Starting phenix.real_space_refine on Sun Feb 18 04:38:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lxm_23571/02_2024/7lxm_23571.pdb" } resolution = 3.41 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= 0.014 sd= 0.103 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 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 381": "OE1" <-> "OE2" 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 TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "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 62": "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 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 381": "OE1" <-> "OE2" 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 "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 62": "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 TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" 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 "P TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.06s 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: "N" 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: "P" 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: "O" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 11.43, per 1000 atoms: 0.55 Number of scatterers: 20820 At special positions: 0 Unit cell: (149.796, 154.926, 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=2.15 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=2.06 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.18 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=2.03 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=2.03 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=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 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=2.15 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=2.05 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=2.16 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=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.15 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=2.07 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 I 1 " - " ASN A 88 " " NAG J 1 " - " ASN A 130 " " NAG K 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: 10.54 Conformation dependent library (CDL) restraints added in 3.2 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: 59 helices and 45 sheets defined 21.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.184A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 351 removed outlier: 3.725A pdb=" N GLU A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.937A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.834A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.140A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 569 through 596 removed outlier: 4.242A pdb=" N GLN B 575 " --> pdb=" O TRP B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.504A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 removed outlier: 3.887A pdb=" N ASN B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.958A pdb=" N ASN B 656 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU B 657 " --> pdb=" O GLN B 653 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.214A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (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 99 through 117 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 351 removed outlier: 3.645A pdb=" N GLU C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.899A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 removed outlier: 3.841A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.133A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 541 Processing helix chain 'D' and resid 569 through 596 removed outlier: 4.354A pdb=" N GLN D 575 " --> pdb=" O TRP D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 636 removed outlier: 3.505A pdb=" N GLU D 634 " --> pdb=" O GLU D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 648 Processing helix chain 'D' and resid 651 through 660 removed outlier: 3.605A pdb=" N ASN D 656 " --> pdb=" O GLN D 652 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N GLU D 657 " --> pdb=" O GLN D 653 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 4.143A pdb=" N ASN N 32 " --> pdb=" O VAL N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 65 No H-bonds generated for 'chain 'N' and resid 63 through 65' Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'N' and resid 100D through 100H Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 3.636A pdb=" N GLU E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.903A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 3.770A pdb=" N SER E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.144A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 569 through 596 removed outlier: 4.502A pdb=" N GLN F 575 " --> pdb=" O TRP F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.508A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 648 Processing helix chain 'F' and resid 651 through 660 removed outlier: 3.607A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 32 removed outlier: 4.173A pdb=" N ASN P 32 " --> pdb=" O VAL P 29 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 56 removed outlier: 4.082A pdb=" N GLY P 55 " --> pdb=" O HIS P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100D through 100H Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.792A 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: 4.641A 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 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: 6.658A 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: 6.631A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.588A 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: 10.588A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 11.786A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.862A 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: 6.198A 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: 6.568A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.754A 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: 7.127A pdb=" N CYS H 92 " --> pdb=" O TRP H 101 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N TRP H 101 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.018A 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: 6.446A pdb=" N THR L 8 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE L 105 " --> pdb=" O THR L 8 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL L 11 " --> pdb=" O ILE L 105 " (cutoff:3.500A) removed outlier: 6.748A 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: 4.750A 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: 4.668A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 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: 6.735A 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: 6.634A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (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: 10.714A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.916A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.750A pdb=" N LEU C 288 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 11.761A pdb=" N LEU C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (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 308 Processing sheet with id=AC8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.499A pdb=" N TRP N 34 " --> pdb=" O TYR N 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR N 50 " --> pdb=" O TRP N 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 11 through 12 removed outlier: 7.127A pdb=" N CYS N 92 " --> pdb=" O TRP N 101 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TRP N 101 " --> pdb=" O CYS N 92 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N THR N 94 " --> pdb=" O ASP N 100Q" (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 8 through 13 removed outlier: 6.397A pdb=" N THR M 8 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE M 105 " --> pdb=" O THR M 8 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL M 11 " --> pdb=" O ILE M 105 " (cutoff:3.500A) removed outlier: 6.741A 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: 4.744A 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: 4.626A 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 Processing sheet with id=AD7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'E' and resid 130 through 133 Processing sheet with id=AD9, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AE1, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.713A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.628A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.709A 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=AE3, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.709A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.910A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.770A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 11.766A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.860A 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=AE4, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AE5, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'P' and resid 11 through 12 removed outlier: 6.517A pdb=" N TRP P 34 " --> pdb=" O TYR P 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR P 50 " --> pdb=" O TRP P 34 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 11 through 12 removed outlier: 7.109A pdb=" N CYS P 92 " --> pdb=" O TRP P 101 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N TRP P 101 " --> pdb=" O CYS P 92 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N THR P 94 " --> pdb=" O ASP P 100Q" (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 8 through 13 removed outlier: 6.391A pdb=" N THR O 8 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE O 105 " --> pdb=" O THR O 8 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL O 11 " --> pdb=" O ILE O 105 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP O 35 " --> pdb=" O ILE O 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 19 through 23 728 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 11.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5038 1.32 - 1.47: 7214 1.47 - 1.61: 8835 1.61 - 1.75: 9 1.75 - 1.89: 138 Bond restraints: 21234 Sorted by residual: bond pdb=" CB CYS C 247 " pdb=" SG CYS C 247 " ideal model delta sigma weight residual 1.808 1.613 0.195 3.30e-02 9.18e+02 3.49e+01 bond pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 1.808 1.615 0.193 3.30e-02 9.18e+02 3.43e+01 bond pdb=" CA THR E 137 " pdb=" C THR E 137 " ideal model delta sigma weight residual 1.528 1.458 0.070 1.33e-02 5.65e+03 2.76e+01 bond pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 1.502 1.384 0.118 2.30e-02 1.89e+03 2.62e+01 bond pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 1.502 1.385 0.117 2.30e-02 1.89e+03 2.61e+01 ... (remaining 21229 not shown) Histogram of bond angle deviations from ideal: 96.92 - 104.39: 356 104.39 - 111.86: 10549 111.86 - 119.33: 7906 119.33 - 126.80: 9749 126.80 - 134.27: 306 Bond angle restraints: 28866 Sorted by residual: angle pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " pdb=" CG PHE A 159 " ideal model delta sigma weight residual 113.80 122.57 -8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " pdb=" CG PHE C 159 " ideal model delta sigma weight residual 113.80 122.51 -8.71 1.00e+00 1.00e+00 7.60e+01 angle pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " pdb=" CG PHE E 159 " ideal model delta sigma weight residual 113.80 122.49 -8.69 1.00e+00 1.00e+00 7.55e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.87 128.09 -8.22 1.04e+00 9.25e-01 6.25e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.87 128.08 -8.21 1.04e+00 9.25e-01 6.23e+01 ... (remaining 28861 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.45: 14110 22.45 - 44.90: 360 44.90 - 67.34: 120 67.34 - 89.79: 104 89.79 - 112.24: 72 Dihedral angle restraints: 14766 sinusoidal: 7890 harmonic: 6876 Sorted by residual: dihedral pdb=" C PHE C 159 " pdb=" N PHE C 159 " pdb=" CA PHE C 159 " pdb=" CB PHE C 159 " ideal model delta harmonic sigma weight residual -122.60 -107.87 -14.73 0 2.50e+00 1.60e-01 3.47e+01 dihedral pdb=" C PHE A 159 " pdb=" N PHE A 159 " pdb=" CA PHE A 159 " pdb=" CB PHE A 159 " ideal model delta harmonic sigma weight residual -122.60 -107.96 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" C PHE E 159 " pdb=" N PHE E 159 " pdb=" CA PHE E 159 " pdb=" CB PHE E 159 " ideal model delta harmonic sigma weight residual -122.60 -108.02 -14.58 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 14763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2533 0.108 - 0.216: 1010 0.216 - 0.324: 142 0.324 - 0.432: 32 0.432 - 0.540: 6 Chirality restraints: 3723 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.66 0.26 2.00e-02 2.50e+03 1.67e+02 chirality pdb=" C1 NAG e 2 " pdb=" O4 NAG e 1 " pdb=" C2 NAG e 2 " pdb=" O5 NAG e 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.54e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.43e+02 ... (remaining 3720 not shown) Planarity restraints: 3480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.094 2.00e-02 2.50e+03 9.89e-02 1.22e+02 pdb=" CG ASN D 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.159 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 611 " -0.094 2.00e-02 2.50e+03 9.87e-02 1.22e+02 pdb=" CG ASN F 611 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN F 611 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN F 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG F 701 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 611 " -0.094 2.00e-02 2.50e+03 9.85e-02 1.21e+02 pdb=" CG ASN B 611 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 611 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN B 611 " 0.158 2.00e-02 2.50e+03 pdb=" C1 NAG B 701 " -0.116 2.00e-02 2.50e+03 ... (remaining 3477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2997 2.73 - 3.28: 18807 3.28 - 3.82: 34213 3.82 - 4.36: 41635 4.36 - 4.90: 67793 Nonbonded interactions: 165445 Sorted by model distance: nonbonded pdb=" O4 MAN G 5 " pdb=" O6 MAN G 5 " model vdw 2.194 2.440 nonbonded pdb=" O4 MAN o 8 " pdb=" O6 MAN o 8 " model vdw 2.232 2.440 nonbonded pdb=" O5 NAG a 2 " pdb=" O6 NAG a 2 " model vdw 2.255 2.432 nonbonded pdb=" O4 MAN o 5 " pdb=" O6 MAN o 5 " model vdw 2.257 2.440 nonbonded pdb=" O4 MAN a 5 " pdb=" O6 MAN a 5 " model vdw 2.270 2.440 ... (remaining 165440 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 'I' selection = chain 'J' selection = chain 'K' 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 'N' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.290 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 56.030 Find NCS groups from input model: 1.340 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 0.195 21234 Z= 1.294 Angle : 1.800 12.734 28866 Z= 1.120 Chirality : 0.111 0.540 3723 Planarity : 0.009 0.051 3429 Dihedral : 15.746 112.236 10203 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 1.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.20 % Favored : 98.54 % Rotamer: Outliers : 0.24 % Allowed : 0.19 % Favored : 99.57 % Cbeta Deviations : 0.18 % 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: 0.80 (0.17), residues: 2325 helix: -0.63 (0.25), residues: 396 sheet: 0.83 (0.19), residues: 708 loop : 0.97 (0.18), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.009 TRP A 96 HIS 0.008 0.002 HIS H 52 PHE 0.057 0.009 PHE A 159 TYR 0.045 0.007 TYR N 100O ARG 0.008 0.001 ARG P 66 *********************** 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 523 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 518 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7849 (mmm160) REVERT: A 99 ASN cc_start: 0.8375 (t0) cc_final: 0.8028 (t0) REVERT: A 325 ASP cc_start: 0.8135 (m-30) cc_final: 0.7866 (m-30) REVERT: H 13 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7799 (mmmt) REVERT: H 100 LYS cc_start: 0.7839 (mttt) cc_final: 0.7502 (mtpp) REVERT: L 58 ILE cc_start: 0.8515 (mm) cc_final: 0.8257 (mm) REVERT: C 46 LYS cc_start: 0.7771 (mmtt) cc_final: 0.7411 (mtmm) REVERT: C 66 ARG cc_start: 0.8168 (mtp180) cc_final: 0.7768 (tpt170) REVERT: C 103 GLN cc_start: 0.8005 (tt0) cc_final: 0.7796 (tt0) REVERT: D 608 VAL cc_start: 0.7631 (t) cc_final: 0.7409 (m) REVERT: D 625 ASN cc_start: 0.7414 (m-40) cc_final: 0.7050 (t0) REVERT: N 13 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7883 (mmmt) REVERT: N 100 LYS cc_start: 0.7946 (mttt) cc_final: 0.7630 (mtpp) REVERT: E 46 LYS cc_start: 0.7764 (mmtt) cc_final: 0.7271 (mtmm) REVERT: E 66 ARG cc_start: 0.8288 (mtp180) cc_final: 0.7920 (mmm160) REVERT: E 99 ASN cc_start: 0.8205 (t0) cc_final: 0.7874 (t0) REVERT: E 348 LYS cc_start: 0.7335 (tptt) cc_final: 0.6508 (mptt) REVERT: E 498 PRO cc_start: 0.6550 (Cg_endo) cc_final: 0.6242 (Cg_exo) REVERT: P 13 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7930 (mmmt) REVERT: P 100 LYS cc_start: 0.7886 (mttt) cc_final: 0.7528 (mtpp) outliers start: 5 outliers final: 5 residues processed: 523 average time/residue: 0.3873 time to fit residues: 291.9988 Evaluate side-chains 284 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 279 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 289 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: 0.7980 chunk 175 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 209 optimal weight: 9.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 567 GLN B 625 ASN B 650 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** D 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 362 ASN ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21234 Z= 0.236 Angle : 0.740 8.501 28866 Z= 0.371 Chirality : 0.051 0.350 3723 Planarity : 0.005 0.055 3429 Dihedral : 12.954 84.392 5755 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.68 % Favored : 98.28 % Rotamer: Outliers : 2.52 % Allowed : 8.02 % Favored : 89.46 % 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: 0.70 (0.28), residues: 351 sheet: 0.56 (0.19), residues: 669 loop : 0.35 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 610 HIS 0.008 0.001 HIS P 52 PHE 0.021 0.002 PHE A 468 TYR 0.016 0.002 TYR N 91 ARG 0.008 0.001 ARG E 350 *********************** 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 407 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 354 time to evaluate : 2.285 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: A 66 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7965 (mmm160) REVERT: A 348 LYS cc_start: 0.7638 (tptt) cc_final: 0.6745 (mptt) REVERT: A 475 MET cc_start: 0.8526 (mmt) cc_final: 0.8251 (mmm) REVERT: B 591 GLN cc_start: 0.7408 (tt0) cc_final: 0.7115 (tt0) REVERT: B 626 MET cc_start: 0.6932 (mtt) cc_final: 0.6568 (mtp) REVERT: H 13 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7815 (mmmt) REVERT: H 77 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7309 (tp) REVERT: H 100 LYS cc_start: 0.7849 (mttt) cc_final: 0.7462 (mtpp) REVERT: L 51 ASN cc_start: 0.7416 (m-40) cc_final: 0.6871 (m-40) REVERT: C 350 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5989 (ttm-80) REVERT: C 502 LYS cc_start: 0.6745 (pttt) cc_final: 0.6491 (tmtt) REVERT: N 13 LYS cc_start: 0.8159 (mmtt) cc_final: 0.7888 (mmmt) REVERT: N 77 LEU cc_start: 0.7616 (mm) cc_final: 0.7346 (mm) REVERT: N 100 LYS cc_start: 0.7972 (mttt) cc_final: 0.7617 (mtpp) REVERT: E 46 LYS cc_start: 0.7614 (mmtt) cc_final: 0.7179 (mtmm) REVERT: E 66 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7745 (mmm160) REVERT: E 99 ASN cc_start: 0.8062 (t0) cc_final: 0.7848 (t0) REVERT: F 653 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8075 (mm-40) REVERT: F 656 ASN cc_start: 0.7301 (p0) cc_final: 0.6775 (p0) REVERT: P 13 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7860 (mmmt) REVERT: P 29 VAL cc_start: 0.7889 (p) cc_final: 0.7584 (t) REVERT: P 77 LEU cc_start: 0.7492 (mt) cc_final: 0.7175 (tp) REVERT: P 81 ARG cc_start: 0.7798 (mtp-110) cc_final: 0.6890 (mtt90) REVERT: P 100 LYS cc_start: 0.7927 (mttt) cc_final: 0.7495 (mtpp) REVERT: O 51 ASN cc_start: 0.7584 (m-40) cc_final: 0.7266 (m110) outliers start: 53 outliers final: 30 residues processed: 393 average time/residue: 0.3403 time to fit residues: 202.0665 Evaluate side-chains 306 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 274 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 567 GLN Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 642 ILE Chi-restraints excluded: chain B residue 649 SER Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 368 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 539 VAL Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 368 ASP Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 644 SER Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 210 optimal weight: 20.0000 chunk 227 optimal weight: 0.6980 chunk 187 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 71 optimal weight: 0.8980 chunk 168 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 577 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN L 37 GLN C 114 GLN D 650 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN F 577 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN O 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21234 Z= 0.222 Angle : 0.673 8.959 28866 Z= 0.332 Chirality : 0.050 0.399 3723 Planarity : 0.004 0.064 3429 Dihedral : 11.143 83.227 5745 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.42 % Allowed : 10.16 % Favored : 87.42 % 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: 0.50 (0.17), residues: 2325 helix: 0.88 (0.28), residues: 351 sheet: 0.51 (0.18), residues: 669 loop : 0.20 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 628 HIS 0.008 0.001 HIS P 52 PHE 0.016 0.002 PHE H 100K TYR 0.014 0.001 TYR F 643 ARG 0.005 0.000 ARG O 20 *********************** 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 348 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 297 time to evaluate : 2.225 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: A 66 ARG cc_start: 0.8407 (mtp180) cc_final: 0.7674 (tpm170) REVERT: A 225 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.8162 (mt) REVERT: A 348 LYS cc_start: 0.7689 (tptt) cc_final: 0.6782 (mptt) REVERT: A 475 MET cc_start: 0.8473 (mmt) cc_final: 0.8261 (mmm) REVERT: B 626 MET cc_start: 0.7126 (mtt) cc_final: 0.6860 (mtp) REVERT: H 13 LYS cc_start: 0.8162 (mmtt) cc_final: 0.7860 (mmmt) REVERT: H 100 LYS cc_start: 0.8043 (mttt) cc_final: 0.7598 (mtpp) REVERT: L 25 GLU cc_start: 0.7836 (pp20) cc_final: 0.7573 (pp20) REVERT: C 66 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.7453 (tpm170) REVERT: C 67 ASN cc_start: 0.7335 (t0) cc_final: 0.6973 (t0) REVERT: N 13 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7921 (mmmt) REVERT: N 77 LEU cc_start: 0.7816 (mm) cc_final: 0.7462 (mm) REVERT: N 100 LYS cc_start: 0.8040 (mttt) cc_final: 0.7655 (mtpp) REVERT: M 25 GLU cc_start: 0.7639 (pp20) cc_final: 0.7187 (pp20) REVERT: E 99 ASN cc_start: 0.8135 (t0) cc_final: 0.7902 (t0) REVERT: E 217 TYR cc_start: 0.8420 (m-80) cc_final: 0.8123 (m-10) REVERT: F 542 ARG cc_start: 0.7774 (tpt-90) cc_final: 0.7552 (ttt-90) REVERT: F 592 LEU cc_start: 0.8593 (tp) cc_final: 0.8380 (mp) REVERT: F 627 THR cc_start: 0.6369 (p) cc_final: 0.6006 (p) REVERT: P 13 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7902 (mmmt) REVERT: P 81 ARG cc_start: 0.7764 (mtp-110) cc_final: 0.6937 (mtt90) REVERT: P 100 LYS cc_start: 0.7995 (mttt) cc_final: 0.7582 (mtpp) REVERT: O 25 GLU cc_start: 0.7661 (pp20) cc_final: 0.7402 (pp20) outliers start: 51 outliers final: 29 residues processed: 330 average time/residue: 0.3381 time to fit residues: 168.1809 Evaluate side-chains 290 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 260 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain F residue 618 SER Chi-restraints excluded: chain F residue 634 GLU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 60 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 575 GLN ** H 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN D 575 GLN ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN F 650 GLN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 21234 Z= 0.457 Angle : 0.803 11.173 28866 Z= 0.395 Chirality : 0.054 0.375 3723 Planarity : 0.006 0.080 3429 Dihedral : 10.921 96.346 5745 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.42 % Allowed : 10.30 % Favored : 86.28 % 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 (0.16), residues: 2325 helix: 0.25 (0.27), residues: 369 sheet: 0.13 (0.19), residues: 615 loop : -0.40 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP D 610 HIS 0.009 0.002 HIS P 52 PHE 0.030 0.004 PHE H 100K TYR 0.021 0.003 TYR L 49 ARG 0.010 0.001 ARG C 504 *********************** 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 356 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 284 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8456 (mtp180) cc_final: 0.7658 (tpt170) REVERT: A 225 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8209 (mt) REVERT: A 348 LYS cc_start: 0.7761 (tptt) cc_final: 0.6897 (mptt) REVERT: B 626 MET cc_start: 0.7192 (mtt) cc_final: 0.6825 (mtp) REVERT: H 30 ARG cc_start: 0.8201 (ttp80) cc_final: 0.7815 (tpp80) REVERT: H 66 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7397 (mtp-110) REVERT: H 73 LYS cc_start: 0.8161 (ttmm) cc_final: 0.7538 (ttmm) REVERT: H 100 LYS cc_start: 0.8150 (mttt) cc_final: 0.7824 (mtpp) REVERT: C 66 ARG cc_start: 0.8376 (mmm-85) cc_final: 0.7500 (tpt170) REVERT: C 67 ASN cc_start: 0.7733 (t0) cc_final: 0.7519 (t0) REVERT: C 69 TRP cc_start: 0.8812 (m-90) cc_final: 0.8512 (m-90) REVERT: C 91 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6538 (mm-30) REVERT: C 92 ASN cc_start: 0.7553 (m-40) cc_final: 0.7115 (t0) REVERT: D 540 GLN cc_start: 0.5635 (OUTLIER) cc_final: 0.5325 (mp10) REVERT: N 77 LEU cc_start: 0.7669 (mm) cc_final: 0.7360 (mm) REVERT: N 100 LYS cc_start: 0.8276 (mttt) cc_final: 0.7855 (mtpp) REVERT: E 159 PHE cc_start: 0.8443 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: E 348 LYS cc_start: 0.7845 (tptt) cc_final: 0.6955 (mptt) REVERT: F 542 ARG cc_start: 0.7924 (tpt-90) cc_final: 0.7708 (ttt-90) REVERT: P 13 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7896 (mmmt) REVERT: P 100 LYS cc_start: 0.8334 (mttt) cc_final: 0.7906 (mtpp) outliers start: 72 outliers final: 46 residues processed: 334 average time/residue: 0.3527 time to fit residues: 176.4935 Evaluate side-chains 300 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 250 time to evaluate : 2.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 540 GLN Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 189 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN O 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 21234 Z= 0.251 Angle : 0.658 8.599 28866 Z= 0.326 Chirality : 0.049 0.350 3723 Planarity : 0.004 0.082 3429 Dihedral : 10.129 91.371 5745 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.85 % Allowed : 11.97 % Favored : 85.19 % 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: -0.26 (0.16), residues: 2325 helix: 0.61 (0.28), residues: 369 sheet: 0.03 (0.19), residues: 612 loop : -0.44 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 571 HIS 0.006 0.001 HIS H 52 PHE 0.016 0.002 PHE H 100K TYR 0.015 0.002 TYR C 486 ARG 0.007 0.001 ARG O 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 335 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 275 time to evaluate : 2.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7633 (tpt170) REVERT: A 225 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8174 (mt) REVERT: A 318 TYR cc_start: 0.8938 (m-80) cc_final: 0.8676 (m-80) REVERT: A 348 LYS cc_start: 0.7557 (tptt) cc_final: 0.6722 (mptt) REVERT: B 577 GLN cc_start: 0.8552 (tp-100) cc_final: 0.8171 (tp-100) REVERT: B 626 MET cc_start: 0.6844 (mtt) cc_final: 0.6558 (mtt) REVERT: H 30 ARG cc_start: 0.8172 (ttp80) cc_final: 0.7798 (tpp80) REVERT: H 66 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7406 (mtp180) REVERT: H 77 LEU cc_start: 0.7942 (mm) cc_final: 0.7684 (mm) REVERT: H 100 LYS cc_start: 0.8217 (mttt) cc_final: 0.7745 (mtpp) REVERT: L 25 GLU cc_start: 0.7642 (pp20) cc_final: 0.7274 (pp20) REVERT: C 66 ARG cc_start: 0.8436 (mmm-85) cc_final: 0.7544 (tpt170) REVERT: C 69 TRP cc_start: 0.8806 (m-90) cc_final: 0.8506 (m-90) REVERT: C 92 ASN cc_start: 0.7615 (m-40) cc_final: 0.7231 (t0) REVERT: C 271 ILE cc_start: 0.8111 (mt) cc_final: 0.7897 (mp) REVERT: N 30 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7943 (tpp80) REVERT: N 77 LEU cc_start: 0.7751 (mm) cc_final: 0.7423 (mm) REVERT: N 100 LYS cc_start: 0.8230 (mttt) cc_final: 0.7896 (mtpp) REVERT: M 25 GLU cc_start: 0.7593 (pp20) cc_final: 0.7152 (pp20) REVERT: E 66 ARG cc_start: 0.8639 (mmm-85) cc_final: 0.7697 (tpt170) REVERT: E 92 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7278 (t0) REVERT: F 542 ARG cc_start: 0.7926 (tpt-90) cc_final: 0.7672 (ttt-90) REVERT: P 13 LYS cc_start: 0.8209 (mmtt) cc_final: 0.7900 (mmmt) REVERT: P 100 LYS cc_start: 0.8257 (mttt) cc_final: 0.7868 (mtpp) outliers start: 60 outliers final: 41 residues processed: 316 average time/residue: 0.3449 time to fit residues: 164.2165 Evaluate side-chains 291 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 247 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 0.0170 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 21234 Z= 0.439 Angle : 0.753 8.579 28866 Z= 0.372 Chirality : 0.053 0.369 3723 Planarity : 0.005 0.083 3429 Dihedral : 10.388 97.887 5745 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.32 % Allowed : 13.06 % Favored : 83.62 % 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: -0.64 (0.16), residues: 2325 helix: 0.27 (0.27), residues: 384 sheet: -0.15 (0.20), residues: 591 loop : -0.72 (0.16), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 610 HIS 0.007 0.001 HIS H 52 PHE 0.024 0.003 PHE H 100K TYR 0.019 0.002 TYR M 49 ARG 0.007 0.001 ARG M 54 *********************** 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 328 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 258 time to evaluate : 2.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ARG cc_start: 0.8452 (mtp180) cc_final: 0.7958 (tpm170) REVERT: A 225 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 318 TYR cc_start: 0.9002 (m-80) cc_final: 0.8778 (m-80) REVERT: A 348 LYS cc_start: 0.7710 (tptt) cc_final: 0.6921 (mptt) REVERT: H 30 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7824 (tpp80) REVERT: H 66 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7524 (mtp180) REVERT: H 77 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7804 (mm) REVERT: H 100 LYS cc_start: 0.8282 (mttt) cc_final: 0.7891 (mtpp) REVERT: C 69 TRP cc_start: 0.8836 (m-90) cc_final: 0.8471 (m-90) REVERT: C 92 ASN cc_start: 0.7647 (m-40) cc_final: 0.7375 (t0) REVERT: D 628 TRP cc_start: 0.7390 (m100) cc_final: 0.7183 (m100) REVERT: N 6 GLU cc_start: 0.6828 (mp0) cc_final: 0.6492 (mp0) REVERT: N 30 ARG cc_start: 0.8194 (ttp80) cc_final: 0.7928 (tpp80) REVERT: N 77 LEU cc_start: 0.7670 (mm) cc_final: 0.7325 (mm) REVERT: N 100 LYS cc_start: 0.8242 (mttt) cc_final: 0.7881 (mtpp) REVERT: E 92 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7365 (t0) REVERT: E 159 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: F 608 VAL cc_start: 0.8439 (m) cc_final: 0.8196 (p) REVERT: P 13 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7957 (mmmt) REVERT: P 100 LYS cc_start: 0.8309 (mttt) cc_final: 0.7899 (mtpp) outliers start: 70 outliers final: 61 residues processed: 308 average time/residue: 0.3534 time to fit residues: 168.8174 Evaluate side-chains 314 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 248 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 591 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 17 THR Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 378 CYS Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 92 CYS Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 188 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 222 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21234 Z= 0.204 Angle : 0.638 8.534 28866 Z= 0.316 Chirality : 0.048 0.327 3723 Planarity : 0.005 0.087 3429 Dihedral : 9.720 90.736 5745 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.23 % Allowed : 13.25 % Favored : 83.52 % 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 (0.16), residues: 2325 helix: 0.69 (0.28), residues: 369 sheet: 0.03 (0.20), residues: 609 loop : -0.57 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 610 HIS 0.006 0.001 HIS H 52 PHE 0.017 0.002 PHE P 100K TYR 0.015 0.001 TYR A 486 ARG 0.008 0.001 ARG O 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 344 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 276 time to evaluate : 2.433 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: A 225 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8129 (mt) REVERT: H 30 ARG cc_start: 0.8152 (ttp80) cc_final: 0.7920 (tpp80) REVERT: H 66 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7327 (mtp180) REVERT: H 77 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7855 (mm) REVERT: H 100 LYS cc_start: 0.8262 (mttt) cc_final: 0.7876 (mtpp) REVERT: C 66 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.7914 (mtm110) REVERT: C 69 TRP cc_start: 0.8811 (m-90) cc_final: 0.8427 (m-90) REVERT: C 92 ASN cc_start: 0.7703 (m-40) cc_final: 0.7465 (t0) REVERT: C 271 ILE cc_start: 0.8076 (mt) cc_final: 0.7853 (mp) REVERT: N 30 ARG cc_start: 0.8166 (ttp80) cc_final: 0.7926 (tpp80) REVERT: N 77 LEU cc_start: 0.7858 (mm) cc_final: 0.7485 (mm) REVERT: N 100 LYS cc_start: 0.8218 (mttt) cc_final: 0.7892 (mtpp) REVERT: E 92 ASN cc_start: 0.7863 (OUTLIER) cc_final: 0.7489 (t0) REVERT: P 13 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7904 (mmmt) REVERT: P 77 LEU cc_start: 0.7732 (mm) cc_final: 0.7473 (mm) REVERT: P 100 LYS cc_start: 0.8297 (mttt) cc_final: 0.7873 (mtpp) outliers start: 68 outliers final: 45 residues processed: 320 average time/residue: 0.3381 time to fit residues: 164.5043 Evaluate side-chains 301 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 642 ILE Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 43 optimal weight: 0.0980 chunk 141 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21234 Z= 0.224 Angle : 0.639 8.630 28866 Z= 0.317 Chirality : 0.048 0.315 3723 Planarity : 0.005 0.087 3429 Dihedral : 9.457 89.265 5745 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.99 % Allowed : 13.77 % Favored : 83.24 % 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: 0.54 (0.27), residues: 384 sheet: 0.17 (0.21), residues: 558 loop : -0.52 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 610 HIS 0.005 0.001 HIS P 52 PHE 0.016 0.002 PHE P 100K TYR 0.012 0.001 TYR A 318 ARG 0.007 0.000 ARG O 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 329 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 266 time to evaluate : 2.215 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: A 225 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8077 (mt) REVERT: H 30 ARG cc_start: 0.8180 (ttp80) cc_final: 0.7947 (tpp80) REVERT: H 66 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7423 (mtp180) REVERT: H 77 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7880 (mm) REVERT: H 100 LYS cc_start: 0.8260 (mttt) cc_final: 0.7872 (mtpp) REVERT: C 66 ARG cc_start: 0.8347 (mmm-85) cc_final: 0.7988 (mtm110) REVERT: C 69 TRP cc_start: 0.8798 (m-90) cc_final: 0.8445 (m-90) REVERT: C 271 ILE cc_start: 0.8070 (mt) cc_final: 0.7835 (mp) REVERT: D 610 TRP cc_start: 0.6992 (m100) cc_final: 0.6765 (m100) REVERT: N 30 ARG cc_start: 0.8147 (ttp80) cc_final: 0.7924 (tpp80) REVERT: N 77 LEU cc_start: 0.7750 (mm) cc_final: 0.7445 (mm) REVERT: N 100 LYS cc_start: 0.8221 (mttt) cc_final: 0.7829 (mtpp) REVERT: E 92 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7506 (t0) REVERT: F 596 TRP cc_start: 0.8726 (m-10) cc_final: 0.8505 (m-10) REVERT: P 13 LYS cc_start: 0.8161 (mmtt) cc_final: 0.7929 (mmmt) REVERT: P 77 LEU cc_start: 0.7781 (OUTLIER) cc_final: 0.7550 (mm) REVERT: P 100 LYS cc_start: 0.8304 (mttt) cc_final: 0.7870 (mtpp) outliers start: 63 outliers final: 51 residues processed: 305 average time/residue: 0.3421 time to fit residues: 157.7399 Evaluate side-chains 310 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 254 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain D residue 642 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 622 ILE Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21234 Z= 0.286 Angle : 0.664 8.580 28866 Z= 0.329 Chirality : 0.049 0.312 3723 Planarity : 0.005 0.087 3429 Dihedral : 9.515 91.621 5745 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.18 % Allowed : 13.72 % Favored : 83.10 % 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: -0.36 (0.16), residues: 2325 helix: 0.47 (0.27), residues: 384 sheet: 0.28 (0.21), residues: 522 loop : -0.62 (0.15), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 571 HIS 0.006 0.001 HIS P 52 PHE 0.019 0.002 PHE H 100K TYR 0.014 0.002 TYR M 49 ARG 0.008 0.001 ARG N 81 *********************** 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 324 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 257 time to evaluate : 2.126 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: A 225 ILE cc_start: 0.8349 (OUTLIER) cc_final: 0.8085 (mt) REVERT: H 30 ARG cc_start: 0.8185 (ttp80) cc_final: 0.7944 (tpp80) REVERT: H 66 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: H 77 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7877 (mm) REVERT: H 100 LYS cc_start: 0.8269 (mttt) cc_final: 0.7871 (mtpp) REVERT: C 66 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7923 (mtm110) REVERT: C 69 TRP cc_start: 0.8819 (m-90) cc_final: 0.8449 (m-90) REVERT: C 271 ILE cc_start: 0.8079 (mt) cc_final: 0.7832 (mp) REVERT: D 610 TRP cc_start: 0.7026 (m100) cc_final: 0.6807 (m100) REVERT: N 30 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7911 (tpp80) REVERT: N 66 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7471 (mtp-110) REVERT: N 77 LEU cc_start: 0.7748 (mm) cc_final: 0.7419 (mm) REVERT: N 81 ARG cc_start: 0.8245 (mtt90) cc_final: 0.7193 (mtm110) REVERT: N 100 LYS cc_start: 0.8260 (mttt) cc_final: 0.7862 (mtpp) REVERT: E 92 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7560 (t0) REVERT: E 159 PHE cc_start: 0.8066 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: P 77 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7538 (mm) REVERT: P 100 LYS cc_start: 0.8305 (mttt) cc_final: 0.7870 (mtpp) outliers start: 67 outliers final: 55 residues processed: 297 average time/residue: 0.3420 time to fit residues: 153.3145 Evaluate side-chains 313 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 251 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 211 optimal weight: 0.0370 chunk 183 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 overall best weight: 3.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 50 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21234 Z= 0.341 Angle : 0.695 8.543 28866 Z= 0.346 Chirality : 0.050 0.309 3723 Planarity : 0.005 0.088 3429 Dihedral : 9.754 94.821 5745 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.13 % Allowed : 14.15 % 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: -0.49 (0.16), residues: 2325 helix: 0.40 (0.27), residues: 384 sheet: 0.15 (0.21), residues: 531 loop : -0.70 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 610 HIS 0.021 0.001 HIS P 52 PHE 0.021 0.002 PHE H 100K TYR 0.015 0.002 TYR M 49 ARG 0.010 0.001 ARG L 54 ********************** 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 316 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 250 time to evaluate : 2.150 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: A 225 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8130 (mt) REVERT: H 30 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7976 (tpp80) REVERT: H 66 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: H 77 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7926 (mm) REVERT: H 100 LYS cc_start: 0.8277 (mttt) cc_final: 0.7858 (mtpp) REVERT: L 20 ARG cc_start: 0.7254 (mmm-85) cc_final: 0.6832 (mmm160) REVERT: C 66 ARG cc_start: 0.8350 (mmm-85) cc_final: 0.7958 (mtm110) REVERT: C 69 TRP cc_start: 0.8810 (m-90) cc_final: 0.8417 (m-90) REVERT: C 271 ILE cc_start: 0.8099 (mt) cc_final: 0.7851 (mp) REVERT: N 30 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7914 (tpp80) REVERT: N 66 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7537 (mtp-110) REVERT: N 77 LEU cc_start: 0.7806 (mm) cc_final: 0.7489 (mm) REVERT: N 81 ARG cc_start: 0.8290 (mtt90) cc_final: 0.7252 (mtm110) REVERT: N 100 LYS cc_start: 0.8270 (mttt) cc_final: 0.7883 (mtpp) REVERT: E 92 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7602 (t0) REVERT: E 159 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7246 (m-80) REVERT: P 77 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (mm) REVERT: P 100 LYS cc_start: 0.8290 (mttt) cc_final: 0.7854 (mtpp) outliers start: 66 outliers final: 56 residues processed: 293 average time/residue: 0.3515 time to fit residues: 157.2094 Evaluate side-chains 303 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 240 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 529 THR Chi-restraints excluded: chain B residue 576 LEU Chi-restraints excluded: chain B residue 622 ILE Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 66 ARG Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 159 PHE Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 308 ARG Chi-restraints excluded: chain C residue 457 ASP Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 637 ASN Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 27 THR Chi-restraints excluded: chain N residue 32 ASN Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 92 CYS Chi-restraints excluded: chain M residue 22 THR Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 92 ASN Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 159 PHE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 217 TYR Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 457 ASP Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 599 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain P residue 27 THR Chi-restraints excluded: chain P residue 32 ASN Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain O residue 22 THR Chi-restraints excluded: chain O residue 97 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 51 ASN ** P 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.161499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.134887 restraints weight = 29904.598| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.78 r_work: 0.3314 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 21234 Z= 0.224 Angle : 0.642 8.783 28866 Z= 0.319 Chirality : 0.048 0.289 3723 Planarity : 0.005 0.089 3429 Dihedral : 9.361 90.733 5745 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.99 % Allowed : 14.48 % Favored : 82.53 % 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: -0.36 (0.16), residues: 2325 helix: 0.49 (0.27), residues: 384 sheet: 0.30 (0.21), residues: 516 loop : -0.64 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 610 HIS 0.008 0.001 HIS P 52 PHE 0.016 0.002 PHE P 100K TYR 0.011 0.001 TYR M 49 ARG 0.013 0.001 ARG P 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4365.99 seconds wall clock time: 80 minutes 49.94 seconds (4849.94 seconds total)