Starting phenix.real_space_refine on Fri Feb 23 10:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upw_26676/02_2024/7upw_26676_neut.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 23952 2.51 5 N 6153 2.21 5 O 7632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 138": "OD1" <-> "OD2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A ASP 936": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 138": "OD1" <-> "OD2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 420": "OD1" <-> "OD2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B ASP 586": "OD1" <-> "OD2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B ASP 745": "OD1" <-> "OD2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 820": "OD1" <-> "OD2" Residue "B ASP 843": "OD1" <-> "OD2" Residue "B PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 985": "OD1" <-> "OD2" Residue "B ASP 1118": "OD1" <-> "OD2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C GLU 309": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ASP 420": "OD1" <-> "OD2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C ASP 571": "OD1" <-> "OD2" Residue "C ASP 574": "OD1" <-> "OD2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 745": "OD1" <-> "OD2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C PHE 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 28": "OD1" <-> "OD2" Residue "E ASP 31": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 81": "OE1" <-> "OE2" Residue "E TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 151": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E ASP 185": "OD1" <-> "OD2" Residue "E PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 72": "OD1" <-> "OD2" Residue "F TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 17": "OD1" <-> "OD2" Residue "G ASP 28": "OD1" <-> "OD2" Residue "G TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G ASP 70": "OD1" <-> "OD2" Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 81": "OE1" <-> "OE2" Residue "G ASP 82": "OD1" <-> "OD2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G GLU 161": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G ASP 170": "OD1" <-> "OD2" Residue "G ASP 185": "OD1" <-> "OD2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 187": "OE1" <-> "OE2" Residue "G PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 72": "OD1" <-> "OD2" Residue "H ASP 85": "OD1" <-> "OD2" Residue "H ARG 96": "NH1" <-> "NH2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 1": "OD1" <-> "OD2" Residue "L ASP 17": "OD1" <-> "OD2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 50": "OD1" <-> "OD2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 92": "OD1" <-> "OD2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 122": "OD1" <-> "OD2" Residue "L PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L ASP 151": "OD1" <-> "OD2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 37893 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "B" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "C" Number of atoms: 8766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8766 Classifications: {'peptide': 1121} Link IDs: {'PTRANS': 53, 'TRANS': 1067} Chain breaks: 3 Chain: "D" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "F" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 213} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1622 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 200} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: {'MAN': 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "c" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "n" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "o" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 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: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} 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 Time building chain proxies: 19.76, per 1000 atoms: 0.52 Number of scatterers: 37893 At special positions: 0 Unit cell: (166, 163.51, 248.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 7632 8.00 N 6153 7.00 C 23952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.01 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.05 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.05 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.01 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.01 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.05 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.01 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.05 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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 Atom "HETATM37167 O5 NAG h 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM37737 O5 NAG B1403 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG M 2 " - " MAN M 3 " " NAG O 2 " - " MAN O 3 " " NAG P 2 " - " MAN P 3 " " NAG R 2 " - " MAN R 3 " " NAG S 2 " - " MAN S 3 " " NAG U 2 " - " MAN U 3 " " NAG W 2 " - " MAN W 3 " " NAG X 2 " - " MAN X 3 " " NAG Y 2 " - " MAN Y 3 " " NAG a 2 " - " MAN a 3 " " NAG b 2 " - " MAN b 3 " " NAG d 2 " - " MAN d 3 " " NAG e 2 " - " MAN e 3 " " NAG g 2 " - " MAN g 3 " " NAG i 2 " - " MAN i 3 " " NAG j 2 " - " MAN j 3 " " NAG k 2 " - " MAN k 3 " " NAG m 2 " - " MAN m 3 " " NAG n 2 " - " MAN n 3 " " NAG p 2 " - " MAN p 3 " " NAG q 2 " - " MAN q 3 " " NAG s 2 " - " MAN s 3 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " BETA1-6 " NAG Q 1 " - " FUC Q 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG T 1 " - " FUC T 3 " " NAG c 1 " - " FUC c 3 " " NAG f 1 " - " FUC f 3 " " NAG o 1 " - " FUC o 3 " " NAG r 1 " - " FUC r 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 149 " " NAG A1403 " - " ASN A 331 " " NAG A1404 " - " ASN A 603 " " NAG A1405 " - " ASN A 657 " " NAG A1406 " - " ASN A 709 " " NAG A1407 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 331 " " NAG B1404 " - " ASN B 603 " " NAG B1405 " - " ASN B 657 " " NAG B1406 " - " ASN B 709 " " NAG B1407 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 603 " " NAG C1405 " - " ASN C 657 " " NAG C1406 " - " ASN C 709 " " NAG C1407 " - " ASN C1158 " " NAG I 1 " - " ASN A 17 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 282 " " NAG N 1 " - " ASN A 616 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN A1134 " " NAG T 1 " - " ASN A 343 " " NAG U 1 " - " ASN A 165 " " NAG V 1 " - " ASN B 17 " " NAG W 1 " - " ASN B 122 " " NAG X 1 " - " ASN B 234 " " NAG Y 1 " - " ASN B 282 " " NAG Z 1 " - " ASN B 616 " " NAG a 1 " - " ASN B 717 " " NAG b 1 " - " ASN B 801 " " NAG c 1 " - " ASN B1074 " " NAG d 1 " - " ASN B1098 " " NAG e 1 " - " ASN B1134 " " NAG f 1 " - " ASN B 343 " " NAG g 1 " - " ASN B 165 " " NAG h 1 " - " ASN C 17 " " NAG i 1 " - " ASN C 122 " " NAG j 1 " - " ASN C 234 " " NAG k 1 " - " ASN C 282 " " NAG l 1 " - " ASN C 616 " " NAG m 1 " - " ASN C 717 " " NAG n 1 " - " ASN C 801 " " NAG o 1 " - " ASN C1074 " " NAG p 1 " - " ASN C1098 " " NAG q 1 " - " ASN C1134 " " NAG r 1 " - " ASN C 343 " " NAG s 1 " - " ASN C 165 " Time building additional restraints: 17.48 Conformation dependent library (CDL) restraints added in 6.9 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8712 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 81 sheets defined 22.2% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.27 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.577A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.802A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.541A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.884A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.833A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.753A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 847 removed outlier: 4.188A pdb=" N ALA A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 842 through 847' Processing helix chain 'A' and resid 849 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.569A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.053A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.868A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.814A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1160 removed outlier: 4.075A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.059A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.432A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.427A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.931A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.560A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 847 removed outlier: 3.622A pdb=" N ALA B 846 " --> pdb=" O GLY B 842 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 855 removed outlier: 3.685A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.626A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.514A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.574A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.938A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA B1016 " --> pdb=" O LEU B1012 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1160 removed outlier: 3.940A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR B1155 " --> pdb=" O GLU B1151 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.821A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.637A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.391A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 4.320A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.030A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 removed outlier: 3.718A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.866A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.653A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 removed outlier: 5.876A pdb=" N LEU C 841 " --> pdb=" O GLY C 838 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 847 removed outlier: 3.899A pdb=" N ALA C 846 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 842 through 847' Processing helix chain 'C' and resid 849 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.641A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.038A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.870A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.565A pdb=" N ARG C 983 " --> pdb=" O ASP C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.845A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 3.913A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.991A pdb=" N THR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.706A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 183 through 187 Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.838A pdb=" N THR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'F' and resid 128 through 132 removed outlier: 3.595A pdb=" N SER F 132 " --> pdb=" O ARG F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 187 through 190 Processing helix chain 'F' and resid 201 through 204 Processing helix chain 'G' and resid 79 through 83 removed outlier: 3.695A pdb=" N ILE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 183 through 187 Processing helix chain 'H' and resid 28 through 32 removed outlier: 4.340A pdb=" N THR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 128 through 132 removed outlier: 3.616A pdb=" N SER H 132 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.464A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 190' Processing helix chain 'H' and resid 201 through 204 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.855A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.537A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.041A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASN A 188 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ILE A 210 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ARG A 190 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 208 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N PHE A 192 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N LYS A 206 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE A 194 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR A 204 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ASN A 196 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LYS A 202 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.156A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.575A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.896A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 116 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 83 through 85 removed outlier: 13.124A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.162A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 143 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 9.827A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.778A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.127A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.344A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.642A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.749A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.182A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.708A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.800A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.768A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.388A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.540A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.014A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 31 removed outlier: 4.014A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.748A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 13.210A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.173A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 143 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 9.784A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N TYR B 144 " --> pdb=" O GLU B 154 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU B 154 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.102A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.278A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.691A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.217A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.166A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.903A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.800A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.440A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.499A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 4.097A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASN C 188 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE C 210 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ARG C 190 " --> pdb=" O THR C 208 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N THR C 208 " --> pdb=" O ARG C 190 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N PHE C 192 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LYS C 206 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE C 194 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR C 204 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N ASN C 196 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LYS C 202 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.770A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.900A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 12.762A pdb=" N PHE C 238 " --> pdb=" O PHE C 133 " (cutoff:3.500A) removed outlier: 12.320A pdb=" N PHE C 135 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 12.879A pdb=" N THR C 240 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 10.448A pdb=" N ASN C 137 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N LEU C 242 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU C 244 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.168A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.661A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.909A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE9, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.155A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.913A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.764A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.428A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AF7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.448A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.535A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.535A pdb=" N ASP D 144 " --> pdb=" O TYR D 176 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 150 through 154 removed outlier: 4.506A pdb=" N TYR D 194 " --> pdb=" O VAL D 211 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.585A pdb=" N ASP E 70 " --> pdb=" O SER E 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.282A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.282A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.640A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 131 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU E 181 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL E 133 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N LEU E 179 " --> pdb=" O VAL E 133 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.664A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.664A pdb=" N GLU F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.180A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 120 through 124 removed outlier: 6.180A pdb=" N TYR F 176 " --> pdb=" O ASP F 144 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 151 through 154 removed outlier: 4.131A pdb=" N TYR F 194 " --> pdb=" O VAL F 211 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.699A pdb=" N ASP G 70 " --> pdb=" O SER G 67 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.259A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AH7, first strand: chain 'G' and resid 114 through 118 removed outlier: 4.905A pdb=" N SER G 131 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU G 181 " --> pdb=" O SER G 131 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL G 133 " --> pdb=" O LEU G 179 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G 179 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 153 through 155 removed outlier: 4.120A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AI1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.696A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.337A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H' and resid 120 through 124 removed outlier: 6.337A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.423A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AI6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.863A pdb=" N GLY L 84 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.820A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N SER L 174 " --> pdb=" O THR L 164 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AI9, first strand: chain 'L' and resid 145 through 150 1573 hydrogen bonds defined for protein. 4182 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: 23.17 Time building geometry restraints manager: 18.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6163 1.30 - 1.43: 10337 1.43 - 1.56: 22036 1.56 - 1.69: 5 1.69 - 1.82: 195 Bond restraints: 38736 Sorted by residual: bond pdb=" CA ARG D 38 " pdb=" C ARG D 38 " ideal model delta sigma weight residual 1.520 1.589 -0.069 1.20e-02 6.94e+03 3.27e+01 bond pdb=" C ARG B1019 " pdb=" O ARG B1019 " ideal model delta sigma weight residual 1.237 1.174 0.062 1.16e-02 7.43e+03 2.90e+01 bond pdb=" CA PRO E 119 " pdb=" C PRO E 119 " ideal model delta sigma weight residual 1.514 1.543 -0.029 5.50e-03 3.31e+04 2.81e+01 bond pdb=" C ARG C 905 " pdb=" O ARG C 905 " ideal model delta sigma weight residual 1.236 1.172 0.065 1.22e-02 6.72e+03 2.80e+01 bond pdb=" C ARG B1039 " pdb=" O ARG B1039 " ideal model delta sigma weight residual 1.235 1.174 0.061 1.20e-02 6.94e+03 2.61e+01 ... (remaining 38731 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.41: 774 105.41 - 113.02: 18818 113.02 - 120.63: 19763 120.63 - 128.24: 13175 128.24 - 135.85: 192 Bond angle restraints: 52722 Sorted by residual: angle pdb=" N ARG C 214 " pdb=" CA ARG C 214 " pdb=" C ARG C 214 " ideal model delta sigma weight residual 110.41 122.91 -12.50 1.18e+00 7.18e-01 1.12e+02 angle pdb=" C GLU H 148 " pdb=" N PRO H 149 " pdb=" CA PRO H 149 " ideal model delta sigma weight residual 119.84 133.02 -13.18 1.25e+00 6.40e-01 1.11e+02 angle pdb=" C GLU F 148 " pdb=" N PRO F 149 " pdb=" CA PRO F 149 " ideal model delta sigma weight residual 119.84 132.98 -13.14 1.25e+00 6.40e-01 1.11e+02 angle pdb=" C GLU D 148 " pdb=" N PRO D 149 " pdb=" CA PRO D 149 " ideal model delta sigma weight residual 119.84 132.95 -13.11 1.25e+00 6.40e-01 1.10e+02 angle pdb=" N ASN L 138 " pdb=" CA ASN L 138 " pdb=" C ASN L 138 " ideal model delta sigma weight residual 111.24 124.17 -12.93 1.38e+00 5.25e-01 8.78e+01 ... (remaining 52717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.00: 23297 25.00 - 50.00: 956 50.00 - 75.00: 225 75.00 - 100.00: 65 100.00 - 125.00: 78 Dihedral angle restraints: 24621 sinusoidal: 11046 harmonic: 13575 Sorted by residual: dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual -86.00 -160.40 74.40 1 1.00e+01 1.00e-02 7.02e+01 dihedral pdb=" CB CYS A 840 " pdb=" SG CYS A 840 " pdb=" SG CYS A 851 " pdb=" CB CYS A 851 " ideal model delta sinusoidal sigma weight residual -86.00 -154.29 68.29 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 840 " pdb=" SG CYS C 840 " pdb=" SG CYS C 851 " pdb=" CB CYS C 851 " ideal model delta sinusoidal sigma weight residual -86.00 -151.94 65.94 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 24618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.310: 6258 0.310 - 0.619: 57 0.619 - 0.929: 3 0.929 - 1.239: 0 1.239 - 1.549: 3 Chirality restraints: 6321 Sorted by residual: chirality pdb=" C1 FUC f 3 " pdb=" O6 NAG f 1 " pdb=" C2 FUC f 3 " pdb=" O5 FUC f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.57e+02 chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.63e+01 ... (remaining 6318 not shown) Planarity restraints: 6693 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " -0.114 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" CG ASN A 61 " 0.067 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " 0.200 2.00e-02 2.50e+03 pdb=" C1 NAG A1401 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1158 " -0.089 2.00e-02 2.50e+03 1.19e-01 1.76e+02 pdb=" CG ASN C1158 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C1158 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C1158 " 0.205 2.00e-02 2.50e+03 pdb=" C1 NAG C1407 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " -0.008 2.00e-02 2.50e+03 1.16e-01 1.67e+02 pdb=" CG ASN B 603 " 0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.097 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " 0.199 2.00e-02 2.50e+03 pdb=" C1 NAG B1404 " -0.129 2.00e-02 2.50e+03 ... (remaining 6690 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 80 2.57 - 3.15: 27902 3.15 - 3.73: 56985 3.73 - 4.32: 85039 4.32 - 4.90: 137992 Nonbonded interactions: 307998 Sorted by model distance: nonbonded pdb=" NH1 ARG H 100A" pdb=" OH TYR L 91 " model vdw 1.984 2.520 nonbonded pdb=" OE1 GLU C 156 " pdb=" NH1 ARG C 158 " model vdw 2.094 2.520 nonbonded pdb=" CD1 TYR G 32 " pdb=" OH TYR G 91 " model vdw 2.102 3.340 nonbonded pdb=" OD1 ASP C 442 " pdb=" OG SER H 100B" model vdw 2.135 2.440 nonbonded pdb=" OG1 THR F 116 " pdb=" CG PRO F 147 " model vdw 2.179 3.440 ... (remaining 307993 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'N' selection = chain 'V' selection = chain 'Z' selection = chain 'h' selection = chain 'l' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'c' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'k' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'n' and resid 1 through 2) selection = (chain 'o' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 's' and resid 1 through 2) } 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: 7.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 26.460 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 111.320 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.014 0.090 38736 Z= 0.944 Angle : 1.869 13.497 52722 Z= 1.225 Chirality : 0.111 1.549 6321 Planarity : 0.012 0.120 6636 Dihedral : 16.960 124.998 15747 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 1.10 % Allowed : 5.86 % Favored : 93.04 % Rotamer: Outliers : 2.59 % Allowed : 5.83 % Favored : 91.58 % Cbeta Deviations : 0.53 % 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: -1.40 (0.11), residues: 4638 helix: -1.54 (0.15), residues: 831 sheet: 0.44 (0.14), residues: 1188 loop : -1.40 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.129 0.020 TRP C 104 HIS 0.013 0.004 HIS C 519 PHE 0.118 0.014 PHE A 718 TYR 0.120 0.020 TYR C 269 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 441 time to evaluate : 4.254 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 780 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7788 (mt-10) REVERT: A 854 LYS cc_start: 0.7710 (tttt) cc_final: 0.7466 (tmtt) REVERT: B 99 ASN cc_start: 0.7402 (m-40) cc_final: 0.7154 (m110) REVERT: B 345 THR cc_start: 0.8185 (m) cc_final: 0.7909 (m) REVERT: B 420 ASP cc_start: 0.6908 (t0) cc_final: 0.6591 (t0) REVERT: B 1038 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8537 (mmtm) REVERT: B 1045 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8288 (tptt) REVERT: C 346 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7596 (ptp-110) REVERT: C 427 ASP cc_start: 0.7459 (m-30) cc_final: 0.7191 (m-30) REVERT: C 634 ARG cc_start: 0.6367 (OUTLIER) cc_final: 0.5850 (mtm180) REVERT: C 758 SER cc_start: 0.7824 (t) cc_final: 0.7472 (m) REVERT: C 1038 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8382 (mmtm) REVERT: F 48 MET cc_start: 0.5664 (mpp) cc_final: 0.5147 (mmm) REVERT: F 71 ARG cc_start: 0.5933 (OUTLIER) cc_final: 0.4085 (ptm-80) REVERT: H 71 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.4537 (ptm-80) REVERT: L 175 LEU cc_start: 0.1812 (OUTLIER) cc_final: 0.1543 (pt) outliers start: 105 outliers final: 28 residues processed: 529 average time/residue: 1.4251 time to fit residues: 921.1575 Evaluate side-chains 342 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 306 time to evaluate : 4.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 841 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 50 TRP Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 96 ARG Chi-restraints excluded: chain H residue 209 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 392 optimal weight: 0.4980 chunk 352 optimal weight: 40.0000 chunk 195 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 237 optimal weight: 4.9990 chunk 188 optimal weight: 0.3980 chunk 364 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 0.6980 chunk 271 optimal weight: 1.9990 chunk 422 optimal weight: 9.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 422 ASN A 437 ASN A 762 GLN A 907 ASN A 957 GLN B 188 ASN B 211 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 907 ASN B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 314 GLN C 422 ASN C 613 GLN C 762 GLN C 907 ASN C1002 GLN E 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38736 Z= 0.214 Angle : 0.739 15.098 52722 Z= 0.370 Chirality : 0.047 0.251 6321 Planarity : 0.004 0.071 6636 Dihedral : 13.928 113.281 7610 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.51 % Favored : 96.08 % Rotamer: Outliers : 2.59 % Allowed : 9.95 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.12), residues: 4638 helix: 0.49 (0.18), residues: 840 sheet: 0.29 (0.13), residues: 1431 loop : -1.01 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 154 HIS 0.006 0.001 HIS L 198 PHE 0.032 0.002 PHE H 146 TYR 0.023 0.002 TYR D 100F ARG 0.004 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 377 time to evaluate : 4.439 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 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.7109 (p90) REVERT: A 378 LYS cc_start: 0.7460 (tppt) cc_final: 0.7212 (tptp) REVERT: A 1005 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: B 309 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 420 ASP cc_start: 0.7080 (t0) cc_final: 0.6868 (t0) REVERT: B 529 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7330 (mttp) REVERT: B 661 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7828 (tt0) REVERT: B 994 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7726 (t70) REVERT: B 1038 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8508 (mmtm) REVERT: C 427 ASP cc_start: 0.7697 (m-30) cc_final: 0.7408 (m-30) REVERT: C 787 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: C 950 ASP cc_start: 0.8521 (m-30) cc_final: 0.8224 (m-30) REVERT: C 1029 MET cc_start: 0.8727 (tpp) cc_final: 0.8476 (tpp) REVERT: C 1038 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8409 (mmtm) REVERT: E 183 LYS cc_start: 0.0887 (mptt) cc_final: 0.0030 (ttmt) REVERT: F 48 MET cc_start: 0.5803 (mpp) cc_final: 0.4808 (mmm) REVERT: F 71 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.4433 (ptm-80) REVERT: H 4 LEU cc_start: 0.3412 (OUTLIER) cc_final: 0.2618 (mp) REVERT: H 48 MET cc_start: 0.5831 (OUTLIER) cc_final: 0.5254 (mmt) REVERT: L 59 PRO cc_start: 0.4488 (Cg_exo) cc_final: 0.4269 (Cg_endo) REVERT: L 124 GLN cc_start: 0.2905 (OUTLIER) cc_final: 0.2669 (pp30) REVERT: L 175 LEU cc_start: 0.2006 (OUTLIER) cc_final: 0.1800 (pp) outliers start: 105 outliers final: 42 residues processed: 444 average time/residue: 1.3772 time to fit residues: 755.2328 Evaluate side-chains 365 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 309 time to evaluate : 3.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 211 ASN Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 975 SER Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 234 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 351 optimal weight: 20.0000 chunk 287 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 423 optimal weight: 0.0020 chunk 456 optimal weight: 3.9990 chunk 376 optimal weight: 40.0000 chunk 419 optimal weight: 5.9990 chunk 144 optimal weight: 0.7980 chunk 339 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 321 GLN A 957 GLN B 99 ASN B 321 GLN B 703 ASN B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 762 GLN E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 38736 Z= 0.177 Angle : 0.658 10.408 52722 Z= 0.324 Chirality : 0.045 0.299 6321 Planarity : 0.004 0.055 6636 Dihedral : 12.680 109.874 7579 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.95 % Favored : 95.80 % Rotamer: Outliers : 2.89 % Allowed : 11.06 % Favored : 86.05 % 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: -0.18 (0.12), residues: 4638 helix: 1.06 (0.19), residues: 849 sheet: 0.47 (0.13), residues: 1422 loop : -0.92 (0.12), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 50 HIS 0.004 0.001 HIS D 200 PHE 0.023 0.001 PHE B 592 TYR 0.024 0.002 TYR L 49 ARG 0.004 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 332 time to evaluate : 4.661 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 309 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 629 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3648 (mp) REVERT: A 950 ASP cc_start: 0.8543 (m-30) cc_final: 0.8240 (m-30) REVERT: A 1005 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: B 309 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 358 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8153 (mt) REVERT: B 420 ASP cc_start: 0.7006 (t0) cc_final: 0.6714 (t0) REVERT: B 529 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7356 (mttp) REVERT: B 916 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8594 (tt) REVERT: B 994 ASP cc_start: 0.8023 (OUTLIER) cc_final: 0.7719 (t70) REVERT: B 1038 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8520 (mmtm) REVERT: C 427 ASP cc_start: 0.7731 (m-30) cc_final: 0.7442 (m-30) REVERT: C 780 GLU cc_start: 0.8766 (mm-30) cc_final: 0.8101 (pt0) REVERT: C 843 ASP cc_start: 0.2171 (OUTLIER) cc_final: 0.0999 (t70) REVERT: C 950 ASP cc_start: 0.8532 (m-30) cc_final: 0.8242 (m-30) REVERT: C 1005 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: C 1038 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8369 (mmtm) REVERT: D 214 LYS cc_start: 0.2172 (pttt) cc_final: 0.0983 (ptpt) REVERT: F 48 MET cc_start: 0.5760 (mpp) cc_final: 0.5309 (mmm) REVERT: H 4 LEU cc_start: 0.3351 (OUTLIER) cc_final: 0.2555 (mp) REVERT: H 138 LEU cc_start: 0.2523 (pt) cc_final: 0.1725 (mp) REVERT: H 201 LYS cc_start: 0.4882 (tptp) cc_final: 0.4523 (mmtt) REVERT: L 124 GLN cc_start: 0.2833 (tt0) cc_final: 0.2044 (tm-30) REVERT: L 175 LEU cc_start: 0.2332 (OUTLIER) cc_final: 0.2111 (pp) REVERT: L 183 LYS cc_start: 0.3686 (ttmm) cc_final: 0.3233 (tttp) outliers start: 117 outliers final: 54 residues processed: 408 average time/residue: 1.3312 time to fit residues: 675.5311 Evaluate side-chains 365 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 297 time to evaluate : 3.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 629 LEU Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 634 ARG Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 843 ASP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain E residue 31 ASP Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 161 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 417 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 424 optimal weight: 20.0000 chunk 449 optimal weight: 30.0000 chunk 221 optimal weight: 0.6980 chunk 402 optimal weight: 30.0000 chunk 121 optimal weight: 6.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 134 GLN A 762 GLN A 957 GLN A1119 ASN B 134 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1113 GLN C 314 GLN E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 38736 Z= 0.366 Angle : 0.739 11.094 52722 Z= 0.362 Chirality : 0.049 0.322 6321 Planarity : 0.005 0.064 6636 Dihedral : 12.425 112.106 7570 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.29 % Favored : 95.47 % Rotamer: Outliers : 3.73 % Allowed : 11.98 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.12), residues: 4638 helix: 0.88 (0.19), residues: 849 sheet: 0.38 (0.13), residues: 1437 loop : -0.97 (0.12), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 152 HIS 0.008 0.001 HIS C1064 PHE 0.025 0.002 PHE H 146 TYR 0.023 0.002 TYR B 265 ARG 0.003 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 295 time to evaluate : 4.442 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 309 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: A 310 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8675 (ttpm) REVERT: A 368 LEU cc_start: 0.8200 (mp) cc_final: 0.7933 (mt) REVERT: A 661 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7771 (tm-30) REVERT: A 780 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8194 (pt0) REVERT: A 787 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: A 1005 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8226 (mt0) REVERT: B 52 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8101 (tt0) REVERT: B 309 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: B 358 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 420 ASP cc_start: 0.7132 (t0) cc_final: 0.6829 (t0) REVERT: B 529 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.7489 (mttp) REVERT: B 661 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 780 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8186 (pt0) REVERT: B 994 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7773 (t70) REVERT: B 1038 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8541 (mmtm) REVERT: C 52 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7931 (tm130) REVERT: C 427 ASP cc_start: 0.7935 (m-30) cc_final: 0.7632 (m-30) REVERT: C 780 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8130 (pt0) REVERT: C 787 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8007 (mt0) REVERT: C 957 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7984 (tt0) REVERT: C 1141 LEU cc_start: 0.8111 (OUTLIER) cc_final: 0.7812 (tm) REVERT: D 214 LYS cc_start: 0.2275 (pttt) cc_final: 0.0994 (ptpt) REVERT: G 24 GLN cc_start: 0.5384 (OUTLIER) cc_final: 0.5074 (tm-30) REVERT: H 4 LEU cc_start: 0.3352 (OUTLIER) cc_final: 0.2489 (mp) REVERT: H 71 ARG cc_start: 0.6131 (OUTLIER) cc_final: 0.4446 (ptm-80) REVERT: H 201 LYS cc_start: 0.4768 (tptp) cc_final: 0.4510 (mmtt) REVERT: L 29 ILE cc_start: 0.6120 (OUTLIER) cc_final: 0.5709 (mp) REVERT: L 42 LYS cc_start: 0.5018 (tptp) cc_final: 0.4815 (mppt) REVERT: L 124 GLN cc_start: 0.2888 (tt0) cc_final: 0.2153 (tm-30) REVERT: L 175 LEU cc_start: 0.2535 (OUTLIER) cc_final: 0.2240 (pp) outliers start: 151 outliers final: 76 residues processed: 396 average time/residue: 1.4062 time to fit residues: 682.5802 Evaluate side-chains 375 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 278 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 374 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 334 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 chunk 383 optimal weight: 20.0000 chunk 310 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 229 optimal weight: 6.9990 chunk 403 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 99 ASN B 146 HIS B 211 ASN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 914 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 38736 Z= 0.349 Angle : 0.718 16.062 52722 Z= 0.350 Chirality : 0.048 0.357 6321 Planarity : 0.004 0.056 6636 Dihedral : 11.989 111.030 7561 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.18 % Favored : 95.60 % Rotamer: Outliers : 3.56 % Allowed : 13.19 % Favored : 83.26 % 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: -0.32 (0.12), residues: 4638 helix: 0.99 (0.19), residues: 834 sheet: 0.41 (0.13), residues: 1428 loop : -1.04 (0.12), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 50 HIS 0.005 0.001 HIS C1058 PHE 0.025 0.002 PHE B 592 TYR 0.023 0.002 TYR B 265 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 287 time to evaluate : 4.270 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 52 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: A 309 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 310 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8687 (ttpm) REVERT: A 368 LEU cc_start: 0.8206 (mp) cc_final: 0.7940 (mt) REVERT: A 378 LYS cc_start: 0.7446 (tppt) cc_final: 0.7173 (tptm) REVERT: A 661 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7754 (tm-30) REVERT: A 780 GLU cc_start: 0.8759 (mm-30) cc_final: 0.8209 (pt0) REVERT: A 787 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8240 (mt0) REVERT: A 1002 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: A 1005 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: B 52 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8093 (tt0) REVERT: B 309 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: B 358 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8200 (mt) REVERT: B 529 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7458 (mttp) REVERT: B 661 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: B 780 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8196 (pt0) REVERT: B 916 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8647 (tt) REVERT: B 994 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7744 (t70) REVERT: B 1038 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8504 (mmtm) REVERT: C 52 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.7939 (tm130) REVERT: C 427 ASP cc_start: 0.8043 (m-30) cc_final: 0.7725 (m-30) REVERT: C 529 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7303 (mptp) REVERT: C 567 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7876 (mtt90) REVERT: C 780 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8114 (pt0) REVERT: C 787 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7940 (mt0) REVERT: C 790 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7558 (mmtm) REVERT: C 1029 MET cc_start: 0.8796 (tpp) cc_final: 0.8489 (tpp) REVERT: C 1141 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7798 (tm) REVERT: D 71 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.4595 (ptm-80) REVERT: D 214 LYS cc_start: 0.2367 (OUTLIER) cc_final: 0.1310 (pttt) REVERT: F 48 MET cc_start: 0.5810 (mpp) cc_final: 0.4856 (mmm) REVERT: G 24 GLN cc_start: 0.5351 (OUTLIER) cc_final: 0.5051 (tm-30) REVERT: H 4 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.2720 (mp) REVERT: H 71 ARG cc_start: 0.6295 (OUTLIER) cc_final: 0.4625 (ptm-80) REVERT: L 29 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5739 (mp) REVERT: L 124 GLN cc_start: 0.3104 (tt0) cc_final: 0.2354 (tm-30) REVERT: L 145 LYS cc_start: 0.3556 (mttt) cc_final: 0.2916 (tptt) REVERT: L 175 LEU cc_start: 0.2656 (OUTLIER) cc_final: 0.2294 (pp) REVERT: L 183 LYS cc_start: 0.3692 (ttmm) cc_final: 0.3208 (tttp) outliers start: 144 outliers final: 82 residues processed: 386 average time/residue: 1.3807 time to fit residues: 657.9343 Evaluate side-chains 388 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 278 time to evaluate : 4.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 567 ARG Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 13 LYS Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 151 optimal weight: 7.9990 chunk 404 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 263 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 449 optimal weight: 9.9990 chunk 373 optimal weight: 0.7980 chunk 208 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 236 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 90 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38736 Z= 0.194 Angle : 0.647 12.113 52722 Z= 0.311 Chirality : 0.044 0.324 6321 Planarity : 0.004 0.068 6636 Dihedral : 11.194 106.386 7561 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.67 % Favored : 96.10 % Rotamer: Outliers : 3.01 % Allowed : 14.77 % Favored : 82.22 % 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: -0.15 (0.12), residues: 4638 helix: 1.36 (0.19), residues: 834 sheet: 0.50 (0.13), residues: 1401 loop : -1.01 (0.12), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 50 HIS 0.004 0.001 HIS H 35 PHE 0.029 0.001 PHE B 592 TYR 0.024 0.001 TYR C 508 ARG 0.003 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 315 time to evaluate : 4.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: A 316 SER cc_start: 0.8131 (OUTLIER) cc_final: 0.7831 (p) REVERT: A 319 ARG cc_start: 0.7933 (ttm170) cc_final: 0.7532 (ttm110) REVERT: A 368 LEU cc_start: 0.8152 (mp) cc_final: 0.7902 (mt) REVERT: A 378 LYS cc_start: 0.7376 (tppt) cc_final: 0.7117 (tptm) REVERT: A 780 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8158 (pt0) REVERT: A 1005 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: B 309 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: B 319 ARG cc_start: 0.7922 (ttm170) cc_final: 0.7523 (ttm110) REVERT: B 358 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8183 (mt) REVERT: B 661 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7887 (tt0) REVERT: B 780 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8203 (pt0) REVERT: B 916 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 994 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7684 (t70) REVERT: B 1038 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8460 (mmtm) REVERT: C 529 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.7299 (mptp) REVERT: C 780 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8120 (pt0) REVERT: C 787 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7912 (mt0) REVERT: C 950 ASP cc_start: 0.8593 (m-30) cc_final: 0.8290 (m-30) REVERT: C 1141 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7759 (tm) REVERT: D 71 ARG cc_start: 0.6167 (OUTLIER) cc_final: 0.4703 (ptm-80) REVERT: D 99 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: D 214 LYS cc_start: 0.2359 (OUTLIER) cc_final: 0.1292 (pttt) REVERT: E 183 LYS cc_start: 0.0744 (mptt) cc_final: -0.0074 (ttmt) REVERT: G 24 GLN cc_start: 0.5470 (OUTLIER) cc_final: 0.5188 (tm-30) REVERT: H 4 LEU cc_start: 0.3447 (OUTLIER) cc_final: 0.2590 (mp) REVERT: H 71 ARG cc_start: 0.6236 (OUTLIER) cc_final: 0.4648 (ptm-80) REVERT: L 29 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5692 (mp) REVERT: L 145 LYS cc_start: 0.3405 (mttt) cc_final: 0.2874 (tptt) REVERT: L 163 VAL cc_start: 0.2798 (OUTLIER) cc_final: 0.2264 (m) REVERT: L 175 LEU cc_start: 0.2785 (OUTLIER) cc_final: 0.2405 (pp) outliers start: 122 outliers final: 65 residues processed: 400 average time/residue: 1.3946 time to fit residues: 688.2898 Evaluate side-chains 379 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 293 time to evaluate : 4.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain D residue 214 LYS Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 433 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 328 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 378 optimal weight: 0.9990 chunk 251 optimal weight: 1.9990 chunk 448 optimal weight: 8.9990 chunk 280 optimal weight: 2.9990 chunk 273 optimal weight: 0.2980 chunk 206 optimal weight: 0.0770 overall best weight: 1.0744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS A 321 GLN ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38736 Z= 0.227 Angle : 0.663 11.615 52722 Z= 0.319 Chirality : 0.045 0.312 6321 Planarity : 0.004 0.061 6636 Dihedral : 10.784 104.893 7561 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.86 % Rotamer: Outliers : 3.31 % Allowed : 15.11 % Favored : 81.58 % 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: -0.09 (0.12), residues: 4638 helix: 1.39 (0.19), residues: 837 sheet: 0.62 (0.14), residues: 1356 loop : -1.00 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 50 HIS 0.003 0.001 HIS C1064 PHE 0.032 0.001 PHE B 592 TYR 0.028 0.002 TYR C 508 ARG 0.002 0.000 ARG A 634 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 300 time to evaluate : 4.291 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 186 PHE cc_start: 0.8207 (m-80) cc_final: 0.8007 (m-80) REVERT: A 190 ARG cc_start: 0.8529 (mtt90) cc_final: 0.8169 (mtt180) REVERT: A 309 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: A 310 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8642 (ttpm) REVERT: A 319 ARG cc_start: 0.7895 (ttm170) cc_final: 0.7527 (ttm110) REVERT: A 368 LEU cc_start: 0.8177 (mp) cc_final: 0.7922 (mt) REVERT: A 378 LYS cc_start: 0.7362 (tppt) cc_final: 0.7122 (tptm) REVERT: A 661 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: A 780 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8236 (pt0) REVERT: A 1005 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: B 309 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7526 (mp0) REVERT: B 319 ARG cc_start: 0.7910 (ttm170) cc_final: 0.7521 (ttm110) REVERT: B 358 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8199 (mt) REVERT: B 661 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (tt0) REVERT: B 780 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8224 (pt0) REVERT: B 916 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8582 (tt) REVERT: B 994 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7673 (t70) REVERT: B 1038 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8480 (mmtm) REVERT: C 52 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: C 529 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7374 (mptp) REVERT: C 780 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8147 (pt0) REVERT: C 787 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: C 950 ASP cc_start: 0.8575 (m-30) cc_final: 0.8211 (m-30) REVERT: C 1141 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7744 (tm) REVERT: D 71 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.4678 (ptm-80) REVERT: D 99 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6970 (m-80) REVERT: E 183 LYS cc_start: 0.0700 (mptt) cc_final: -0.0088 (ttmt) REVERT: G 24 GLN cc_start: 0.5527 (OUTLIER) cc_final: 0.5218 (tm-30) REVERT: H 4 LEU cc_start: 0.3481 (OUTLIER) cc_final: 0.2614 (mp) REVERT: H 71 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.4639 (ptm-80) REVERT: H 83 LYS cc_start: 0.6531 (mttm) cc_final: 0.6320 (mttm) REVERT: L 29 ILE cc_start: 0.6102 (OUTLIER) cc_final: 0.5647 (mp) REVERT: L 145 LYS cc_start: 0.3305 (mttt) cc_final: 0.2885 (tptt) REVERT: L 163 VAL cc_start: 0.2844 (OUTLIER) cc_final: 0.2294 (m) REVERT: L 175 LEU cc_start: 0.2809 (OUTLIER) cc_final: 0.2459 (pp) REVERT: L 183 LYS cc_start: 0.3672 (ttmm) cc_final: 0.2959 (tttp) REVERT: L 207 LYS cc_start: 0.1801 (OUTLIER) cc_final: 0.1060 (ptpt) outliers start: 134 outliers final: 78 residues processed: 396 average time/residue: 1.3966 time to fit residues: 682.2775 Evaluate side-chains 387 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 286 time to evaluate : 4.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 408 ARG Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain H residue 172 SER Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 277 optimal weight: 3.9990 chunk 178 optimal weight: 3.9990 chunk 267 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 284 optimal weight: 0.0770 chunk 305 optimal weight: 3.9990 chunk 221 optimal weight: 0.0270 chunk 41 optimal weight: 20.0000 chunk 352 optimal weight: 0.1980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 146 HIS ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 90 GLN ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 53 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 38736 Z= 0.177 Angle : 0.635 12.691 52722 Z= 0.302 Chirality : 0.044 0.303 6321 Planarity : 0.004 0.065 6636 Dihedral : 10.005 102.054 7560 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.56 % Favored : 96.21 % Rotamer: Outliers : 2.74 % Allowed : 15.98 % Favored : 81.28 % 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: 0.01 (0.12), residues: 4638 helix: 1.55 (0.19), residues: 837 sheet: 0.62 (0.14), residues: 1371 loop : -0.93 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 50 HIS 0.003 0.001 HIS H 35 PHE 0.033 0.001 PHE B 592 TYR 0.026 0.001 TYR D 100F ARG 0.007 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 310 time to evaluate : 4.157 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 190 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8146 (mtt180) REVERT: A 309 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: A 310 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8652 (ttpm) REVERT: A 316 SER cc_start: 0.8057 (OUTLIER) cc_final: 0.7777 (p) REVERT: A 319 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7541 (ttm110) REVERT: A 368 LEU cc_start: 0.8126 (mp) cc_final: 0.7886 (mt) REVERT: A 378 LYS cc_start: 0.7312 (tppt) cc_final: 0.7076 (tptm) REVERT: A 420 ASP cc_start: 0.6366 (m-30) cc_final: 0.6142 (m-30) REVERT: A 661 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7741 (tm-30) REVERT: A 740 MET cc_start: 0.8763 (tpt) cc_final: 0.8247 (tpt) REVERT: A 780 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8210 (pt0) REVERT: B 309 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: B 319 ARG cc_start: 0.7855 (ttm170) cc_final: 0.7528 (ttm110) REVERT: B 358 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8246 (mt) REVERT: B 378 LYS cc_start: 0.7587 (tptm) cc_final: 0.7311 (tppt) REVERT: B 568 ASP cc_start: 0.7097 (m-30) cc_final: 0.6764 (m-30) REVERT: B 661 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: B 780 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8261 (pt0) REVERT: B 916 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8529 (tt) REVERT: B 994 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7573 (t70) REVERT: B 1038 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8457 (mmtm) REVERT: C 52 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: C 420 ASP cc_start: 0.6395 (m-30) cc_final: 0.6180 (m-30) REVERT: C 529 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7372 (mptp) REVERT: C 780 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8177 (pt0) REVERT: C 787 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7926 (mt0) REVERT: C 950 ASP cc_start: 0.8577 (m-30) cc_final: 0.8288 (m-30) REVERT: C 1141 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7738 (tm) REVERT: D 71 ARG cc_start: 0.6161 (OUTLIER) cc_final: 0.4781 (ptm-80) REVERT: D 99 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: E 183 LYS cc_start: 0.0648 (mptt) cc_final: -0.0128 (ttmt) REVERT: G 24 GLN cc_start: 0.5648 (OUTLIER) cc_final: 0.5335 (tm-30) REVERT: G 45 LYS cc_start: 0.6204 (tmtm) cc_final: 0.5197 (mppt) REVERT: H 4 LEU cc_start: 0.3550 (OUTLIER) cc_final: 0.2656 (mp) REVERT: H 71 ARG cc_start: 0.6235 (OUTLIER) cc_final: 0.4687 (ptm-80) REVERT: H 83 LYS cc_start: 0.6508 (mttm) cc_final: 0.6288 (mttm) REVERT: L 29 ILE cc_start: 0.5987 (OUTLIER) cc_final: 0.5512 (mp) REVERT: L 145 LYS cc_start: 0.3241 (mttt) cc_final: 0.2883 (tptt) REVERT: L 163 VAL cc_start: 0.2944 (OUTLIER) cc_final: 0.2414 (m) REVERT: L 175 LEU cc_start: 0.2864 (OUTLIER) cc_final: 0.2589 (pp) REVERT: L 183 LYS cc_start: 0.3685 (ttmm) cc_final: 0.2969 (tttp) REVERT: L 207 LYS cc_start: 0.2044 (OUTLIER) cc_final: 0.1723 (ptpt) outliers start: 111 outliers final: 61 residues processed: 389 average time/residue: 1.4474 time to fit residues: 700.2095 Evaluate side-chains 376 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 292 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 130 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 71 ARG Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 407 optimal weight: 20.0000 chunk 429 optimal weight: 0.9980 chunk 391 optimal weight: 0.0970 chunk 417 optimal weight: 30.0000 chunk 251 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 377 optimal weight: 2.9990 chunk 395 optimal weight: 8.9990 chunk 416 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 GLN B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38736 Z= 0.179 Angle : 0.648 12.969 52722 Z= 0.309 Chirality : 0.047 1.177 6321 Planarity : 0.004 0.063 6636 Dihedral : 9.635 111.054 7558 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.86 % Favored : 95.92 % Rotamer: Outliers : 2.64 % Allowed : 16.22 % Favored : 81.14 % Cbeta Deviations : 0.02 % 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: 0.04 (0.12), residues: 4638 helix: 1.60 (0.19), residues: 837 sheet: 0.63 (0.14), residues: 1365 loop : -0.90 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 50 HIS 0.002 0.000 HIS H 35 PHE 0.020 0.001 PHE A1075 TYR 0.026 0.001 TYR F 100F ARG 0.005 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 306 time to evaluate : 4.823 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 190 ARG cc_start: 0.8510 (mtt90) cc_final: 0.8130 (mtt180) REVERT: A 309 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: A 310 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8648 (ttpm) REVERT: A 319 ARG cc_start: 0.7820 (ttm170) cc_final: 0.7536 (ttm110) REVERT: A 368 LEU cc_start: 0.8118 (mp) cc_final: 0.7871 (mt) REVERT: A 378 LYS cc_start: 0.7339 (tppt) cc_final: 0.7098 (tptm) REVERT: A 661 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: A 740 MET cc_start: 0.8765 (tpt) cc_final: 0.8258 (tpt) REVERT: A 780 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8211 (pt0) REVERT: B 309 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 319 ARG cc_start: 0.7836 (ttm170) cc_final: 0.7533 (ttm110) REVERT: B 358 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8254 (mt) REVERT: B 568 ASP cc_start: 0.7116 (m-30) cc_final: 0.6826 (m-30) REVERT: B 661 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: B 780 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8273 (pt0) REVERT: B 878 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8861 (OUTLIER) REVERT: B 916 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8530 (tt) REVERT: B 994 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7574 (t70) REVERT: B 1038 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8467 (mmtm) REVERT: C 346 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7490 (ptp90) REVERT: C 420 ASP cc_start: 0.6385 (m-30) cc_final: 0.6182 (m-30) REVERT: C 529 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7393 (mptp) REVERT: C 567 ARG cc_start: 0.8057 (mtt90) cc_final: 0.7851 (mtt90) REVERT: C 747 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8039 (m) REVERT: C 780 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8182 (pt0) REVERT: C 787 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: C 950 ASP cc_start: 0.8587 (m-30) cc_final: 0.8289 (m-30) REVERT: C 1141 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7731 (tm) REVERT: D 71 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.4786 (ptm-80) REVERT: D 99 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: G 24 GLN cc_start: 0.5653 (OUTLIER) cc_final: 0.5341 (tm-30) REVERT: H 4 LEU cc_start: 0.3604 (OUTLIER) cc_final: 0.2716 (mp) REVERT: H 83 LYS cc_start: 0.6501 (mttm) cc_final: 0.6291 (mttm) REVERT: H 201 LYS cc_start: 0.4479 (mmpt) cc_final: 0.3534 (mtmm) REVERT: L 29 ILE cc_start: 0.5966 (OUTLIER) cc_final: 0.5481 (mp) REVERT: L 145 LYS cc_start: 0.3259 (mttt) cc_final: 0.2969 (tptt) REVERT: L 163 VAL cc_start: 0.3139 (OUTLIER) cc_final: 0.2611 (m) REVERT: L 175 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2626 (pp) REVERT: L 183 LYS cc_start: 0.3758 (ttmm) cc_final: 0.3029 (tttp) REVERT: L 207 LYS cc_start: 0.1937 (OUTLIER) cc_final: 0.1510 (ptpt) outliers start: 107 outliers final: 71 residues processed: 383 average time/residue: 1.4408 time to fit residues: 677.9261 Evaluate side-chains 389 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 296 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 207 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 274 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 chunk 269 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 463 optimal weight: 10.0000 chunk 426 optimal weight: 20.0000 chunk 368 optimal weight: 3.9990 chunk 38 optimal weight: 0.0040 chunk 284 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 overall best weight: 2.0156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN C 314 GLN C 321 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 27 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 38736 Z= 0.343 Angle : 0.717 12.494 52722 Z= 0.347 Chirality : 0.050 1.083 6321 Planarity : 0.004 0.064 6636 Dihedral : 9.426 96.000 7558 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.14 % Favored : 95.64 % Rotamer: Outliers : 2.74 % Allowed : 16.25 % Favored : 81.01 % 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: -0.12 (0.12), residues: 4638 helix: 1.32 (0.19), residues: 837 sheet: 0.57 (0.14), residues: 1368 loop : -0.98 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.005 0.001 HIS C1058 PHE 0.022 0.002 PHE B 898 TYR 0.022 0.002 TYR C 508 ARG 0.006 0.001 ARG A 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 293 time to evaluate : 4.114 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 190 ARG cc_start: 0.8551 (mtt90) cc_final: 0.8199 (mtt180) REVERT: A 309 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 310 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8653 (ttpm) REVERT: A 368 LEU cc_start: 0.8214 (mp) cc_final: 0.7951 (mt) REVERT: A 378 LYS cc_start: 0.7366 (tppt) cc_final: 0.7117 (tptm) REVERT: A 661 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7766 (tm-30) REVERT: A 780 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8234 (pt0) REVERT: B 309 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 319 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7559 (ttm110) REVERT: B 358 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 661 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7908 (tt0) REVERT: B 780 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8270 (pt0) REVERT: B 916 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 994 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7734 (t70) REVERT: B 1038 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8495 (mmtm) REVERT: C 52 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: C 346 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7483 (ptp90) REVERT: C 529 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.7793 (mptp) REVERT: C 780 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8150 (pt0) REVERT: C 787 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: C 790 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7550 (mmtm) REVERT: C 1141 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7742 (tm) REVERT: D 71 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.4841 (ptm-80) REVERT: D 99 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7235 (m-80) REVERT: E 183 LYS cc_start: 0.0674 (tptt) cc_final: -0.0152 (ttpt) REVERT: G 24 GLN cc_start: 0.5654 (OUTLIER) cc_final: 0.5341 (tm-30) REVERT: H 83 LYS cc_start: 0.6500 (mttm) cc_final: 0.6288 (mttm) REVERT: H 201 LYS cc_start: 0.4564 (mmpt) cc_final: 0.3564 (mtmm) REVERT: L 29 ILE cc_start: 0.5995 (OUTLIER) cc_final: 0.5486 (mp) REVERT: L 145 LYS cc_start: 0.3395 (mttt) cc_final: 0.2949 (tptt) REVERT: L 175 LEU cc_start: 0.2981 (OUTLIER) cc_final: 0.2593 (pp) REVERT: L 183 LYS cc_start: 0.3755 (ttmm) cc_final: 0.3008 (tttp) outliers start: 111 outliers final: 75 residues processed: 375 average time/residue: 1.4479 time to fit residues: 666.3953 Evaluate side-chains 378 residues out of total 4059 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 283 time to evaluate : 4.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 634 ARG Chi-restraints excluded: chain A residue 658 ASN Chi-restraints excluded: chain A residue 661 GLU Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 309 GLU Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 52 GLN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 785 VAL Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 71 ARG Chi-restraints excluded: chain D residue 99 TYR Chi-restraints excluded: chain D residue 205 THR Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 110 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 99 TYR Chi-restraints excluded: chain F residue 100 ARG Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 197 ASN Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 181 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 211 ARG Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain L residue 29 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 122 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 163 VAL Chi-restraints excluded: chain L residue 175 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 465 random chunks: chunk 293 optimal weight: 0.9980 chunk 392 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 369 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 379 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN ** A 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 957 GLN B 99 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 321 GLN ** C 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN E 166 GLN G 53 ASN ** G 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.218392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.161383 restraints weight = 42112.368| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.42 r_work: 0.3189 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 38736 Z= 0.319 Angle : 0.706 11.908 52722 Z= 0.341 Chirality : 0.049 1.005 6321 Planarity : 0.004 0.064 6636 Dihedral : 9.122 96.046 7558 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.12 % Favored : 95.71 % Rotamer: Outliers : 2.81 % Allowed : 16.25 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.18 (0.12), residues: 4638 helix: 1.24 (0.19), residues: 840 sheet: 0.56 (0.14), residues: 1362 loop : -1.02 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 64 HIS 0.004 0.001 HIS B 519 PHE 0.021 0.002 PHE B 898 TYR 0.025 0.002 TYR C 508 ARG 0.005 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13535.78 seconds wall clock time: 244 minutes 20.24 seconds (14660.24 seconds total)