17), residues: 2325 helix: 0.81 (0.28), residues: 372 sheet: 0.79 (0.20), residues: 645 loop : -0.18 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 91 HIS 0.006 0.001 HIS C 330 PHE 0.015 0.002 PHE N 98 TYR 0.049 0.002 TYR F 643 ARG 0.009 0.001 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 205 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TRP cc_start: 0.8745 (m-90) cc_final: 0.8469 (m-10) REVERT: A 159 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.8191 (m-10) REVERT: A 260 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8648 (mm) REVERT: A 475 MET cc_start: 0.8307 (tpp) cc_final: 0.8083 (tpp) REVERT: B 584 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8356 (mt-10) REVERT: B 623 TRP cc_start: 0.7180 (m-10) cc_final: 0.6827 (m-10) REVERT: B 629 MET cc_start: 0.8994 (mmm) cc_final: 0.8490 (mmm) REVERT: H 16 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6929 (tt0) REVERT: H 43 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7918 (mmmt) REVERT: H 100 MET cc_start: 0.9060 (mpp) cc_final: 0.8720 (mpp) REVERT: L 79 GLU cc_start: 0.8567 (mp0) cc_final: 0.8257 (mp0) REVERT: C 475 MET cc_start: 0.8113 (mmm) cc_final: 0.7705 (tpp) REVERT: D 584 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8492 (mt-10) REVERT: D 626 MET cc_start: 0.8476 (tpp) cc_final: 0.8241 (tpp) REVERT: D 630 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8339 (mm-30) REVERT: M 79 GLU cc_start: 0.8582 (mp0) cc_final: 0.8258 (mp0) REVERT: M 104 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7603 (mp) REVERT: E 195 ASN cc_start: 0.8329 (m-40) cc_final: 0.8011 (t0) REVERT: F 577 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8382 (tm-30) REVERT: F 584 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8587 (mt-10) REVERT: F 629 MET cc_start: 0.9061 (mmm) cc_final: 0.8837 (mmt) REVERT: N 79 GLU cc_start: 0.8537 (mp0) cc_final: 0.8305 (mp0) outliers start: 87 outliers final: 61 residues processed: 272 average time/residue: 0.3274 time to fit residues: 138.7317 Evaluate side-chains 253 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 188 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 30 ARG Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 222 optimal weight: 20.0000 chunk 139 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 HIS ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21234 Z= 0.315 Angle : 0.715 10.221 28866 Z= 0.345 Chirality : 0.049 0.482 3723 Planarity : 0.005 0.071 3429 Dihedral : 9.890 81.673 5761 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.13 % Allowed : 12.01 % Favored : 83.86 % 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: 0.22 (0.17), residues: 2325 helix: 0.79 (0.28), residues: 372 sheet: 0.67 (0.20), residues: 645 loop : -0.25 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 69 HIS 0.007 0.001 HIS I 3 PHE 0.016 0.002 PHE N 98 TYR 0.042 0.002 TYR F 643 ARG 0.009 0.001 ARG L 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 191 time to evaluate : 2.462 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 69 TRP cc_start: 0.8797 (m-90) cc_final: 0.8468 (m-10) REVERT: A 159 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8190 (m-10) REVERT: A 260 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8557 (mm) REVERT: B 584 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: B 629 MET cc_start: 0.8992 (mmm) cc_final: 0.8619 (mmm) REVERT: H 16 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7024 (tt0) REVERT: H 100 MET cc_start: 0.9054 (mpp) cc_final: 0.8700 (mpp) REVERT: L 79 GLU cc_start: 0.8597 (mp0) cc_final: 0.8329 (mp0) REVERT: C 475 MET cc_start: 0.8136 (mmm) cc_final: 0.7816 (tpp) REVERT: D 584 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8502 (mt-10) REVERT: D 629 MET cc_start: 0.8620 (mmm) cc_final: 0.8390 (mmt) REVERT: M 79 GLU cc_start: 0.8573 (mp0) cc_final: 0.8211 (mp0) REVERT: M 104 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7835 (mp) REVERT: E 159 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: E 195 ASN cc_start: 0.8437 (m-40) cc_final: 0.8141 (t0) REVERT: E 283 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8521 (p) REVERT: F 577 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8405 (tm-30) REVERT: F 584 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8567 (mt-10) REVERT: F 629 MET cc_start: 0.9025 (mmm) cc_final: 0.8672 (mmm) REVERT: N 79 GLU cc_start: 0.8502 (mp0) cc_final: 0.8292 (mp0) REVERT: N 83 GLU cc_start: 0.8217 (pp20) cc_final: 0.7760 (pp20) outliers start: 87 outliers final: 63 residues processed: 254 average time/residue: 0.3158 time to fit residues: 125.3135 Evaluate side-chains 248 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 179 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 593 LEU Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 75 LYS Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 536 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 574 LYS Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain D residue 640 ASP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain M residue 51 ASN Chi-restraints excluded: chain M residue 104 LEU Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 345 VAL Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain J residue 89 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 39 ARG Chi-restraints excluded: chain N residue 51 ASN Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 20.0000 chunk 67 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 175 optimal weight: 0.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 279 ASN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN E 425 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21234 Z= 0.189 Angle : 0.657 13.601 28866 Z= 0.315 Chirality : 0.048 0.412 3723 Planarity : 0.004 0.053 3429 Dihedral : 9.411 75.874 5761 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 13.63 % Favored : 83.67 % 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: 0.39 (0.17), residues: 2325 helix: 0.93 (0.28), residues: 372 sheet: 0.69 (0.20), residues: 651 loop : -0.08 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 69 HIS 0.006 0.001 HIS H 3 PHE 0.014 0.001 PHE C 233 TYR 0.024 0.001 TYR F 643 ARG 0.007 0.000 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 201 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 69 TRP cc_start: 0.8796 (m-90) cc_final: 0.8428 (m-10) REVERT: A 260 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8560 (mm) REVERT: B 584 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: H 16 GLU cc_start: 0.7355 (mt-10) cc_final: 0.7101 (tt0) REVERT: H 100 MET cc_start: 0.8976 (mpp) cc_final: 0.8659 (mpp) REVERT: L 79 GLU cc_start: 0.8654 (mp0) cc_final: 0.8414 (mp0) REVERT: C 475 MET cc_start: 0.8025 (mmm) cc_final: 0.7729 (tpp) REVERT: D 584 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8442 (mt-10) REVERT: M 79 GLU cc_start: 0.8593 (mp0) cc_final: 0.8280 (mp0) REVERT: E 195 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7934 (t0) REVERT: E 283 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8466 (p) REVERT: F 577 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8341 (tm-30) REVERT: F 584 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8566 (mt-10) REVERT: N 79 GLU cc_start: 0.8598 (mp0) cc_final: 0.8385 (mp0) REVERT: N 83 GLU cc_start: 0.8201 (pp20) cc_final: 0.7753 (pp20) outliers start: 57 outliers final: 44 residues processed: 245 average time/residue: 0.3301 time to fit residues: 125.3733 Evaluate side-chains 234 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 186 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 97 LYS Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 196 optimal weight: 0.9990 chunk 206 optimal weight: 0.3980 chunk 136 optimal weight: 5.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 656 ASN I 5 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 21234 Z= 0.280 Angle : 0.690 11.311 28866 Z= 0.332 Chirality : 0.048 0.436 3723 Planarity : 0.004 0.053 3429 Dihedral : 9.496 77.324 5761 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.13 % Allowed : 13.53 % Favored : 83.33 % 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: 0.29 (0.17), residues: 2325 helix: 0.84 (0.28), residues: 372 sheet: 0.64 (0.20), residues: 651 loop : -0.17 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 631 HIS 0.005 0.001 HIS C 330 PHE 0.013 0.001 PHE C 233 TYR 0.022 0.002 TYR B 643 ARG 0.007 0.001 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 192 time to evaluate : 2.492 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 69 TRP cc_start: 0.8771 (m-90) cc_final: 0.8377 (m-10) REVERT: A 159 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8062 (m-10) REVERT: A 201 ILE cc_start: 0.8824 (tt) cc_final: 0.8608 (tt) REVERT: A 260 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8575 (mm) REVERT: B 584 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: B 656 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7855 (p0) REVERT: H 16 GLU cc_start: 0.7325 (mt-10) cc_final: 0.6975 (tt0) REVERT: H 100 MET cc_start: 0.9035 (mpp) cc_final: 0.8695 (mpp) REVERT: H 100 ASP cc_start: 0.8501 (t0) cc_final: 0.8294 (t0) REVERT: L 79 GLU cc_start: 0.8646 (mp0) cc_final: 0.8306 (mp0) REVERT: C 475 MET cc_start: 0.8127 (mmm) cc_final: 0.7814 (tpp) REVERT: D 584 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8478 (mt-10) REVERT: M 79 GLU cc_start: 0.8565 (mp0) cc_final: 0.8195 (mp0) REVERT: E 195 ASN cc_start: 0.8306 (OUTLIER) cc_final: 0.7913 (t0) REVERT: E 283 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8478 (p) REVERT: F 577 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8364 (tm-30) REVERT: F 584 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8573 (mt-10) REVERT: N 79 GLU cc_start: 0.8567 (mp0) cc_final: 0.8351 (mp0) REVERT: N 83 GLU cc_start: 0.8236 (pp20) cc_final: 0.7779 (pp20) outliers start: 66 outliers final: 52 residues processed: 242 average time/residue: 0.3189 time to fit residues: 120.6234 Evaluate side-chains 238 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 180 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain B residue 640 ASP Chi-restraints excluded: chain B residue 656 ASN Chi-restraints excluded: chain H residue 32 ASN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain L residue 51 ASN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 195 ASN Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 491 ILE Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 183 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21234 Z= 0.187 Angle : 0.667 10.439 28866 Z= 0.319 Chirality : 0.048 0.398 3723 Planarity : 0.004 0.067 3429 Dihedral : 9.126 72.379 5759 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.52 % Allowed : 14.48 % Favored : 83.00 % 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: 0.42 (0.18), residues: 2325 helix: 0.88 (0.28), residues: 369 sheet: 0.69 (0.20), residues: 651 loop : -0.04 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP D 631 HIS 0.005 0.001 HIS H 3 PHE 0.016 0.001 PHE C 233 TYR 0.024 0.001 TYR B 643 ARG 0.008 0.001 ARG M 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 197 time to evaluate : 2.288 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 69 TRP cc_start: 0.8751 (m-90) cc_final: 0.8353 (m-10) REVERT: A 159 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: A 260 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8563 (mm) REVERT: B 584 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8224 (mt-10) REVERT: H 16 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6969 (tt0) REVERT: H 100 MET cc_start: 0.8978 (mpp) cc_final: 0.8675 (mpp) REVERT: L 79 GLU cc_start: 0.8668 (mp0) cc_final: 0.8325 (mp0) REVERT: C 475 MET cc_start: 0.8011 (mmm) cc_final: 0.7729 (tpp) REVERT: D 584 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8425 (mt-10) REVERT: D 629 MET cc_start: 0.8530 (mmm) cc_final: 0.8166 (mmt) REVERT: I 43 LYS cc_start: 0.8307 (mmmm) cc_final: 0.7954 (mmmt) REVERT: M 79 GLU cc_start: 0.8610 (mp0) cc_final: 0.8299 (mp0) REVERT: E 195 ASN cc_start: 0.8407 (m-40) cc_final: 0.7975 (t0) REVERT: E 283 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8447 (p) REVERT: F 577 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8338 (tm-30) REVERT: F 584 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8597 (mt-10) REVERT: N 79 GLU cc_start: 0.8647 (mp0) cc_final: 0.8424 (mp0) REVERT: N 83 GLU cc_start: 0.8230 (pp20) cc_final: 0.7786 (pp20) outliers start: 53 outliers final: 44 residues processed: 238 average time/residue: 0.3493 time to fit residues: 129.9891 Evaluate side-chains 233 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 197 ASN Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 598 CYS Chi-restraints excluded: chain H residue 58 ASN Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 105 THR Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 119 CYS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 598 CYS Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 97 HIS Chi-restraints excluded: chain E residue 95 MET Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 234 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain E residue 326 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 587 LEU Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain F residue 641 ILE Chi-restraints excluded: chain J residue 105 THR Chi-restraints excluded: chain N residue 78 VAL Chi-restraints excluded: chain N residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 591 GLN ** E 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.098174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078807 restraints weight = 63286.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.080247 restraints weight = 38904.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.080581 restraints weight = 33323.935| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21234 Z= 0.227 Angle : 0.670 10.079 28866 Z= 0.320 Chirality : 0.048 0.399 3723 Planarity : 0.004 0.076 3429 Dihedral : 9.109 72.530 5759 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.37 % Allowed : 14.91 % Favored : 82.72 % 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: 0.41 (0.18), residues: 2325 helix: 0.90 (0.28), residues: 369 sheet: 0.69 (0.20), residues: 651 loop : -0.06 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 631 HIS 0.009 0.001 HIS I 3 PHE 0.013 0.001 PHE C 233 TYR 0.036 0.002 TYR B 643 ARG 0.010 0.001 ARG F 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.95 seconds wall clock time: 69 minutes 35.46 seconds (4175.46 seconds total)