Starting phenix.real_space_refine on Sun Mar 24 08:35:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x6l_22077/03_2024/6x6l_22077.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 102 5.16 5 C 25619 2.51 5 N 6868 2.21 5 O 8024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "AX ARG 36": "NH1" <-> "NH2" Residue "AX ARG 38": "NH1" <-> "NH2" Residue "AX ASP 51": "OD1" <-> "OD2" Residue "AX ASP 62": "OD1" <-> "OD2" Residue "AX GLU 70": "OE1" <-> "OE2" Residue "AX GLU 124": "OE1" <-> "OE2" Residue "AX GLU 317": "OE1" <-> "OE2" Residue "AX GLU 324": "OE1" <-> "OE2" Residue "BX ARG 36": "NH1" <-> "NH2" Residue "BX ARG 38": "NH1" <-> "NH2" Residue "BX ASP 72": "OD1" <-> "OD2" Residue "BX GLU 124": "OE1" <-> "OE2" Residue "BX GLU 268": "OE1" <-> "OE2" Residue "CX ARG 36": "NH1" <-> "NH2" Residue "CX ARG 38": "NH1" <-> "NH2" Residue "CX GLU 70": "OE1" <-> "OE2" Residue "CX GLU 124": "OE1" <-> "OE2" Residue "DX ARG 36": "NH1" <-> "NH2" Residue "DX ARG 38": "NH1" <-> "NH2" Residue "DX ASP 51": "OD1" <-> "OD2" Residue "DX ASP 62": "OD1" <-> "OD2" Residue "DX GLU 124": "OE1" <-> "OE2" Residue "EX ARG 36": "NH1" <-> "NH2" Residue "EX ARG 38": "NH1" <-> "NH2" Residue "EX ASP 51": "OD1" <-> "OD2" Residue "EX GLU 124": "OE1" <-> "OE2" Residue "EX GLU 324": "OE1" <-> "OE2" Residue "FX ARG 36": "NH1" <-> "NH2" Residue "FX ARG 38": "NH1" <-> "NH2" Residue "FX ASP 62": "OD1" <-> "OD2" Residue "FX GLU 124": "OE1" <-> "OE2" Residue "FX GLU 268": "OE1" <-> "OE2" Residue "GX ARG 36": "NH1" <-> "NH2" Residue "GX ARG 38": "NH1" <-> "NH2" Residue "GX ASP 62": "OD1" <-> "OD2" Residue "GX GLU 124": "OE1" <-> "OE2" Residue "GX GLU 268": "OE1" <-> "OE2" Residue "GX GLU 324": "OE1" <-> "OE2" Residue "HX ARG 36": "NH1" <-> "NH2" Residue "HX ARG 38": "NH1" <-> "NH2" Residue "HX ASP 51": "OD1" <-> "OD2" Residue "HX ASP 62": "OD1" <-> "OD2" Residue "HX GLU 124": "OE1" <-> "OE2" Residue "HX GLU 268": "OE1" <-> "OE2" Residue "IX ARG 36": "NH1" <-> "NH2" Residue "IX ARG 38": "NH1" <-> "NH2" Residue "IX ASP 62": "OD1" <-> "OD2" Residue "IX ASP 72": "OD1" <-> "OD2" Residue "IX GLU 124": "OE1" <-> "OE2" Residue "JX ARG 36": "NH1" <-> "NH2" Residue "JX ARG 38": "NH1" <-> "NH2" Residue "JX ASP 62": "OD1" <-> "OD2" Residue "JX GLU 124": "OE1" <-> "OE2" Residue "JX GLU 268": "OE1" <-> "OE2" Residue "KX ARG 36": "NH1" <-> "NH2" Residue "KX ARG 38": "NH1" <-> "NH2" Residue "KX ASP 62": "OD1" <-> "OD2" Residue "KX ASP 72": "OD1" <-> "OD2" Residue "KX GLU 124": "OE1" <-> "OE2" Residue "KX GLU 268": "OE1" <-> "OE2" Residue "KX GLU 324": "OE1" <-> "OE2" Residue "LX ARG 36": "NH1" <-> "NH2" Residue "LX ARG 38": "NH1" <-> "NH2" Residue "LX ASP 62": "OD1" <-> "OD2" Residue "LX ASP 72": "OD1" <-> "OD2" Residue "LX GLU 124": "OE1" <-> "OE2" Residue "LX GLU 268": "OE1" <-> "OE2" Residue "LX GLU 324": "OE1" <-> "OE2" Residue "MX ARG 36": "NH1" <-> "NH2" Residue "MX ARG 38": "NH1" <-> "NH2" Residue "MX ASP 72": "OD1" <-> "OD2" Residue "MX GLU 124": "OE1" <-> "OE2" Residue "MX GLU 268": "OE1" <-> "OE2" Residue "MX GLU 324": "OE1" <-> "OE2" Residue "NX ARG 36": "NH1" <-> "NH2" Residue "NX ARG 38": "NH1" <-> "NH2" Residue "NX ASP 51": "OD1" <-> "OD2" Residue "NX ASP 62": "OD1" <-> "OD2" Residue "NX ASP 72": "OD1" <-> "OD2" Residue "NX GLU 124": "OE1" <-> "OE2" Residue "NX GLU 317": "OE1" <-> "OE2" Residue "OX ARG 36": "NH1" <-> "NH2" Residue "OX ARG 38": "NH1" <-> "NH2" Residue "OX ASP 51": "OD1" <-> "OD2" Residue "OX GLU 70": "OE1" <-> "OE2" Residue "OX GLU 124": "OE1" <-> "OE2" Residue "PX ARG 36": "NH1" <-> "NH2" Residue "PX ARG 38": "NH1" <-> "NH2" Residue "PX ASP 51": "OD1" <-> "OD2" Residue "PX GLU 124": "OE1" <-> "OE2" Residue "PX GLU 317": "OE1" <-> "OE2" Residue "QX ARG 36": "NH1" <-> "NH2" Residue "QX ARG 38": "NH1" <-> "NH2" Residue "QX ASP 62": "OD1" <-> "OD2" Residue "QX GLU 70": "OE1" <-> "OE2" Residue "QX ASP 72": "OD1" <-> "OD2" Residue "QX GLU 124": "OE1" <-> "OE2" Residue "QX GLU 324": "OE1" <-> "OE2" Residue "AY GLU 1518": "OE1" <-> "OE2" Residue "AY ASP 1525": "OD1" <-> "OD2" Residue "AY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY ASP 1533": "OD1" <-> "OD2" Residue "AY ASP 1546": "OD1" <-> "OD2" Residue "AY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AY GLU 1585": "OE1" <-> "OE2" Residue "BY ASP 1517": "OD1" <-> "OD2" Residue "BY GLU 1518": "OE1" <-> "OE2" Residue "BY ASP 1525": "OD1" <-> "OD2" Residue "BY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BY ASP 1533": "OD1" <-> "OD2" Residue "BY ASP 1546": "OD1" <-> "OD2" Residue "BY ASP 1564": "OD1" <-> "OD2" Residue "BY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY GLU 1492": "OE1" <-> "OE2" Residue "CY GLU 1495": "OE1" <-> "OE2" Residue "CY ASP 1525": "OD1" <-> "OD2" Residue "CY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY ASP 1533": "OD1" <-> "OD2" Residue "CY ASP 1546": "OD1" <-> "OD2" Residue "CY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "CY ASP 1579": "OD1" <-> "OD2" Residue "CY GLU 1585": "OE1" <-> "OE2" Residue "DY GLU 1495": "OE1" <-> "OE2" Residue "DY ASP 1517": "OD1" <-> "OD2" Residue "DY GLU 1518": "OE1" <-> "OE2" Residue "DY ASP 1525": "OD1" <-> "OD2" Residue "DY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY ASP 1564": "OD1" <-> "OD2" Residue "DY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DY GLU 1577": "OE1" <-> "OE2" Residue "DY GLU 1585": "OE1" <-> "OE2" Residue "EY GLU 1492": "OE1" <-> "OE2" Residue "EY GLU 1495": "OE1" <-> "OE2" Residue "EY ASP 1503": "OD1" <-> "OD2" Residue "EY GLU 1518": "OE1" <-> "OE2" Residue "EY ASP 1525": "OD1" <-> "OD2" Residue "EY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "EY ASP 1533": "OD1" <-> "OD2" Residue "EY ASP 1546": "OD1" <-> "OD2" Residue "EY ASP 1552": "OD1" <-> "OD2" Residue "EY ASP 1569": "OD1" <-> "OD2" Residue "EY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FY GLU 1492": "OE1" <-> "OE2" Residue "FY ASP 1517": "OD1" <-> "OD2" Residue "FY GLU 1518": "OE1" <-> "OE2" Residue "FY ASP 1525": "OD1" <-> "OD2" Residue "FY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FY ASP 1533": "OD1" <-> "OD2" Residue "FY ASP 1546": "OD1" <-> "OD2" Residue "FY ASP 1552": "OD1" <-> "OD2" Residue "FY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GY ASP 1486": "OD1" <-> "OD2" Residue "GY GLU 1492": "OE1" <-> "OE2" Residue "GY GLU 1495": "OE1" <-> "OE2" Residue "GY ASP 1525": "OD1" <-> "OD2" Residue "GY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GY ASP 1552": "OD1" <-> "OD2" Residue "GY ASP 1569": "OD1" <-> "OD2" Residue "GY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "GY ASP 1579": "OD1" <-> "OD2" Residue "GY GLU 1585": "OE1" <-> "OE2" Residue "HY GLU 1495": "OE1" <-> "OE2" Residue "HY ASP 1503": "OD1" <-> "OD2" Residue "HY GLU 1518": "OE1" <-> "OE2" Residue "HY ASP 1525": "OD1" <-> "OD2" Residue "HY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HY ASP 1533": "OD1" <-> "OD2" Residue "HY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HY ASP 1552": "OD1" <-> "OD2" Residue "HY ASP 1564": "OD1" <-> "OD2" Residue "HY ASP 1569": "OD1" <-> "OD2" Residue "HY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HY ASP 1579": "OD1" <-> "OD2" Residue "IY GLU 1492": "OE1" <-> "OE2" Residue "IY ASP 1517": "OD1" <-> "OD2" Residue "IY GLU 1518": "OE1" <-> "OE2" Residue "IY ASP 1525": "OD1" <-> "OD2" Residue "IY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "IY ASP 1546": "OD1" <-> "OD2" Residue "IY ASP 1569": "OD1" <-> "OD2" Residue "IY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JY GLU 1518": "OE1" <-> "OE2" Residue "JY ASP 1525": "OD1" <-> "OD2" Residue "JY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JY ASP 1533": "OD1" <-> "OD2" Residue "JY ASP 1546": "OD1" <-> "OD2" Residue "JY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JY ASP 1552": "OD1" <-> "OD2" Residue "JY ASP 1569": "OD1" <-> "OD2" Residue "JY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KY ASP 1490": "OD1" <-> "OD2" Residue "KY GLU 1492": "OE1" <-> "OE2" Residue "KY ASP 1503": "OD1" <-> "OD2" Residue "KY ASP 1517": "OD1" <-> "OD2" Residue "KY GLU 1518": "OE1" <-> "OE2" Residue "KY ASP 1525": "OD1" <-> "OD2" Residue "KY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KY ASP 1564": "OD1" <-> "OD2" Residue "KY ASP 1569": "OD1" <-> "OD2" Residue "KY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "KY GLU 1585": "OE1" <-> "OE2" Residue "LY ASP 1486": "OD1" <-> "OD2" Residue "LY GLU 1492": "OE1" <-> "OE2" Residue "LY GLU 1495": "OE1" <-> "OE2" Residue "LY GLU 1518": "OE1" <-> "OE2" Residue "LY ASP 1525": "OD1" <-> "OD2" Residue "LY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LY ASP 1533": "OD1" <-> "OD2" Residue "LY ASP 1546": "OD1" <-> "OD2" Residue "LY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MY GLU 1492": "OE1" <-> "OE2" Residue "MY GLU 1495": "OE1" <-> "OE2" Residue "MY ASP 1503": "OD1" <-> "OD2" Residue "MY GLU 1518": "OE1" <-> "OE2" Residue "MY ASP 1525": "OD1" <-> "OD2" Residue "MY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MY ASP 1533": "OD1" <-> "OD2" Residue "MY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "MY GLU 1585": "OE1" <-> "OE2" Residue "NY GLU 1495": "OE1" <-> "OE2" Residue "NY ASP 1503": "OD1" <-> "OD2" Residue "NY ASP 1525": "OD1" <-> "OD2" Residue "NY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NY ASP 1546": "OD1" <-> "OD2" Residue "NY ASP 1569": "OD1" <-> "OD2" Residue "NY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OY GLU 1492": "OE1" <-> "OE2" Residue "OY GLU 1518": "OE1" <-> "OE2" Residue "OY ASP 1525": "OD1" <-> "OD2" Residue "OY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OY ASP 1546": "OD1" <-> "OD2" Residue "OY ASP 1564": "OD1" <-> "OD2" Residue "OY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "OY GLU 1585": "OE1" <-> "OE2" Residue "PY GLU 1495": "OE1" <-> "OE2" Residue "PY ASP 1503": "OD1" <-> "OD2" Residue "PY ASP 1517": "OD1" <-> "OD2" Residue "PY GLU 1518": "OE1" <-> "OE2" Residue "PY ASP 1525": "OD1" <-> "OD2" Residue "PY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PY ASP 1533": "OD1" <-> "OD2" Residue "PY ASP 1546": "OD1" <-> "OD2" Residue "PY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PY ASP 1564": "OD1" <-> "OD2" Residue "PY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PY GLU 1585": "OE1" <-> "OE2" Residue "QY GLU 1492": "OE1" <-> "OE2" Residue "QY ASP 1503": "OD1" <-> "OD2" Residue "QY GLU 1518": "OE1" <-> "OE2" Residue "QY ASP 1525": "OD1" <-> "OD2" Residue "QY PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QY ASP 1533": "OD1" <-> "OD2" Residue "QY ASP 1546": "OD1" <-> "OD2" Residue "QY PHE 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QY TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "QY ASP 1579": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40613 Number of models: 1 Model: "" Number of chains: 34 Chain: "AX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "BX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "CX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "DX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "EX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "FX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "GX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "HX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "IX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "JX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "KX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "LX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "MX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "NX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "OX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "PX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "QX" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1339 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain breaks: 1 Chain: "AY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "BY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "CY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "DY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "EY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "FY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "GY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "HY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "IY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "JY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "KY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "LY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "MY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "NY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "OY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "PY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Chain: "QY" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1050 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 5, 'TRANS': 129} Time building chain proxies: 20.05, per 1000 atoms: 0.49 Number of scatterers: 40613 At special positions: 0 Unit cell: (202, 201, 98, 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 102 16.00 O 8024 8.00 N 6868 7.00 C 25619 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYSAY1481 " - pdb=" SG CYSAY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSBY1481 " - pdb=" SG CYSBY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSCY1481 " - pdb=" SG CYSCY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSDY1481 " - pdb=" SG CYSDY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSEY1481 " - pdb=" SG CYSEY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSFY1481 " - pdb=" SG CYSFY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSGY1481 " - pdb=" SG CYSGY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSHY1481 " - pdb=" SG CYSHY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSIY1481 " - pdb=" SG CYSIY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSJY1481 " - pdb=" SG CYSJY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSKY1481 " - pdb=" SG CYSKY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSLY1481 " - pdb=" SG CYSLY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSMY1481 " - pdb=" SG CYSMY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSNY1481 " - pdb=" SG CYSNY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSOY1481 " - pdb=" SG CYSOY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSPY1481 " - pdb=" SG CYSPY1497 " distance=2.03 Simple disulfide: pdb=" SG CYSQY1481 " - pdb=" SG CYSQY1497 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.14 Conformation dependent library (CDL) restraints added in 7.2 seconds 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9860 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 68 sheets defined 43.4% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'AX' and resid 82 through 84 No H-bonds generated for 'chain 'AX' and resid 82 through 84' Processing helix chain 'AX' and resid 111 through 129 Processing helix chain 'AX' and resid 272 through 277 Processing helix chain 'AX' and resid 312 through 324 Processing helix chain 'BX' and resid 82 through 84 No H-bonds generated for 'chain 'BX' and resid 82 through 84' Processing helix chain 'BX' and resid 111 through 129 Processing helix chain 'BX' and resid 272 through 277 Processing helix chain 'BX' and resid 312 through 324 Processing helix chain 'CX' and resid 82 through 84 No H-bonds generated for 'chain 'CX' and resid 82 through 84' Processing helix chain 'CX' and resid 111 through 130 Processing helix chain 'CX' and resid 272 through 277 Processing helix chain 'CX' and resid 312 through 324 Processing helix chain 'DX' and resid 82 through 84 No H-bonds generated for 'chain 'DX' and resid 82 through 84' Processing helix chain 'DX' and resid 111 through 129 Processing helix chain 'DX' and resid 272 through 277 Processing helix chain 'DX' and resid 312 through 324 Processing helix chain 'EX' and resid 82 through 84 No H-bonds generated for 'chain 'EX' and resid 82 through 84' Processing helix chain 'EX' and resid 111 through 129 Processing helix chain 'EX' and resid 272 through 277 Processing helix chain 'EX' and resid 312 through 324 Processing helix chain 'FX' and resid 82 through 84 No H-bonds generated for 'chain 'FX' and resid 82 through 84' Processing helix chain 'FX' and resid 111 through 130 Processing helix chain 'FX' and resid 272 through 277 Processing helix chain 'FX' and resid 312 through 324 Processing helix chain 'GX' and resid 82 through 84 No H-bonds generated for 'chain 'GX' and resid 82 through 84' Processing helix chain 'GX' and resid 111 through 130 Processing helix chain 'GX' and resid 272 through 277 Processing helix chain 'GX' and resid 312 through 324 Processing helix chain 'HX' and resid 82 through 84 No H-bonds generated for 'chain 'HX' and resid 82 through 84' Processing helix chain 'HX' and resid 111 through 129 Processing helix chain 'HX' and resid 272 through 277 Processing helix chain 'HX' and resid 312 through 324 Processing helix chain 'IX' and resid 82 through 84 No H-bonds generated for 'chain 'IX' and resid 82 through 84' Processing helix chain 'IX' and resid 110 through 129 removed outlier: 4.687A pdb=" N ASNIX 114 " --> pdb=" O LYSIX 110 " (cutoff:3.500A) Processing helix chain 'IX' and resid 272 through 277 Processing helix chain 'IX' and resid 312 through 324 Processing helix chain 'JX' and resid 82 through 84 No H-bonds generated for 'chain 'JX' and resid 82 through 84' Processing helix chain 'JX' and resid 111 through 129 Processing helix chain 'JX' and resid 272 through 277 Processing helix chain 'JX' and resid 312 through 324 Processing helix chain 'KX' and resid 82 through 84 No H-bonds generated for 'chain 'KX' and resid 82 through 84' Processing helix chain 'KX' and resid 111 through 129 Processing helix chain 'KX' and resid 272 through 277 Processing helix chain 'KX' and resid 312 through 324 Processing helix chain 'LX' and resid 82 through 84 No H-bonds generated for 'chain 'LX' and resid 82 through 84' Processing helix chain 'LX' and resid 111 through 129 Processing helix chain 'LX' and resid 272 through 277 Processing helix chain 'LX' and resid 312 through 324 Processing helix chain 'MX' and resid 82 through 84 No H-bonds generated for 'chain 'MX' and resid 82 through 84' Processing helix chain 'MX' and resid 111 through 129 Processing helix chain 'MX' and resid 272 through 277 Processing helix chain 'MX' and resid 312 through 324 Processing helix chain 'NX' and resid 82 through 84 No H-bonds generated for 'chain 'NX' and resid 82 through 84' Processing helix chain 'NX' and resid 111 through 129 Processing helix chain 'NX' and resid 272 through 277 Processing helix chain 'NX' and resid 312 through 324 Processing helix chain 'OX' and resid 82 through 84 No H-bonds generated for 'chain 'OX' and resid 82 through 84' Processing helix chain 'OX' and resid 111 through 129 Processing helix chain 'OX' and resid 272 through 277 Processing helix chain 'OX' and resid 312 through 324 Processing helix chain 'PX' and resid 82 through 84 No H-bonds generated for 'chain 'PX' and resid 82 through 84' Processing helix chain 'PX' and resid 110 through 129 removed outlier: 4.685A pdb=" N ASNPX 114 " --> pdb=" O LYSPX 110 " (cutoff:3.500A) Processing helix chain 'PX' and resid 272 through 277 Processing helix chain 'PX' and resid 312 through 324 Processing helix chain 'QX' and resid 82 through 84 No H-bonds generated for 'chain 'QX' and resid 82 through 84' Processing helix chain 'QX' and resid 111 through 129 Processing helix chain 'QX' and resid 272 through 277 Processing helix chain 'QX' and resid 312 through 324 Processing helix chain 'AY' and resid 1472 through 1484 Processing helix chain 'AY' and resid 1490 through 1498 Processing helix chain 'AY' and resid 1502 through 1530 removed outlier: 4.558A pdb=" N LYSAY1530 " --> pdb=" O LEUAY1526 " (cutoff:3.500A) Processing helix chain 'AY' and resid 1531 through 1538 Processing helix chain 'AY' and resid 1562 through 1566 removed outlier: 3.508A pdb=" N ILEAY1566 " --> pdb=" O ALAAY1563 " (cutoff:3.500A) Processing helix chain 'AY' and resid 1579 through 1603 Processing helix chain 'BY' and resid 1472 through 1484 Processing helix chain 'BY' and resid 1490 through 1498 Processing helix chain 'BY' and resid 1502 through 1529 Processing helix chain 'BY' and resid 1531 through 1538 Processing helix chain 'BY' and resid 1562 through 1566 Processing helix chain 'BY' and resid 1579 through 1603 Processing helix chain 'CY' and resid 1472 through 1484 Processing helix chain 'CY' and resid 1490 through 1498 Processing helix chain 'CY' and resid 1502 through 1529 Processing helix chain 'CY' and resid 1531 through 1538 Processing helix chain 'CY' and resid 1562 through 1566 Processing helix chain 'CY' and resid 1579 through 1603 Processing helix chain 'DY' and resid 1472 through 1484 Processing helix chain 'DY' and resid 1490 through 1498 Processing helix chain 'DY' and resid 1502 through 1530 removed outlier: 4.531A pdb=" N LYSDY1530 " --> pdb=" O LEUDY1526 " (cutoff:3.500A) Processing helix chain 'DY' and resid 1531 through 1538 Processing helix chain 'DY' and resid 1562 through 1566 Processing helix chain 'DY' and resid 1579 through 1603 Processing helix chain 'EY' and resid 1472 through 1484 Processing helix chain 'EY' and resid 1490 through 1498 Processing helix chain 'EY' and resid 1502 through 1529 Processing helix chain 'EY' and resid 1531 through 1538 Processing helix chain 'EY' and resid 1562 through 1566 removed outlier: 3.503A pdb=" N ILEEY1566 " --> pdb=" O ALAEY1563 " (cutoff:3.500A) Processing helix chain 'EY' and resid 1579 through 1603 Processing helix chain 'FY' and resid 1472 through 1484 Processing helix chain 'FY' and resid 1490 through 1498 Processing helix chain 'FY' and resid 1502 through 1529 Processing helix chain 'FY' and resid 1531 through 1538 Processing helix chain 'FY' and resid 1562 through 1566 Processing helix chain 'FY' and resid 1579 through 1603 Processing helix chain 'GY' and resid 1472 through 1484 Processing helix chain 'GY' and resid 1490 through 1498 Processing helix chain 'GY' and resid 1502 through 1529 Processing helix chain 'GY' and resid 1531 through 1538 Processing helix chain 'GY' and resid 1562 through 1566 Processing helix chain 'GY' and resid 1579 through 1603 Processing helix chain 'HY' and resid 1472 through 1484 Processing helix chain 'HY' and resid 1490 through 1498 Processing helix chain 'HY' and resid 1502 through 1530 removed outlier: 4.546A pdb=" N LYSHY1530 " --> pdb=" O LEUHY1526 " (cutoff:3.500A) Processing helix chain 'HY' and resid 1531 through 1538 Processing helix chain 'HY' and resid 1562 through 1566 Processing helix chain 'HY' and resid 1579 through 1603 Processing helix chain 'IY' and resid 1472 through 1484 Processing helix chain 'IY' and resid 1490 through 1498 Processing helix chain 'IY' and resid 1502 through 1529 Processing helix chain 'IY' and resid 1531 through 1538 Processing helix chain 'IY' and resid 1562 through 1566 Processing helix chain 'IY' and resid 1579 through 1603 Processing helix chain 'JY' and resid 1472 through 1484 Processing helix chain 'JY' and resid 1490 through 1498 Processing helix chain 'JY' and resid 1502 through 1529 Processing helix chain 'JY' and resid 1531 through 1538 Processing helix chain 'JY' and resid 1562 through 1566 Processing helix chain 'JY' and resid 1579 through 1603 Processing helix chain 'KY' and resid 1472 through 1484 Processing helix chain 'KY' and resid 1490 through 1498 Processing helix chain 'KY' and resid 1502 through 1529 Processing helix chain 'KY' and resid 1531 through 1538 Processing helix chain 'KY' and resid 1562 through 1566 Processing helix chain 'KY' and resid 1579 through 1603 Processing helix chain 'LY' and resid 1472 through 1484 Processing helix chain 'LY' and resid 1490 through 1498 Processing helix chain 'LY' and resid 1502 through 1530 removed outlier: 4.596A pdb=" N LYSLY1530 " --> pdb=" O LEULY1526 " (cutoff:3.500A) Processing helix chain 'LY' and resid 1531 through 1538 Processing helix chain 'LY' and resid 1562 through 1566 Processing helix chain 'LY' and resid 1579 through 1603 Processing helix chain 'MY' and resid 1472 through 1484 Processing helix chain 'MY' and resid 1490 through 1498 Processing helix chain 'MY' and resid 1502 through 1530 removed outlier: 4.571A pdb=" N LYSMY1530 " --> pdb=" O LEUMY1526 " (cutoff:3.500A) Processing helix chain 'MY' and resid 1531 through 1538 Processing helix chain 'MY' and resid 1562 through 1566 Processing helix chain 'MY' and resid 1579 through 1603 Processing helix chain 'NY' and resid 1472 through 1484 Processing helix chain 'NY' and resid 1490 through 1498 Processing helix chain 'NY' and resid 1502 through 1529 Processing helix chain 'NY' and resid 1531 through 1538 Processing helix chain 'NY' and resid 1562 through 1566 Processing helix chain 'NY' and resid 1579 through 1603 Processing helix chain 'OY' and resid 1472 through 1484 Processing helix chain 'OY' and resid 1490 through 1498 Processing helix chain 'OY' and resid 1502 through 1529 Processing helix chain 'OY' and resid 1531 through 1538 Processing helix chain 'OY' and resid 1562 through 1566 Processing helix chain 'OY' and resid 1579 through 1603 Processing helix chain 'PY' and resid 1472 through 1484 Processing helix chain 'PY' and resid 1490 through 1498 Processing helix chain 'PY' and resid 1502 through 1530 removed outlier: 4.590A pdb=" N LYSPY1530 " --> pdb=" O LEUPY1526 " (cutoff:3.500A) Processing helix chain 'PY' and resid 1531 through 1538 Processing helix chain 'PY' and resid 1562 through 1566 Processing helix chain 'PY' and resid 1579 through 1603 Processing helix chain 'QY' and resid 1472 through 1484 Processing helix chain 'QY' and resid 1490 through 1498 Processing helix chain 'QY' and resid 1502 through 1529 Processing helix chain 'QY' and resid 1531 through 1538 Processing helix chain 'QY' and resid 1562 through 1566 Processing helix chain 'QY' and resid 1579 through 1603 Processing sheet with id=AA1, first strand: chain 'AX' and resid 41 through 47 removed outlier: 7.754A pdb=" N VALAX 42 " --> pdb=" O THRAX 307 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N LYSAX 309 " --> pdb=" O VALAX 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYSAX 44 " --> pdb=" O LYSAX 309 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLUAX 311 " --> pdb=" O LYSAX 44 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILEAX 46 " --> pdb=" O GLUAX 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'AX' and resid 55 through 59 removed outlier: 6.392A pdb=" N ILEAX 55 " --> pdb=" O ILEAX 292 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARGAX 294 " --> pdb=" O ILEAX 55 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILEAX 57 " --> pdb=" O ARGAX 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'AX' and resid 102 through 104 Processing sheet with id=AA4, first strand: chain 'AX' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'BX' and resid 41 through 47 removed outlier: 7.695A pdb=" N VALBX 42 " --> pdb=" O THRBX 307 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N LYSBX 309 " --> pdb=" O VALBX 42 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LYSBX 44 " --> pdb=" O LYSBX 309 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N GLUBX 311 " --> pdb=" O LYSBX 44 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILEBX 46 " --> pdb=" O GLUBX 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BX' and resid 55 through 59 removed outlier: 6.399A pdb=" N ILEBX 55 " --> pdb=" O ILEBX 292 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ARGBX 294 " --> pdb=" O ILEBX 55 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILEBX 57 " --> pdb=" O ARGBX 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'BX' and resid 102 through 104 Processing sheet with id=AA8, first strand: chain 'BX' and resid 106 through 108 Processing sheet with id=AA9, first strand: chain 'CX' and resid 41 through 47 removed outlier: 7.720A pdb=" N VALCX 42 " --> pdb=" O THRCX 307 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N LYSCX 309 " --> pdb=" O VALCX 42 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYSCX 44 " --> pdb=" O LYSCX 309 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLUCX 311 " --> pdb=" O LYSCX 44 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILECX 46 " --> pdb=" O GLUCX 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'CX' and resid 55 through 59 removed outlier: 6.336A pdb=" N ILECX 55 " --> pdb=" O ILECX 292 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARGCX 294 " --> pdb=" O ILECX 55 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILECX 57 " --> pdb=" O ARGCX 294 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'CX' and resid 102 through 104 Processing sheet with id=AB3, first strand: chain 'CX' and resid 106 through 108 Processing sheet with id=AB4, first strand: chain 'DX' and resid 41 through 47 removed outlier: 7.728A pdb=" N VALDX 42 " --> pdb=" O THRDX 307 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N LYSDX 309 " --> pdb=" O VALDX 42 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYSDX 44 " --> pdb=" O LYSDX 309 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLUDX 311 " --> pdb=" O LYSDX 44 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILEDX 46 " --> pdb=" O GLUDX 311 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'DX' and resid 55 through 59 removed outlier: 6.343A pdb=" N ILEDX 55 " --> pdb=" O ILEDX 292 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARGDX 294 " --> pdb=" O ILEDX 55 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ILEDX 57 " --> pdb=" O ARGDX 294 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'DX' and resid 102 through 104 Processing sheet with id=AB7, first strand: chain 'DX' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'EX' and resid 41 through 47 removed outlier: 7.728A pdb=" N VALEX 42 " --> pdb=" O THREX 307 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LYSEX 309 " --> pdb=" O VALEX 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LYSEX 44 " --> pdb=" O LYSEX 309 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLUEX 311 " --> pdb=" O LYSEX 44 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILEEX 46 " --> pdb=" O GLUEX 311 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'EX' and resid 55 through 59 removed outlier: 6.329A pdb=" N ILEEX 55 " --> pdb=" O ILEEX 292 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARGEX 294 " --> pdb=" O ILEEX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEEX 57 " --> pdb=" O ARGEX 294 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'EX' and resid 102 through 104 Processing sheet with id=AC2, first strand: chain 'EX' and resid 106 through 108 Processing sheet with id=AC3, first strand: chain 'FX' and resid 41 through 47 removed outlier: 7.712A pdb=" N VALFX 42 " --> pdb=" O THRFX 307 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N LYSFX 309 " --> pdb=" O VALFX 42 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYSFX 44 " --> pdb=" O LYSFX 309 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLUFX 311 " --> pdb=" O LYSFX 44 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILEFX 46 " --> pdb=" O GLUFX 311 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'FX' and resid 55 through 59 Processing sheet with id=AC5, first strand: chain 'FX' and resid 102 through 104 Processing sheet with id=AC6, first strand: chain 'FX' and resid 106 through 108 Processing sheet with id=AC7, first strand: chain 'GX' and resid 41 through 47 removed outlier: 7.673A pdb=" N VALGX 42 " --> pdb=" O THRGX 307 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LYSGX 309 " --> pdb=" O VALGX 42 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LYSGX 44 " --> pdb=" O LYSGX 309 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLUGX 311 " --> pdb=" O LYSGX 44 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILEGX 46 " --> pdb=" O GLUGX 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'GX' and resid 55 through 59 removed outlier: 6.393A pdb=" N ILEGX 55 " --> pdb=" O ILEGX 292 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARGGX 294 " --> pdb=" O ILEGX 55 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ILEGX 57 " --> pdb=" O ARGGX 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'GX' and resid 102 through 104 Processing sheet with id=AD1, first strand: chain 'GX' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'HX' and resid 41 through 47 removed outlier: 7.749A pdb=" N VALHX 42 " --> pdb=" O THRHX 307 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LYSHX 309 " --> pdb=" O VALHX 42 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYSHX 44 " --> pdb=" O LYSHX 309 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLUHX 311 " --> pdb=" O LYSHX 44 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILEHX 46 " --> pdb=" O GLUHX 311 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'HX' and resid 55 through 59 removed outlier: 6.385A pdb=" N ILEHX 55 " --> pdb=" O ILEHX 292 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARGHX 294 " --> pdb=" O ILEHX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEHX 57 " --> pdb=" O ARGHX 294 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'HX' and resid 102 through 104 Processing sheet with id=AD5, first strand: chain 'HX' and resid 106 through 108 Processing sheet with id=AD6, first strand: chain 'IX' and resid 41 through 47 removed outlier: 7.697A pdb=" N VALIX 42 " --> pdb=" O THRIX 307 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYSIX 309 " --> pdb=" O VALIX 42 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYSIX 44 " --> pdb=" O LYSIX 309 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLUIX 311 " --> pdb=" O LYSIX 44 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ILEIX 46 " --> pdb=" O GLUIX 311 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'IX' and resid 55 through 59 removed outlier: 6.414A pdb=" N ILEIX 55 " --> pdb=" O ILEIX 292 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ARGIX 294 " --> pdb=" O ILEIX 55 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ILEIX 57 " --> pdb=" O ARGIX 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'IX' and resid 102 through 104 Processing sheet with id=AD9, first strand: chain 'IX' and resid 106 through 108 Processing sheet with id=AE1, first strand: chain 'JX' and resid 41 through 47 removed outlier: 7.712A pdb=" N VALJX 42 " --> pdb=" O THRJX 307 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYSJX 309 " --> pdb=" O VALJX 42 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYSJX 44 " --> pdb=" O LYSJX 309 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLUJX 311 " --> pdb=" O LYSJX 44 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILEJX 46 " --> pdb=" O GLUJX 311 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'JX' and resid 55 through 59 removed outlier: 6.327A pdb=" N ILEJX 55 " --> pdb=" O ILEJX 292 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ARGJX 294 " --> pdb=" O ILEJX 55 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N ILEJX 57 " --> pdb=" O ARGJX 294 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'JX' and resid 102 through 104 Processing sheet with id=AE4, first strand: chain 'JX' and resid 106 through 108 Processing sheet with id=AE5, first strand: chain 'KX' and resid 41 through 47 removed outlier: 7.713A pdb=" N VALKX 42 " --> pdb=" O THRKX 307 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYSKX 309 " --> pdb=" O VALKX 42 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LYSKX 44 " --> pdb=" O LYSKX 309 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N GLUKX 311 " --> pdb=" O LYSKX 44 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILEKX 46 " --> pdb=" O GLUKX 311 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KX' and resid 55 through 59 removed outlier: 6.403A pdb=" N ILEKX 55 " --> pdb=" O ILEKX 292 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ARGKX 294 " --> pdb=" O ILEKX 55 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILEKX 57 " --> pdb=" O ARGKX 294 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'KX' and resid 102 through 104 Processing sheet with id=AE8, first strand: chain 'KX' and resid 106 through 108 Processing sheet with id=AE9, first strand: chain 'LX' and resid 41 through 47 removed outlier: 7.678A pdb=" N VALLX 42 " --> pdb=" O THRLX 307 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N LYSLX 309 " --> pdb=" O VALLX 42 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYSLX 44 " --> pdb=" O LYSLX 309 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLULX 311 " --> pdb=" O LYSLX 44 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILELX 46 " --> pdb=" O GLULX 311 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LX' and resid 55 through 59 removed outlier: 6.365A pdb=" N ILELX 55 " --> pdb=" O ILELX 292 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ARGLX 294 " --> pdb=" O ILELX 55 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILELX 57 " --> pdb=" O ARGLX 294 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LX' and resid 102 through 104 Processing sheet with id=AF3, first strand: chain 'LX' and resid 106 through 108 Processing sheet with id=AF4, first strand: chain 'MX' and resid 41 through 47 removed outlier: 7.697A pdb=" N VALMX 42 " --> pdb=" O THRMX 307 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LYSMX 309 " --> pdb=" O VALMX 42 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYSMX 44 " --> pdb=" O LYSMX 309 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N GLUMX 311 " --> pdb=" O LYSMX 44 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILEMX 46 " --> pdb=" O GLUMX 311 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'MX' and resid 55 through 59 removed outlier: 6.377A pdb=" N ILEMX 55 " --> pdb=" O ILEMX 292 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ARGMX 294 " --> pdb=" O ILEMX 55 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ILEMX 57 " --> pdb=" O ARGMX 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'MX' and resid 102 through 104 Processing sheet with id=AF7, first strand: chain 'MX' and resid 106 through 108 Processing sheet with id=AF8, first strand: chain 'NX' and resid 41 through 47 removed outlier: 7.741A pdb=" N VALNX 42 " --> pdb=" O THRNX 307 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N LYSNX 309 " --> pdb=" O VALNX 42 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYSNX 44 " --> pdb=" O LYSNX 309 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLUNX 311 " --> pdb=" O LYSNX 44 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILENX 46 " --> pdb=" O GLUNX 311 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'NX' and resid 55 through 59 removed outlier: 6.384A pdb=" N ILENX 55 " --> pdb=" O ILENX 292 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ARGNX 294 " --> pdb=" O ILENX 55 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILENX 57 " --> pdb=" O ARGNX 294 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'NX' and resid 102 through 104 Processing sheet with id=AG2, first strand: chain 'NX' and resid 106 through 108 Processing sheet with id=AG3, first strand: chain 'OX' and resid 41 through 47 removed outlier: 7.685A pdb=" N VALOX 42 " --> pdb=" O THROX 307 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N LYSOX 309 " --> pdb=" O VALOX 42 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYSOX 44 " --> pdb=" O LYSOX 309 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLUOX 311 " --> pdb=" O LYSOX 44 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ILEOX 46 " --> pdb=" O GLUOX 311 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'OX' and resid 55 through 59 removed outlier: 6.357A pdb=" N ILEOX 55 " --> pdb=" O ILEOX 292 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARGOX 294 " --> pdb=" O ILEOX 55 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILEOX 57 " --> pdb=" O ARGOX 294 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'OX' and resid 102 through 104 Processing sheet with id=AG6, first strand: chain 'OX' and resid 106 through 108 Processing sheet with id=AG7, first strand: chain 'PX' and resid 41 through 47 removed outlier: 7.739A pdb=" N VALPX 42 " --> pdb=" O THRPX 307 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N LYSPX 309 " --> pdb=" O VALPX 42 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYSPX 44 " --> pdb=" O LYSPX 309 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLUPX 311 " --> pdb=" O LYSPX 44 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILEPX 46 " --> pdb=" O GLUPX 311 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'PX' and resid 55 through 59 removed outlier: 6.331A pdb=" N ILEPX 55 " --> pdb=" O ILEPX 292 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ARGPX 294 " --> pdb=" O ILEPX 55 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N ILEPX 57 " --> pdb=" O ARGPX 294 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'PX' and resid 102 through 104 Processing sheet with id=AH1, first strand: chain 'PX' and resid 106 through 108 Processing sheet with id=AH2, first strand: chain 'QX' and resid 41 through 47 removed outlier: 7.738A pdb=" N VALQX 42 " --> pdb=" O THRQX 307 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYSQX 309 " --> pdb=" O VALQX 42 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYSQX 44 " --> pdb=" O LYSQX 309 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLUQX 311 " --> pdb=" O LYSQX 44 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILEQX 46 " --> pdb=" O GLUQX 311 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'QX' and resid 55 through 59 removed outlier: 6.344A pdb=" N ILEQX 55 " --> pdb=" O ILEQX 292 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ARGQX 294 " --> pdb=" O ILEQX 55 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILEQX 57 " --> pdb=" O ARGQX 294 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'QX' and resid 102 through 104 Processing sheet with id=AH5, first strand: chain 'QX' and resid 106 through 108 2029 hydrogen bonds defined for protein. 5784 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.77 Time building geometry restraints manager: 17.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12880 1.34 - 1.45: 5041 1.45 - 1.57: 23151 1.57 - 1.68: 0 1.68 - 1.80: 170 Bond restraints: 41242 Sorted by residual: bond pdb=" C VALKX 89 " pdb=" N PROKX 90 " ideal model delta sigma weight residual 1.335 1.316 0.019 8.70e-03 1.32e+04 4.74e+00 bond pdb=" C VALNX 89 " pdb=" N PRONX 90 " ideal model delta sigma weight residual 1.335 1.317 0.018 8.70e-03 1.32e+04 4.33e+00 bond pdb=" C VALGX 89 " pdb=" N PROGX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 4.00e+00 bond pdb=" C VALJX 89 " pdb=" N PROJX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.99e+00 bond pdb=" C VALMX 89 " pdb=" N PROMX 90 " ideal model delta sigma weight residual 1.335 1.318 0.017 8.70e-03 1.32e+04 3.93e+00 ... (remaining 41237 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.76: 1014 106.76 - 113.60: 23381 113.60 - 120.45: 15622 120.45 - 127.29: 15359 127.29 - 134.13: 333 Bond angle restraints: 55709 Sorted by residual: angle pdb=" CA GLUAX 268 " pdb=" CB GLUAX 268 " pdb=" CG GLUAX 268 " ideal model delta sigma weight residual 114.10 122.57 -8.47 2.00e+00 2.50e-01 1.79e+01 angle pdb=" C METGY1545 " pdb=" N ASPGY1546 " pdb=" CA ASPGY1546 " ideal model delta sigma weight residual 122.07 128.12 -6.05 1.43e+00 4.89e-01 1.79e+01 angle pdb=" CA GLULX 268 " pdb=" CB GLULX 268 " pdb=" CG GLULX 268 " ideal model delta sigma weight residual 114.10 122.00 -7.90 2.00e+00 2.50e-01 1.56e+01 angle pdb=" CA GLUNX 268 " pdb=" CB GLUNX 268 " pdb=" CG GLUNX 268 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLUFX 268 " pdb=" CB GLUFX 268 " pdb=" CG GLUFX 268 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 ... (remaining 55704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.17: 21932 18.17 - 36.34: 2706 36.34 - 54.51: 768 54.51 - 72.69: 163 72.69 - 90.86: 67 Dihedral angle restraints: 25636 sinusoidal: 10574 harmonic: 15062 Sorted by residual: dihedral pdb=" CB CYSNY1481 " pdb=" SG CYSNY1481 " pdb=" SG CYSNY1497 " pdb=" CB CYSNY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.66 86.66 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYSQY1481 " pdb=" SG CYSQY1481 " pdb=" SG CYSQY1497 " pdb=" CB CYSQY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.63 86.63 1 1.00e+01 1.00e-02 9.04e+01 dihedral pdb=" CB CYSAY1481 " pdb=" SG CYSAY1481 " pdb=" SG CYSAY1497 " pdb=" CB CYSAY1497 " ideal model delta sinusoidal sigma weight residual -86.00 -172.55 86.55 1 1.00e+01 1.00e-02 9.02e+01 ... (remaining 25633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5666 0.080 - 0.159: 642 0.159 - 0.239: 52 0.239 - 0.318: 14 0.318 - 0.398: 1 Chirality restraints: 6375 Sorted by residual: chirality pdb=" CB ILEFX 78 " pdb=" CA ILEFX 78 " pdb=" CG1 ILEFX 78 " pdb=" CG2 ILEFX 78 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CB ILEGY1576 " pdb=" CA ILEGY1576 " pdb=" CG1 ILEGY1576 " pdb=" CG2 ILEGY1576 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB THRPY1555 " pdb=" CA THRPY1555 " pdb=" OG1 THRPY1555 " pdb=" CG2 THRPY1555 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 6372 not shown) Planarity restraints: 7191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASPFY1552 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.91e+00 pdb=" C ASPFY1552 " -0.038 2.00e-02 2.50e+03 pdb=" O ASPFY1552 " 0.015 2.00e-02 2.50e+03 pdb=" N ILEFY1553 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALJX 66 " 0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" C VALJX 66 " -0.037 2.00e-02 2.50e+03 pdb=" O VALJX 66 " 0.014 2.00e-02 2.50e+03 pdb=" N ILEJX 67 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VALFX 66 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C VALFX 66 " -0.036 2.00e-02 2.50e+03 pdb=" O VALFX 66 " 0.014 2.00e-02 2.50e+03 pdb=" N ILEFX 67 " 0.012 2.00e-02 2.50e+03 ... (remaining 7188 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 10778 2.79 - 3.32: 38303 3.32 - 3.85: 74084 3.85 - 4.37: 83372 4.37 - 4.90: 145496 Nonbonded interactions: 352033 Sorted by model distance: nonbonded pdb=" OG1 THRPX 65 " pdb=" O TYRPX 305 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THRJX 65 " pdb=" O TYRJX 305 " model vdw 2.272 2.440 nonbonded pdb=" OG1 THRQX 65 " pdb=" O TYRQX 305 " model vdw 2.274 2.440 nonbonded pdb=" OG1 THRCX 65 " pdb=" O TYRCX 305 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THRMX 65 " pdb=" O TYRMX 305 " model vdw 2.275 2.440 ... (remaining 352028 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 'AX' selection = chain 'BX' selection = chain 'CX' selection = chain 'DX' selection = chain 'EX' selection = chain 'FX' selection = chain 'GX' selection = chain 'HX' selection = chain 'IX' selection = chain 'JX' selection = chain 'KX' selection = chain 'LX' selection = chain 'MX' selection = chain 'NX' selection = chain 'OX' selection = chain 'PX' selection = chain 'QX' } ncs_group { reference = chain 'AY' selection = chain 'BY' selection = chain 'CY' selection = chain 'DY' selection = chain 'EY' selection = chain 'FY' selection = chain 'GY' selection = chain 'HY' selection = chain 'IY' selection = chain 'JY' selection = chain 'KY' selection = chain 'LY' selection = chain 'MY' selection = chain 'NY' selection = chain 'OY' selection = chain 'PY' selection = chain 'QY' } 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: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 30.980 Check model and map are aligned: 0.600 Set scattering table: 0.390 Process input model: 104.170 Find NCS groups from input model: 3.100 Set up NCS constraints: 0.480 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:11.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 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 : 0.007 0.052 41242 Z= 0.444 Angle : 0.782 13.033 55709 Z= 0.448 Chirality : 0.053 0.398 6375 Planarity : 0.006 0.049 7191 Dihedral : 17.967 90.858 15725 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 10.29 % Allowed : 22.38 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.79 (0.09), residues: 4981 helix: -2.16 (0.08), residues: 2074 sheet: -2.81 (0.15), residues: 680 loop : -2.66 (0.10), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRPAX 58 HIS 0.005 0.001 HISNX 94 PHE 0.018 0.003 PHECY1547 TYR 0.011 0.002 TYREX 122 ARG 0.011 0.001 ARGBX 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1701 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 467 poor density : 1234 time to evaluate : 5.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 83 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (m-40) REVERT: BX 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (pp) REVERT: BX 130 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6510 (tppt) REVERT: CX 77 TYR cc_start: 0.8624 (t80) cc_final: 0.8105 (t80) REVERT: CX 273 ASP cc_start: 0.8157 (t70) cc_final: 0.7685 (t0) REVERT: DX 91 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8311 (t0) REVERT: DX 114 ASN cc_start: 0.8100 (t0) cc_final: 0.7880 (m-40) REVERT: DX 130 LYS cc_start: 0.6563 (OUTLIER) cc_final: 0.5867 (tppt) REVERT: EX 91 ASN cc_start: 0.8579 (OUTLIER) cc_final: 0.8139 (t0) REVERT: HX 130 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6020 (tppt) REVERT: HX 273 ASP cc_start: 0.8152 (t70) cc_final: 0.7937 (t0) REVERT: IX 77 TYR cc_start: 0.8517 (t80) cc_final: 0.7880 (t80) REVERT: IX 273 ASP cc_start: 0.8085 (t70) cc_final: 0.7600 (t0) REVERT: KX 273 ASP cc_start: 0.8222 (t70) cc_final: 0.7803 (t0) REVERT: LX 91 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8397 (t0) REVERT: OX 77 TYR cc_start: 0.8522 (t80) cc_final: 0.8297 (t80) REVERT: OX 91 ASN cc_start: 0.8578 (OUTLIER) cc_final: 0.8284 (t0) REVERT: OX 130 LYS cc_start: 0.6538 (OUTLIER) cc_final: 0.5853 (tppt) REVERT: OX 273 ASP cc_start: 0.8128 (t70) cc_final: 0.7677 (t0) REVERT: OX 324 GLU cc_start: 0.7322 (mp0) cc_final: 0.7120 (mp0) REVERT: PX 91 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8401 (t0) REVERT: AY 1480 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8021 (mm-30) REVERT: AY 1549 ASN cc_start: 0.7466 (m110) cc_final: 0.6437 (m110) REVERT: AY 1596 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7473 (mt-10) REVERT: BY 1528 ASN cc_start: 0.8475 (t0) cc_final: 0.8148 (t0) REVERT: BY 1549 ASN cc_start: 0.7689 (m110) cc_final: 0.7465 (m110) REVERT: BY 1570 ASN cc_start: 0.8300 (p0) cc_final: 0.7981 (p0) REVERT: CY 1480 GLU cc_start: 0.8270 (mm-30) cc_final: 0.8019 (tp30) REVERT: CY 1528 ASN cc_start: 0.8361 (t0) cc_final: 0.8113 (t0) REVERT: CY 1549 ASN cc_start: 0.7383 (m110) cc_final: 0.6062 (m-40) REVERT: CY 1570 ASN cc_start: 0.8323 (p0) cc_final: 0.8104 (p0) REVERT: CY 1601 LYS cc_start: 0.8146 (tmmt) cc_final: 0.7826 (tmmm) REVERT: DY 1480 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7876 (mm-30) REVERT: DY 1570 ASN cc_start: 0.8183 (p0) cc_final: 0.7895 (p0) REVERT: EY 1480 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7919 (mm-30) REVERT: EY 1528 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.7677 (t0) REVERT: EY 1596 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7551 (mt-10) REVERT: FY 1480 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7825 (mm-30) REVERT: FY 1518 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: FY 1528 ASN cc_start: 0.8322 (t0) cc_final: 0.7947 (t0) REVERT: FY 1549 ASN cc_start: 0.7547 (m110) cc_final: 0.6304 (m-40) REVERT: FY 1570 ASN cc_start: 0.8069 (p0) cc_final: 0.7841 (p0) REVERT: FY 1596 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7396 (mt-10) REVERT: GY 1480 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7605 (mm-30) REVERT: GY 1517 ASP cc_start: 0.7604 (p0) cc_final: 0.6886 (p0) REVERT: GY 1518 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: GY 1570 ASN cc_start: 0.8365 (p0) cc_final: 0.8107 (p0) REVERT: GY 1596 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7462 (mt-10) REVERT: HY 1480 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7707 (mm-30) REVERT: HY 1549 ASN cc_start: 0.7481 (m110) cc_final: 0.6627 (m110) REVERT: HY 1570 ASN cc_start: 0.8202 (p0) cc_final: 0.7961 (p0) REVERT: IY 1480 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7836 (mm-30) REVERT: IY 1596 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7389 (mt-10) REVERT: JY 1480 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7804 (mm-30) REVERT: JY 1570 ASN cc_start: 0.8204 (p0) cc_final: 0.7935 (p0) REVERT: KY 1480 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7592 (mm-30) REVERT: LY 1480 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7882 (mm-30) REVERT: LY 1499 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7844 (mt-10) REVERT: LY 1513 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8197 (tttp) REVERT: LY 1528 ASN cc_start: 0.8440 (t0) cc_final: 0.8172 (t0) REVERT: LY 1570 ASN cc_start: 0.8323 (p0) cc_final: 0.8068 (p0) REVERT: LY 1596 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7187 (mm-30) REVERT: MY 1480 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7654 (mm-30) REVERT: MY 1517 ASP cc_start: 0.7687 (p0) cc_final: 0.7217 (p0) REVERT: MY 1518 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: MY 1549 ASN cc_start: 0.7926 (m-40) cc_final: 0.6814 (m-40) REVERT: MY 1570 ASN cc_start: 0.8196 (p0) cc_final: 0.7958 (p0) REVERT: MY 1596 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7536 (mt-10) REVERT: NY 1480 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7868 (mm-30) REVERT: NY 1549 ASN cc_start: 0.7461 (m110) cc_final: 0.7240 (m110) REVERT: NY 1570 ASN cc_start: 0.8179 (p0) cc_final: 0.7919 (p0) REVERT: NY 1596 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7229 (mm-30) REVERT: OY 1480 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7792 (mm-30) REVERT: OY 1517 ASP cc_start: 0.8152 (p0) cc_final: 0.7923 (p0) REVERT: OY 1528 ASN cc_start: 0.8303 (t0) cc_final: 0.7971 (t0) REVERT: OY 1596 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7213 (mm-30) REVERT: PY 1549 ASN cc_start: 0.7376 (m110) cc_final: 0.7071 (m-40) REVERT: PY 1570 ASN cc_start: 0.8294 (p0) cc_final: 0.7945 (p0) REVERT: QY 1480 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7783 (mm-30) REVERT: QY 1499 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7874 (mt-10) REVERT: QY 1549 ASN cc_start: 0.7502 (m110) cc_final: 0.6798 (m-40) REVERT: QY 1570 ASN cc_start: 0.8352 (p0) cc_final: 0.8132 (p0) outliers start: 467 outliers final: 255 residues processed: 1617 average time/residue: 1.4817 time to fit residues: 2915.0523 Evaluate side-chains 1116 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 845 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 56 THR Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 87 SER Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 130 LYS Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 56 THR Chi-restraints excluded: chain CX residue 83 ASN Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 87 SER Chi-restraints excluded: chain DX residue 91 ASN Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 130 LYS Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain DX residue 319 SER Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 56 THR Chi-restraints excluded: chain EX residue 87 SER Chi-restraints excluded: chain EX residue 91 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 319 SER Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 56 THR Chi-restraints excluded: chain FX residue 87 SER Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 274 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 49 LEU Chi-restraints excluded: chain GX residue 56 THR Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 319 SER Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 56 THR Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 130 LYS Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 274 SER Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 317 GLU Chi-restraints excluded: chain HX residue 319 SER Chi-restraints excluded: chain HX residue 321 VAL Chi-restraints excluded: chain IX residue 39 VAL Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 56 THR Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 87 SER Chi-restraints excluded: chain IX residue 91 ASN Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 303 SER Chi-restraints excluded: chain IX residue 319 SER Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 87 SER Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 319 SER Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 49 LEU Chi-restraints excluded: chain KX residue 56 THR Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 272 SER Chi-restraints excluded: chain KX residue 274 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 56 THR Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 91 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 274 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 319 SER Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 56 THR Chi-restraints excluded: chain MX residue 83 ASN Chi-restraints excluded: chain MX residue 87 SER Chi-restraints excluded: chain MX residue 91 ASN Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 56 THR Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 303 SER Chi-restraints excluded: chain NX residue 319 SER Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 49 LEU Chi-restraints excluded: chain OX residue 56 THR Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 87 SER Chi-restraints excluded: chain OX residue 89 VAL Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 130 LYS Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 319 SER Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 62 ASP Chi-restraints excluded: chain PX residue 87 SER Chi-restraints excluded: chain PX residue 91 ASN Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 274 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 319 SER Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 40 LYS Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 56 THR Chi-restraints excluded: chain QX residue 87 SER Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 91 ASN Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 319 SER Chi-restraints excluded: chain AY residue 1470 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1504 SER Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1526 LEU Chi-restraints excluded: chain AY residue 1562 ASP Chi-restraints excluded: chain BY residue 1479 SER Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1518 GLU Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1526 LEU Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1502 SER Chi-restraints excluded: chain CY residue 1526 LEU Chi-restraints excluded: chain CY residue 1561 VAL Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1555 THR Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1526 LEU Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1479 SER Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1518 GLU Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1526 LEU Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1479 SER Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1502 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1526 LEU Chi-restraints excluded: chain GY residue 1561 VAL Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain GY residue 1564 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1504 SER Chi-restraints excluded: chain HY residue 1524 SER Chi-restraints excluded: chain HY residue 1526 LEU Chi-restraints excluded: chain HY residue 1561 VAL Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1564 ASP Chi-restraints excluded: chain HY residue 1585 GLU Chi-restraints excluded: chain IY residue 1479 SER Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1561 VAL Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1504 SER Chi-restraints excluded: chain JY residue 1526 LEU Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain JY residue 1603 LEU Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1479 SER Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1504 SER Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1526 LEU Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1479 SER Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1513 LYS Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1479 SER Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1526 LEU Chi-restraints excluded: chain NY residue 1561 VAL Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1470 SER Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1524 SER Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1470 SER Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1502 SER Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1526 LEU Chi-restraints excluded: chain PY residue 1561 VAL Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1479 SER Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1518 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1526 LEU Chi-restraints excluded: chain QY residue 1561 VAL Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 416 optimal weight: 0.9990 chunk 373 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 chunk 199 optimal weight: 3.9990 chunk 386 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 287 optimal weight: 5.9990 chunk 447 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN CX 297 GLN DX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** DX 297 GLN ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 83 ASN GX 83 ASN IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** IX 297 GLN JX 83 ASN JX 91 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 297 GLN KX 83 ASN ** KX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** KX 297 GLN ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** OX 297 GLN ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1476 HIS AY1484 ASN AY1549 ASN BY1476 HIS BY1583 GLN CY1476 HIS CY1484 ASN CY1549 ASN DY1476 HIS DY1484 ASN DY1528 ASN DY1549 ASN EY1476 HIS EY1583 GLN FY1476 HIS FY1549 ASN GY1476 HIS HY1476 HIS HY1484 ASN HY1549 ASN IY1476 HIS IY1583 GLN JY1476 HIS KY1476 HIS KY1484 ASN KY1515 GLN KY1549 ASN LY1476 HIS LY1484 ASN MY1476 HIS MY1484 ASN NY1476 HIS NY1528 ASN NY1549 ASN OY1476 HIS OY1528 ASN OY1549 ASN PY1476 HIS PY1515 GLN PY1528 ASN PY1549 ASN QY1476 HIS QY1549 ASN QY1583 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 41242 Z= 0.242 Angle : 0.586 9.954 55709 Z= 0.314 Chirality : 0.044 0.244 6375 Planarity : 0.005 0.046 7191 Dihedral : 9.773 160.610 5793 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 9.56 % Allowed : 26.37 % Favored : 64.07 % 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: -1.98 (0.10), residues: 4981 helix: 0.09 (0.10), residues: 2074 sheet: -2.61 (0.16), residues: 714 loop : -2.21 (0.11), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRPJX 86 HIS 0.008 0.001 HISJX 94 PHE 0.011 0.001 PHEEX 96 TYR 0.018 0.001 TYRAX 77 ARG 0.011 0.001 ARGIX 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 434 poor density : 964 time to evaluate : 4.682 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: AX 120 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7519 (ttp-110) REVERT: AX 324 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: BX 49 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8479 (pp) REVERT: BX 83 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7952 (m-40) REVERT: CX 89 VAL cc_start: 0.9179 (p) cc_final: 0.8979 (m) REVERT: CX 120 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7434 (tmm160) REVERT: CX 273 ASP cc_start: 0.8117 (t70) cc_final: 0.7718 (t0) REVERT: CX 324 GLU cc_start: 0.7291 (mp0) cc_final: 0.7039 (mp0) REVERT: DX 91 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8102 (t0) REVERT: EX 91 ASN cc_start: 0.8393 (OUTLIER) cc_final: 0.8018 (t0) REVERT: FX 130 LYS cc_start: 0.6917 (OUTLIER) cc_final: 0.5933 (mmtm) REVERT: FX 294 ARG cc_start: 0.7429 (mtp85) cc_final: 0.6604 (mtp85) REVERT: HX 273 ASP cc_start: 0.8074 (t70) cc_final: 0.7867 (t0) REVERT: IX 273 ASP cc_start: 0.7989 (t70) cc_final: 0.7769 (t0) REVERT: JX 130 LYS cc_start: 0.6883 (OUTLIER) cc_final: 0.5831 (mmtm) REVERT: JX 324 GLU cc_start: 0.7373 (mp0) cc_final: 0.7126 (mp0) REVERT: KX 87 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8459 (p) REVERT: KX 120 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7602 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8261 (t70) cc_final: 0.7609 (t0) REVERT: LX 130 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.5921 (mmtm) REVERT: MX 130 LYS cc_start: 0.6362 (OUTLIER) cc_final: 0.5994 (mmtm) REVERT: NX 87 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8579 (p) REVERT: OX 69 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8916 (mt) REVERT: OX 273 ASP cc_start: 0.8134 (t70) cc_final: 0.7614 (t0) REVERT: PX 91 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8239 (t0) REVERT: PX 130 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.5831 (mmtm) REVERT: QX 130 LYS cc_start: 0.6886 (OUTLIER) cc_final: 0.5907 (mmtm) REVERT: AY 1549 ASN cc_start: 0.7133 (m-40) cc_final: 0.6867 (m-40) REVERT: AY 1596 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7346 (mt-10) REVERT: BY 1480 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7907 (mm-30) REVERT: CY 1480 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7768 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8141 (t70) REVERT: CY 1572 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8282 (mm) REVERT: CY 1601 LYS cc_start: 0.8212 (tmmt) cc_final: 0.7891 (tmmm) REVERT: EY 1480 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7861 (mm-30) REVERT: EY 1528 ASN cc_start: 0.8270 (OUTLIER) cc_final: 0.7634 (OUTLIER) REVERT: FY 1480 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7840 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8081 (t70) REVERT: GY 1480 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7738 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8026 (t70) REVERT: GY 1517 ASP cc_start: 0.7606 (p0) cc_final: 0.6867 (p0) REVERT: GY 1518 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: GY 1523 TYR cc_start: 0.8919 (t80) cc_final: 0.8693 (t80) REVERT: HY 1479 SER cc_start: 0.8709 (OUTLIER) cc_final: 0.8449 (p) REVERT: HY 1499 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7647 (mt-10) REVERT: HY 1503 ASP cc_start: 0.8531 (m-30) cc_final: 0.8233 (t70) REVERT: IY 1498 LEU cc_start: 0.8190 (mt) cc_final: 0.7970 (mt) REVERT: IY 1503 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8177 (t70) REVERT: IY 1549 ASN cc_start: 0.7732 (m-40) cc_final: 0.6598 (m-40) REVERT: IY 1596 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7391 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8497 (m-30) cc_final: 0.8149 (t70) REVERT: JY 1505 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8582 (mt-10) REVERT: KY 1480 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7737 (mm-30) REVERT: KY 1549 ASN cc_start: 0.7157 (m-40) cc_final: 0.6635 (m110) REVERT: LY 1480 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7893 (mm-30) REVERT: LY 1528 ASN cc_start: 0.8244 (t0) cc_final: 0.8029 (t0) REVERT: MY 1505 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8478 (mt-10) REVERT: MY 1517 ASP cc_start: 0.7665 (p0) cc_final: 0.7067 (p0) REVERT: MY 1518 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7111 (mp0) REVERT: MY 1523 TYR cc_start: 0.8810 (t80) cc_final: 0.8607 (t80) REVERT: MY 1549 ASN cc_start: 0.7373 (m-40) cc_final: 0.6887 (m-40) REVERT: NY 1480 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7838 (mm-30) REVERT: NY 1572 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8243 (mm) REVERT: NY 1596 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7227 (mm-30) REVERT: OY 1503 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7956 (t70) REVERT: OY 1528 ASN cc_start: 0.8120 (t0) cc_final: 0.7919 (t0) REVERT: PY 1523 TYR cc_start: 0.8972 (t80) cc_final: 0.8708 (t80) REVERT: PY 1528 ASN cc_start: 0.8203 (t0) cc_final: 0.7514 (t0) REVERT: QY 1572 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8194 (mm) outliers start: 434 outliers final: 177 residues processed: 1300 average time/residue: 1.4083 time to fit residues: 2251.3225 Evaluate side-chains 1068 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 860 time to evaluate : 4.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 32 LYS Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 283 ARG Chi-restraints excluded: chain AX residue 324 GLU Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 91 ASN Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 272 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 91 ASN Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 83 ASN Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 91 ASN Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 91 ASN Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 130 LYS Chi-restraints excluded: chain JX residue 264 ASP Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 264 ASP Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 83 ASN Chi-restraints excluded: chain LX residue 91 ASN Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 91 ASN Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 130 LYS Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain MX residue 283 ARG Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 264 ASP Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 91 ASN Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 130 LYS Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 130 LYS Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1572 ILE Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1479 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1518 GLU Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1505 GLU Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain KY residue 1473 GLU Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1503 ASP Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1518 GLU Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1572 ILE Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1498 LEU Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1518 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Chi-restraints excluded: chain QY residue 1572 ILE Chi-restraints excluded: chain QY residue 1580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 372 optimal weight: 6.9990 chunk 304 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 448 optimal weight: 0.8980 chunk 484 optimal weight: 5.9990 chunk 399 optimal weight: 6.9990 chunk 444 optimal weight: 7.9990 chunk 152 optimal weight: 0.7980 chunk 359 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN AX 297 GLN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** DX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** FX 83 ASN ** FX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 91 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN MX 297 GLN ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1515 GLN ** BY1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** BY1583 GLN CY1484 ASN DY1484 ASN EY1583 GLN HY1484 ASN JY1583 GLN KY1583 GLN LY1484 ASN MY1484 ASN PY1515 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41242 Z= 0.224 Angle : 0.565 9.994 55709 Z= 0.299 Chirality : 0.043 0.210 6375 Planarity : 0.004 0.053 7191 Dihedral : 7.700 72.724 5562 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 9.19 % Allowed : 27.10 % Favored : 63.71 % 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: -1.20 (0.11), residues: 4981 helix: 0.96 (0.11), residues: 2074 sheet: -2.45 (0.16), residues: 714 loop : -1.94 (0.11), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPPX 58 HIS 0.007 0.001 HISDX 94 PHE 0.022 0.001 PHELX 96 TYR 0.016 0.001 TYRFX 77 ARG 0.011 0.001 ARGHY1514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 975 time to evaluate : 4.836 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: AX 120 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7551 (ttp-110) REVERT: AX 316 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7665 (m-70) REVERT: BX 49 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8447 (pp) REVERT: CX 91 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7976 (m-40) REVERT: CX 265 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8080 (t0) REVERT: CX 273 ASP cc_start: 0.8105 (t70) cc_final: 0.7779 (t0) REVERT: DX 94 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7166 (p90) REVERT: DX 120 ARG cc_start: 0.7927 (OUTLIER) cc_final: 0.7618 (ttp-110) REVERT: EX 120 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7584 (ttp-110) REVERT: FX 89 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9032 (m) REVERT: FX 130 LYS cc_start: 0.6922 (OUTLIER) cc_final: 0.5905 (mmtm) REVERT: GX 316 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7866 (m-70) REVERT: HX 277 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8026 (ttt-90) REVERT: IX 273 ASP cc_start: 0.7998 (t0) cc_final: 0.7794 (t0) REVERT: IX 316 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7710 (m-70) REVERT: KX 87 SER cc_start: 0.8779 (OUTLIER) cc_final: 0.8448 (p) REVERT: KX 120 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7632 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8155 (t0) cc_final: 0.7686 (t0) REVERT: LX 130 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.5877 (mmtm) REVERT: NX 87 SER cc_start: 0.8843 (OUTLIER) cc_final: 0.8556 (p) REVERT: NX 103 LYS cc_start: 0.8584 (mppt) cc_final: 0.8304 (mmtt) REVERT: NX 120 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7368 (tmm160) REVERT: OX 69 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8911 (mt) REVERT: OX 92 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7910 (p) REVERT: OX 93 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8547 (p0) REVERT: OX 273 ASP cc_start: 0.8021 (t70) cc_final: 0.7586 (t0) REVERT: PX 316 HIS cc_start: 0.7931 (OUTLIER) cc_final: 0.7679 (m-70) REVERT: QX 316 HIS cc_start: 0.8030 (OUTLIER) cc_final: 0.7803 (m-70) REVERT: AY 1585 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7383 (pm20) REVERT: BY 1480 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7890 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8030 (t70) REVERT: CY 1517 ASP cc_start: 0.8205 (p0) cc_final: 0.7953 (p0) REVERT: DY 1505 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8632 (mt-10) REVERT: DY 1549 ASN cc_start: 0.6700 (m-40) cc_final: 0.6463 (m110) REVERT: EY 1503 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8227 (t70) REVERT: EY 1528 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7634 (OUTLIER) REVERT: EY 1549 ASN cc_start: 0.7554 (m-40) cc_final: 0.7091 (m-40) REVERT: EY 1587 GLU cc_start: 0.8436 (tp30) cc_final: 0.8139 (tp30) REVERT: FY 1480 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7825 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.8069 (t70) REVERT: FY 1596 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7299 (mt-10) REVERT: GY 1480 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7797 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8084 (t70) REVERT: GY 1514 ARG cc_start: 0.7625 (mtm110) cc_final: 0.7407 (ttp80) REVERT: GY 1517 ASP cc_start: 0.7615 (p0) cc_final: 0.6866 (p0) REVERT: GY 1518 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: HY 1503 ASP cc_start: 0.8487 (m-30) cc_final: 0.8201 (t70) REVERT: HY 1527 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7192 (ttm170) REVERT: HY 1528 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7848 (t0) REVERT: HY 1549 ASN cc_start: 0.7216 (m-40) cc_final: 0.6928 (m110) REVERT: IY 1503 ASP cc_start: 0.8319 (OUTLIER) cc_final: 0.8088 (t70) REVERT: IY 1596 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7368 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8479 (OUTLIER) cc_final: 0.8137 (t70) REVERT: KY 1480 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7754 (mm-30) REVERT: LY 1528 ASN cc_start: 0.8149 (t0) cc_final: 0.7924 (t0) REVERT: LY 1596 GLU cc_start: 0.7509 (mt-10) cc_final: 0.7134 (mm-30) REVERT: MY 1480 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7809 (mm-30) REVERT: MY 1505 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8470 (mt-10) REVERT: MY 1517 ASP cc_start: 0.7643 (p0) cc_final: 0.6999 (p0) REVERT: MY 1518 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: MY 1523 TYR cc_start: 0.8843 (t80) cc_final: 0.8618 (t80) REVERT: NY 1480 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7894 (mm-30) REVERT: NY 1596 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7205 (mm-30) REVERT: OY 1503 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8067 (t70) REVERT: OY 1528 ASN cc_start: 0.8066 (t0) cc_final: 0.7522 (t0) REVERT: PY 1528 ASN cc_start: 0.8068 (t0) cc_final: 0.7833 (t0) REVERT: QY 1480 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7874 (mm-30) outliers start: 417 outliers final: 189 residues processed: 1297 average time/residue: 1.4283 time to fit residues: 2271.2244 Evaluate side-chains 1049 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 824 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 91 ASN Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 56 THR Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 91 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 264 ASP Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain GX residue 316 HIS Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 270 SER Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 264 ASP Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 41 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 83 ASN Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 270 SER Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 92 SER Chi-restraints excluded: chain OX residue 93 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 264 ASP Chi-restraints excluded: chain OX residue 265 ASN Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 270 SER Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain QX residue 316 HIS Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1505 GLU Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1503 ASP Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1518 GLU Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1528 ASN Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain PY residue 1470 SER Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1555 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 443 optimal weight: 0.7980 chunk 337 optimal weight: 0.9980 chunk 232 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 450 optimal weight: 6.9990 chunk 476 optimal weight: 4.9990 chunk 235 optimal weight: 1.9990 chunk 426 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** GX 297 GLN ** HX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** HX 297 GLN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 91 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LX 83 ASN ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LX 297 GLN ** MX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** NX 297 GLN ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1484 ASN ** BY1549 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** CY1484 ASN DY1484 ASN EY1583 GLN GY1583 GLN HY1484 ASN JY1549 ASN KY1583 GLN LY1484 ASN LY1549 ASN MY1484 ASN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 41242 Z= 0.309 Angle : 0.596 10.325 55709 Z= 0.318 Chirality : 0.044 0.212 6375 Planarity : 0.004 0.060 7191 Dihedral : 7.438 74.447 5528 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 9.87 % Allowed : 27.34 % Favored : 62.79 % 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: -0.87 (0.11), residues: 4981 helix: 1.26 (0.11), residues: 2074 sheet: -2.42 (0.16), residues: 714 loop : -1.76 (0.11), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPPX 58 HIS 0.009 0.002 HISJX 94 PHE 0.020 0.002 PHEPX 96 TYR 0.014 0.001 TYRFX 77 ARG 0.013 0.001 ARGMX 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 448 poor density : 880 time to evaluate : 5.182 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: AX 120 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7668 (ttp-110) REVERT: AX 316 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7755 (m-70) REVERT: BX 49 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8513 (pp) REVERT: CX 265 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8082 (t0) REVERT: CX 273 ASP cc_start: 0.8132 (t0) cc_final: 0.7807 (t0) REVERT: DX 92 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8153 (p) REVERT: DX 120 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7627 (ttp-110) REVERT: DX 324 GLU cc_start: 0.7160 (mp0) cc_final: 0.6836 (mp0) REVERT: EX 120 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7614 (ttp-110) REVERT: FX 130 LYS cc_start: 0.7014 (OUTLIER) cc_final: 0.6074 (mmtm) REVERT: FX 273 ASP cc_start: 0.8099 (t0) cc_final: 0.6950 (t0) REVERT: FX 294 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6601 (mtp85) REVERT: GX 120 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7628 (ttp-110) REVERT: GX 316 HIS cc_start: 0.8120 (OUTLIER) cc_final: 0.7914 (m-70) REVERT: HX 49 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8692 (pp) REVERT: HX 120 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7680 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8082 (ttt-90) REVERT: HX 310 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8159 (mp) REVERT: IX 273 ASP cc_start: 0.8011 (t0) cc_final: 0.7795 (t0) REVERT: IX 316 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7763 (m-70) REVERT: IX 324 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: JX 91 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.8015 (t0) REVERT: KX 120 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7662 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8169 (t0) cc_final: 0.7703 (t0) REVERT: KX 316 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7736 (m-70) REVERT: LX 49 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8706 (pp) REVERT: LX 130 LYS cc_start: 0.6956 (OUTLIER) cc_final: 0.5938 (mmtm) REVERT: NX 103 LYS cc_start: 0.8611 (mppt) cc_final: 0.8343 (mmtt) REVERT: NX 120 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7449 (tmm160) REVERT: NX 316 HIS cc_start: 0.7976 (OUTLIER) cc_final: 0.7747 (m-70) REVERT: OX 273 ASP cc_start: 0.8078 (t70) cc_final: 0.7672 (t0) REVERT: OX 277 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8153 (ttt-90) REVERT: OX 316 HIS cc_start: 0.8081 (OUTLIER) cc_final: 0.7813 (m-70) REVERT: PX 316 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7815 (m-70) REVERT: QX 49 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8703 (pp) REVERT: QX 316 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7840 (m-70) REVERT: AY 1585 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: BY 1480 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7943 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8042 (t70) REVERT: CY 1517 ASP cc_start: 0.8256 (p0) cc_final: 0.7979 (p0) REVERT: CY 1572 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8229 (mm) REVERT: DY 1480 GLU cc_start: 0.8250 (mm-30) cc_final: 0.8018 (mm-30) REVERT: DY 1505 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8607 (mt-10) REVERT: DY 1523 TYR cc_start: 0.8965 (t80) cc_final: 0.8725 (t80) REVERT: EY 1523 TYR cc_start: 0.8924 (t80) cc_final: 0.8707 (t80) REVERT: EY 1528 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7664 (t0) REVERT: FY 1480 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7848 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8063 (t70) REVERT: GY 1480 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7876 (mm-30) REVERT: GY 1499 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7613 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8056 (t70) REVERT: GY 1517 ASP cc_start: 0.7639 (p0) cc_final: 0.6989 (p0) REVERT: GY 1518 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7064 (mp0) REVERT: HY 1503 ASP cc_start: 0.8471 (m-30) cc_final: 0.8175 (t70) REVERT: HY 1527 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.7192 (ttm170) REVERT: IY 1503 ASP cc_start: 0.8339 (OUTLIER) cc_final: 0.8102 (t70) REVERT: IY 1596 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7374 (mt-10) REVERT: JY 1499 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7885 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8112 (t70) REVERT: JY 1505 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8503 (mt-10) REVERT: MY 1505 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8420 (mt-10) REVERT: MY 1517 ASP cc_start: 0.7685 (p0) cc_final: 0.7205 (p0) REVERT: MY 1518 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7182 (mp0) REVERT: NY 1538 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7941 (mptp) REVERT: OY 1503 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8199 (t70) REVERT: OY 1528 ASN cc_start: 0.8071 (t0) cc_final: 0.7477 (t0) REVERT: PY 1528 ASN cc_start: 0.8078 (t0) cc_final: 0.7349 (t0) REVERT: QY 1505 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8144 (mt-10) outliers start: 448 outliers final: 214 residues processed: 1224 average time/residue: 1.4199 time to fit residues: 2138.5432 Evaluate side-chains 1017 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 759 time to evaluate : 5.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 56 THR Chi-restraints excluded: chain BX residue 62 ASP Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 39 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain DX residue 39 VAL Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 120 ARG Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 270 SER Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain GX residue 316 HIS Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 41 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 310 LEU Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 49 LEU Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain IX residue 324 GLU Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 91 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 264 ASP Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain KX residue 322 ILE Chi-restraints excluded: chain LX residue 39 VAL Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 316 HIS Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 264 ASP Chi-restraints excluded: chain OX residue 265 ASN Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 322 ILE Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 56 THR Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain QX residue 316 HIS Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1505 GLU Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1572 ILE Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1518 GLU Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1505 GLU Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1497 CYS Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1561 VAL Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1503 ASP Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1470 SER Chi-restraints excluded: chain PY residue 1497 CYS Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 396 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 354 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 406 optimal weight: 2.9990 chunk 329 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 427 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** FX 297 GLN ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 91 ASN ** JX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 265 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** MX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1484 ASN CY1484 ASN DY1484 ASN EY1583 GLN HY1484 ASN LY1484 ASN LY1549 ASN MY1484 ASN MY1549 ASN NY1549 ASN OY1583 GLN PY1515 GLN PY1549 ASN PY1583 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 41242 Z= 0.332 Angle : 0.606 10.099 55709 Z= 0.324 Chirality : 0.044 0.213 6375 Planarity : 0.004 0.063 7191 Dihedral : 7.324 76.242 5521 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 9.52 % Allowed : 28.51 % Favored : 61.97 % 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: -0.67 (0.11), residues: 4981 helix: 1.39 (0.11), residues: 2074 sheet: -2.30 (0.19), residues: 544 loop : -1.71 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPPX 58 HIS 0.007 0.002 HISPX 94 PHE 0.018 0.002 PHEPX 96 TYR 0.015 0.001 TYRDX 289 ARG 0.014 0.001 ARGFY1514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 432 poor density : 804 time to evaluate : 5.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 120 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7340 (ttp-170) REVERT: AX 316 HIS cc_start: 0.8074 (OUTLIER) cc_final: 0.7780 (m-70) REVERT: BX 49 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8567 (pp) REVERT: BX 120 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7698 (ttp80) REVERT: BX 310 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8267 (mp) REVERT: CX 49 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8676 (pp) REVERT: CX 265 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8070 (t0) REVERT: CX 273 ASP cc_start: 0.8126 (t0) cc_final: 0.7817 (t0) REVERT: CX 316 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7879 (m-70) REVERT: DX 92 SER cc_start: 0.8498 (OUTLIER) cc_final: 0.8297 (p) REVERT: DX 120 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7683 (ttp-110) REVERT: DX 277 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.8023 (ttt-90) REVERT: DX 310 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8432 (mp) REVERT: EX 120 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7624 (ttp-110) REVERT: FX 130 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6048 (mmtm) REVERT: FX 273 ASP cc_start: 0.8141 (t0) cc_final: 0.7888 (t0) REVERT: FX 310 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8199 (mp) REVERT: GX 120 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7340 (ttp-170) REVERT: GX 277 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8352 (ttt-90) REVERT: HX 49 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8724 (pp) REVERT: HX 120 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7673 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8087 (ttt-90) REVERT: HX 310 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8164 (mp) REVERT: IX 277 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8235 (ttm-80) REVERT: IX 316 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7788 (m-70) REVERT: IX 324 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: KX 120 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7673 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8204 (t0) cc_final: 0.7729 (t0) REVERT: KX 316 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7792 (m-70) REVERT: LX 49 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8754 (pp) REVERT: LX 130 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.5930 (mmtm) REVERT: LX 316 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7658 (m-70) REVERT: MX 103 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7664 (mppt) REVERT: NX 103 LYS cc_start: 0.8619 (mppt) cc_final: 0.8338 (mmtt) REVERT: NX 120 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7483 (tmm160) REVERT: OX 277 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8152 (ttt-90) REVERT: OX 316 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7818 (m-70) REVERT: PX 316 HIS cc_start: 0.8080 (OUTLIER) cc_final: 0.7833 (m-70) REVERT: QX 49 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8740 (pp) REVERT: QX 103 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7044 (mmpt) REVERT: QX 316 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7819 (m-70) REVERT: AY 1585 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7459 (pm20) REVERT: BY 1480 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7987 (mm-30) REVERT: CY 1503 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8045 (t70) REVERT: CY 1517 ASP cc_start: 0.8308 (p0) cc_final: 0.8050 (p0) REVERT: DY 1480 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8012 (mm-30) REVERT: DY 1505 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8622 (mt-10) REVERT: DY 1523 TYR cc_start: 0.8991 (t80) cc_final: 0.8781 (t80) REVERT: DY 1572 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8347 (mm) REVERT: EY 1528 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7662 (t0) REVERT: FY 1480 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7944 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (t70) REVERT: FY 1596 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7401 (mt-10) REVERT: GY 1499 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7605 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8302 (OUTLIER) cc_final: 0.8067 (t70) REVERT: GY 1517 ASP cc_start: 0.7676 (p0) cc_final: 0.7065 (p0) REVERT: GY 1518 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: GY 1549 ASN cc_start: 0.7107 (m-40) cc_final: 0.6655 (m110) REVERT: HY 1527 ARG cc_start: 0.7678 (ttm-80) cc_final: 0.7087 (ttm170) REVERT: HY 1572 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8322 (mm) REVERT: IY 1503 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.8094 (t70) REVERT: JY 1499 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7930 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8157 (t70) REVERT: JY 1505 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: MY 1505 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8385 (mt-10) REVERT: MY 1517 ASP cc_start: 0.7760 (p0) cc_final: 0.7342 (p0) REVERT: MY 1518 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: NY 1480 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7975 (mm-30) REVERT: NY 1538 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7905 (mptp) REVERT: NY 1596 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7175 (mm-30) REVERT: OY 1503 ASP cc_start: 0.8420 (OUTLIER) cc_final: 0.8204 (t70) REVERT: OY 1517 ASP cc_start: 0.8420 (p0) cc_final: 0.8203 (p0) REVERT: OY 1528 ASN cc_start: 0.8071 (t0) cc_final: 0.7470 (t0) REVERT: PY 1528 ASN cc_start: 0.8134 (t0) cc_final: 0.7401 (t0) REVERT: QY 1505 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8100 (mt-10) outliers start: 432 outliers final: 223 residues processed: 1152 average time/residue: 1.3794 time to fit residues: 1964.9490 Evaluate side-chains 979 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 702 time to evaluate : 5.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 56 THR Chi-restraints excluded: chain BX residue 62 ASP Chi-restraints excluded: chain BX residue 94 HIS Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 310 LEU Chi-restraints excluded: chain BX residue 319 SER Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 49 LEU Chi-restraints excluded: chain CX residue 89 VAL Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 83 ASN Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain DX residue 310 LEU Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 120 ARG Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 277 ARG Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 310 LEU Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain IX residue 324 GLU Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 264 ASP Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 103 LYS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 299 ASP Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 264 ASP Chi-restraints excluded: chain OX residue 265 ASN Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 322 ILE Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 56 THR Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 39 VAL Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 103 LYS Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain QX residue 303 SER Chi-restraints excluded: chain QX residue 316 HIS Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1505 GLU Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1518 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1572 ILE Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1469 LEU Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1505 GLU Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1555 THR Chi-restraints excluded: chain MY residue 1561 VAL Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1512 ILE Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 160 optimal weight: 7.9990 chunk 429 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 476 optimal weight: 0.5980 chunk 395 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** HX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 91 ASN JX 265 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1583 GLN CY1484 ASN DY1484 ASN GY1583 GLN HY1484 ASN IY1583 GLN LY1484 ASN LY1549 ASN MY1484 ASN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41242 Z= 0.265 Angle : 0.594 10.325 55709 Z= 0.317 Chirality : 0.044 0.243 6375 Planarity : 0.004 0.064 7191 Dihedral : 7.065 74.421 5515 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 9.25 % Allowed : 29.30 % Favored : 61.45 % 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: -0.56 (0.11), residues: 4981 helix: 1.44 (0.11), residues: 2074 sheet: -2.26 (0.20), residues: 544 loop : -1.60 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRPPX 58 HIS 0.007 0.001 HISDX 94 PHE 0.015 0.001 PHEQX 96 TYR 0.012 0.001 TYRJX 289 ARG 0.015 0.001 ARGFY1514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 420 poor density : 820 time to evaluate : 5.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9343 (OUTLIER) cc_final: 0.9116 (p) REVERT: AX 120 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.7656 (ttp-110) REVERT: AX 316 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7748 (m-70) REVERT: BX 49 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8549 (pp) REVERT: BX 120 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7693 (ttp80) REVERT: CX 265 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8037 (t0) REVERT: CX 273 ASP cc_start: 0.8103 (t0) cc_final: 0.7818 (t0) REVERT: CX 316 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7843 (m-70) REVERT: DX 92 SER cc_start: 0.8554 (OUTLIER) cc_final: 0.8299 (p) REVERT: DX 103 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8377 (mppt) REVERT: DX 120 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7698 (ttp-110) REVERT: DX 277 ARG cc_start: 0.9022 (OUTLIER) cc_final: 0.7976 (ttt-90) REVERT: EX 120 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7613 (ttp-110) REVERT: FX 130 LYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6017 (mmtm) REVERT: FX 273 ASP cc_start: 0.7996 (t0) cc_final: 0.6943 (t0) REVERT: FX 294 ARG cc_start: 0.7193 (mtp85) cc_final: 0.6468 (mtp85) REVERT: FX 310 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8249 (mp) REVERT: FX 316 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7806 (m-70) REVERT: GX 120 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7334 (ttp-170) REVERT: HX 49 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8647 (pp) REVERT: HX 120 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7698 (ttp-110) REVERT: HX 277 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8060 (ttt-90) REVERT: IX 277 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8215 (ttm-80) REVERT: IX 316 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7729 (m-70) REVERT: IX 324 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: JX 91 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7947 (t0) REVERT: KX 87 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8605 (t) REVERT: KX 120 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7680 (ttp-110) REVERT: KX 273 ASP cc_start: 0.8177 (t0) cc_final: 0.7747 (t0) REVERT: KX 316 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7723 (m-70) REVERT: LX 49 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8680 (pp) REVERT: LX 130 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.5903 (mmtm) REVERT: LX 316 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7676 (m-70) REVERT: MX 130 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.5940 (mmtm) REVERT: NX 103 LYS cc_start: 0.8616 (mppt) cc_final: 0.8342 (mmtt) REVERT: NX 120 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7476 (tmm160) REVERT: OX 273 ASP cc_start: 0.8039 (t0) cc_final: 0.7636 (t0) REVERT: OX 277 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8138 (ttt-90) REVERT: OX 316 HIS cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (m-70) REVERT: PX 316 HIS cc_start: 0.8027 (OUTLIER) cc_final: 0.7778 (m-70) REVERT: QX 89 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.8951 (m) REVERT: QX 316 HIS cc_start: 0.8016 (OUTLIER) cc_final: 0.7760 (m-70) REVERT: AY 1585 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7456 (pm20) REVERT: CY 1503 ASP cc_start: 0.8291 (OUTLIER) cc_final: 0.8050 (t70) REVERT: CY 1517 ASP cc_start: 0.8335 (p0) cc_final: 0.8061 (p0) REVERT: CY 1528 ASN cc_start: 0.8189 (t0) cc_final: 0.7571 (t0) REVERT: DY 1505 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8665 (mt-10) REVERT: DY 1583 GLN cc_start: 0.8739 (mt0) cc_final: 0.8529 (mt0) REVERT: EY 1528 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7637 (t0) REVERT: FY 1480 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7898 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8068 (t70) REVERT: GY 1499 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7623 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.8027 (t70) REVERT: GY 1514 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7296 (ttp80) REVERT: GY 1517 ASP cc_start: 0.7693 (p0) cc_final: 0.7023 (p0) REVERT: GY 1518 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: GY 1545 MET cc_start: 0.8562 (tpp) cc_final: 0.8292 (mmm) REVERT: HY 1503 ASP cc_start: 0.8470 (OUTLIER) cc_final: 0.8147 (t70) REVERT: HY 1527 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7202 (ttm170) REVERT: HY 1528 ASN cc_start: 0.8232 (t0) cc_final: 0.7853 (t0) REVERT: HY 1572 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8336 (mm) REVERT: IY 1503 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8036 (t70) REVERT: JY 1499 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7846 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8118 (t0) REVERT: JY 1505 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: LY 1549 ASN cc_start: 0.6994 (m-40) cc_final: 0.6752 (m110) REVERT: MY 1505 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8411 (mt-10) REVERT: MY 1514 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7277 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.7759 (p0) cc_final: 0.7285 (p0) REVERT: MY 1518 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: NY 1528 ASN cc_start: 0.8274 (t0) cc_final: 0.7971 (t0) REVERT: NY 1538 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.7927 (mptp) REVERT: OY 1503 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8200 (t70) REVERT: OY 1517 ASP cc_start: 0.8415 (p0) cc_final: 0.8153 (p0) REVERT: OY 1528 ASN cc_start: 0.8037 (t0) cc_final: 0.7481 (t0) REVERT: PY 1528 ASN cc_start: 0.8102 (t0) cc_final: 0.7384 (t0) outliers start: 420 outliers final: 229 residues processed: 1149 average time/residue: 1.3633 time to fit residues: 1935.5747 Evaluate side-chains 1016 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 735 time to evaluate : 4.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 93 ASN Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 39 VAL Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 62 ASP Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 62 ASP Chi-restraints excluded: chain CX residue 89 VAL Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 103 LYS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 272 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain EX residue 39 VAL Chi-restraints excluded: chain EX residue 42 VAL Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 39 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 272 SER Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 299 ASP Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain FX residue 316 HIS Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 94 HIS Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 120 ARG Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 39 VAL Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 93 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 317 GLU Chi-restraints excluded: chain HX residue 320 SER Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 283 ARG Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain IX residue 324 GLU Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 91 ASN Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 323 GLU Chi-restraints excluded: chain KX residue 39 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 120 ARG Chi-restraints excluded: chain KX residue 264 ASP Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 310 LEU Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 130 LYS Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 39 VAL Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 130 LYS Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 299 ASP Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 83 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 264 ASP Chi-restraints excluded: chain OX residue 265 ASN Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 320 SER Chi-restraints excluded: chain PX residue 56 THR Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain QX residue 316 HIS Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1479 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1502 SER Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1561 VAL Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1512 ILE Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1498 LEU Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1505 GLU Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1497 CYS Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1479 SER Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1561 VAL Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1503 ASP Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1503 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1502 SER Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1505 GLU Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1505 GLU Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1526 LEU Chi-restraints excluded: chain MY residue 1561 VAL Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1473 GLU Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1512 ILE Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 459 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 271 optimal weight: 5.9990 chunk 348 optimal weight: 0.5980 chunk 269 optimal weight: 1.9990 chunk 401 optimal weight: 5.9990 chunk 266 optimal weight: 4.9990 chunk 475 optimal weight: 0.0770 chunk 297 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 219 optimal weight: 0.6980 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN JX 91 ASN JX 265 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN DY1484 ASN DY1557 ASN DY1583 GLN GY1549 ASN HY1484 ASN LY1484 ASN MY1484 ASN OY1583 GLN PY1515 GLN PY1583 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41242 Z= 0.229 Angle : 0.586 10.355 55709 Z= 0.312 Chirality : 0.043 0.226 6375 Planarity : 0.004 0.048 7191 Dihedral : 6.833 73.262 5509 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 8.09 % Allowed : 30.89 % Favored : 61.03 % 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: -0.45 (0.11), residues: 4981 helix: 1.54 (0.11), residues: 2074 sheet: -2.20 (0.20), residues: 544 loop : -1.54 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPPX 58 HIS 0.007 0.001 HISIX 94 PHE 0.015 0.001 PHEAX 82 TYR 0.013 0.001 TYRDX 289 ARG 0.013 0.001 ARGQY1514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 828 time to evaluate : 4.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9127 (p) REVERT: AX 120 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: AX 316 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7716 (m-70) REVERT: BX 49 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8517 (pp) REVERT: BX 120 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: CX 120 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7691 (ttp-110) REVERT: CX 265 ASN cc_start: 0.8399 (OUTLIER) cc_final: 0.8029 (t0) REVERT: CX 273 ASP cc_start: 0.8082 (t0) cc_final: 0.7836 (t0) REVERT: CX 316 HIS cc_start: 0.8093 (OUTLIER) cc_final: 0.7802 (m-70) REVERT: DX 92 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (p) REVERT: DX 103 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8169 (mppt) REVERT: DX 120 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7658 (ttp-110) REVERT: EX 89 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8969 (m) REVERT: EX 118 MET cc_start: 0.8178 (ttm) cc_final: 0.7825 (ttt) REVERT: EX 120 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7578 (ttp-110) REVERT: FX 130 LYS cc_start: 0.6854 (OUTLIER) cc_final: 0.5961 (mmtm) REVERT: FX 273 ASP cc_start: 0.7914 (t0) cc_final: 0.6864 (t0) REVERT: FX 294 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6450 (mtp85) REVERT: FX 310 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8231 (mp) REVERT: GX 77 TYR cc_start: 0.8148 (t80) cc_final: 0.7898 (t80) REVERT: HX 120 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7690 (ttp-110) REVERT: HX 277 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8038 (ttt-90) REVERT: IX 83 ASN cc_start: 0.8863 (OUTLIER) cc_final: 0.8632 (t0) REVERT: IX 277 ARG cc_start: 0.8943 (OUTLIER) cc_final: 0.8117 (ttt-90) REVERT: IX 316 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7690 (m-70) REVERT: KX 87 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8540 (t) REVERT: KX 103 LYS cc_start: 0.8484 (mppt) cc_final: 0.8145 (mmtt) REVERT: KX 273 ASP cc_start: 0.8114 (t0) cc_final: 0.7717 (t0) REVERT: KX 316 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.7690 (m-70) REVERT: LX 49 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8645 (pp) REVERT: LX 89 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9018 (m) REVERT: LX 316 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7645 (m-70) REVERT: MX 130 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.5904 (mmtm) REVERT: NX 103 LYS cc_start: 0.8608 (mppt) cc_final: 0.8333 (mmtt) REVERT: NX 120 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7477 (tmm160) REVERT: OX 69 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8947 (mt) REVERT: OX 273 ASP cc_start: 0.8038 (t0) cc_final: 0.7550 (t0) REVERT: OX 277 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8081 (ttt-90) REVERT: OX 316 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7740 (m-70) REVERT: PX 316 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7707 (m-70) REVERT: QX 89 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.8965 (m) REVERT: AY 1518 GLU cc_start: 0.7516 (mm-30) cc_final: 0.7119 (mp0) REVERT: AY 1585 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: BY 1499 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7799 (pm20) REVERT: BY 1523 TYR cc_start: 0.8945 (t80) cc_final: 0.8637 (t80) REVERT: BY 1545 MET cc_start: 0.8322 (tpp) cc_final: 0.8068 (mmm) REVERT: BY 1585 GLU cc_start: 0.7963 (tp30) cc_final: 0.7753 (tp30) REVERT: CY 1503 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8018 (t0) REVERT: CY 1517 ASP cc_start: 0.8329 (p0) cc_final: 0.8078 (p0) REVERT: DY 1505 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8634 (mt-10) REVERT: DY 1523 TYR cc_start: 0.8979 (t80) cc_final: 0.8639 (t80) REVERT: DY 1527 ARG cc_start: 0.7632 (ttm-80) cc_final: 0.7426 (ttm-80) REVERT: EY 1514 ARG cc_start: 0.7784 (ttp80) cc_final: 0.7549 (ttp80) REVERT: EY 1528 ASN cc_start: 0.8290 (OUTLIER) cc_final: 0.7654 (OUTLIER) REVERT: FY 1480 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7891 (mm-30) REVERT: FY 1503 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8124 (t70) REVERT: FY 1527 ARG cc_start: 0.7681 (ttm-80) cc_final: 0.7479 (ttm-80) REVERT: FY 1596 GLU cc_start: 0.7587 (mt-10) cc_final: 0.7248 (mm-30) REVERT: GY 1499 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7732 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7978 (t70) REVERT: GY 1514 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7144 (ttp80) REVERT: GY 1517 ASP cc_start: 0.7693 (p0) cc_final: 0.6984 (p0) REVERT: GY 1518 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: GY 1545 MET cc_start: 0.8525 (tpp) cc_final: 0.8267 (mmm) REVERT: HY 1527 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.7278 (ttm110) REVERT: HY 1528 ASN cc_start: 0.8229 (t0) cc_final: 0.7847 (t0) REVERT: HY 1572 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8330 (mm) REVERT: IY 1515 GLN cc_start: 0.8657 (mm-40) cc_final: 0.8452 (mm-40) REVERT: JY 1499 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7755 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8056 (t0) REVERT: JY 1505 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: LY 1523 TYR cc_start: 0.9003 (t80) cc_final: 0.8656 (t80) REVERT: MY 1514 ARG cc_start: 0.7642 (ttp80) cc_final: 0.7343 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.7765 (p0) cc_final: 0.7277 (p0) REVERT: MY 1518 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.7115 (mp0) REVERT: NY 1480 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7926 (mm-30) REVERT: NY 1528 ASN cc_start: 0.8242 (t0) cc_final: 0.7961 (t0) REVERT: NY 1538 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7916 (mptp) REVERT: OY 1503 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8199 (t70) REVERT: OY 1517 ASP cc_start: 0.8410 (p0) cc_final: 0.8196 (p0) REVERT: PY 1528 ASN cc_start: 0.8107 (t0) cc_final: 0.7370 (t0) outliers start: 367 outliers final: 205 residues processed: 1112 average time/residue: 1.3927 time to fit residues: 1910.4061 Evaluate side-chains 990 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 741 time to evaluate : 4.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 39 VAL Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 264 ASP Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 319 SER Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 265 ASN Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 310 LEU Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 103 LYS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 120 ARG Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 49 LEU Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 94 HIS Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 299 ASP Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 93 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 320 SER Chi-restraints excluded: chain HX residue 321 VAL Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 94 HIS Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 283 ARG Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain KX residue 42 VAL Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 94 HIS Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 264 ASP Chi-restraints excluded: chain KX residue 265 ASN Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 42 VAL Chi-restraints excluded: chain MX residue 93 ASN Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 130 LYS Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 317 GLU Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 83 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 277 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 320 SER Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 56 THR Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 88 ILE Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain QX residue 323 GLU Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1479 SER Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1561 VAL Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1512 ILE Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1504 SER Chi-restraints excluded: chain CY residue 1505 GLU Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1575 SER Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1469 LEU Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain HY residue 1572 ILE Chi-restraints excluded: chain IY residue 1497 CYS Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1505 GLU Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1561 VAL Chi-restraints excluded: chain MY residue 1562 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain OY residue 1562 ASP Chi-restraints excluded: chain PY residue 1473 GLU Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 293 optimal weight: 0.0570 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 302 optimal weight: 0.7980 chunk 323 optimal weight: 7.9990 chunk 234 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 373 optimal weight: 5.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** DX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** EX 265 ASN ** FX 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 265 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN ** OX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN DY1557 ASN EY1528 ASN EY1583 GLN HY1484 ASN LY1484 ASN MY1484 ASN OY1583 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 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 0.050 41242 Z= 0.206 Angle : 0.592 12.468 55709 Z= 0.314 Chirality : 0.043 0.230 6375 Planarity : 0.004 0.049 7191 Dihedral : 6.557 70.896 5496 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 7.25 % Allowed : 32.39 % Favored : 60.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.11), residues: 4981 helix: 1.59 (0.11), residues: 2074 sheet: -2.13 (0.20), residues: 544 loop : -1.47 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRPKX 58 HIS 0.008 0.001 HISIX 94 PHE 0.017 0.001 PHEIX 82 TYR 0.034 0.001 TYRCX 122 ARG 0.013 0.001 ARGOY1514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 872 time to evaluate : 5.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9321 (OUTLIER) cc_final: 0.9030 (m) REVERT: AX 107 MET cc_start: 0.8694 (ttm) cc_final: 0.8445 (ptm) REVERT: AX 120 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7641 (ttp-110) REVERT: AX 316 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7675 (m-70) REVERT: BX 49 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8485 (pp) REVERT: BX 120 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7728 (ttp80) REVERT: CX 316 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7684 (m-70) REVERT: DX 92 SER cc_start: 0.8388 (OUTLIER) cc_final: 0.8040 (p) REVERT: DX 120 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7611 (ttp-110) REVERT: DX 277 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7950 (ttt-90) REVERT: EX 89 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8960 (m) REVERT: EX 94 HIS cc_start: 0.6413 (OUTLIER) cc_final: 0.6158 (p90) REVERT: EX 118 MET cc_start: 0.8184 (ttm) cc_final: 0.7855 (ttt) REVERT: EX 323 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7260 (mt-10) REVERT: EX 324 GLU cc_start: 0.7712 (mp0) cc_final: 0.7256 (mp0) REVERT: FX 89 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.9029 (m) REVERT: FX 130 LYS cc_start: 0.6795 (OUTLIER) cc_final: 0.5917 (mmtm) REVERT: FX 273 ASP cc_start: 0.7855 (t0) cc_final: 0.6828 (t0) REVERT: FX 294 ARG cc_start: 0.7079 (mtp85) cc_final: 0.6411 (mtp85) REVERT: FX 310 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8153 (mp) REVERT: GX 77 TYR cc_start: 0.8068 (t80) cc_final: 0.7849 (t80) REVERT: HX 120 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7680 (ttp-110) REVERT: HX 277 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.7968 (ttt-90) REVERT: IX 89 VAL cc_start: 0.9316 (OUTLIER) cc_final: 0.9020 (m) REVERT: IX 277 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8093 (ttm-80) REVERT: IX 316 HIS cc_start: 0.7927 (OUTLIER) cc_final: 0.7681 (m-70) REVERT: JX 314 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7438 (pp30) REVERT: KX 87 SER cc_start: 0.8800 (OUTLIER) cc_final: 0.8578 (t) REVERT: KX 103 LYS cc_start: 0.8433 (mppt) cc_final: 0.8127 (mmtt) REVERT: KX 273 ASP cc_start: 0.8093 (t0) cc_final: 0.7798 (t0) REVERT: KX 316 HIS cc_start: 0.7854 (OUTLIER) cc_final: 0.7626 (m-70) REVERT: LX 49 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8632 (pp) REVERT: LX 89 VAL cc_start: 0.9287 (OUTLIER) cc_final: 0.9019 (m) REVERT: LX 316 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7582 (m-70) REVERT: NX 87 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8541 (p) REVERT: NX 120 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7511 (tmm160) REVERT: OX 69 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8953 (mt) REVERT: OX 91 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8112 (t0) REVERT: OX 273 ASP cc_start: 0.8086 (t0) cc_final: 0.7639 (t0) REVERT: OX 316 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7736 (m-70) REVERT: PX 316 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7658 (m-70) REVERT: PX 324 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: QX 89 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8971 (m) REVERT: AY 1585 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7429 (pm20) REVERT: BY 1545 MET cc_start: 0.8277 (tpp) cc_final: 0.8049 (mmm) REVERT: BY 1585 GLU cc_start: 0.7964 (tp30) cc_final: 0.7689 (tp30) REVERT: CY 1503 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7999 (t0) REVERT: CY 1517 ASP cc_start: 0.8303 (p0) cc_final: 0.8029 (p0) REVERT: DY 1505 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: EY 1528 ASN cc_start: 0.8272 (OUTLIER) cc_final: 0.7658 (OUTLIER) REVERT: FY 1503 ASP cc_start: 0.8293 (m-30) cc_final: 0.8067 (t0) REVERT: GY 1499 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7678 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7975 (t0) REVERT: GY 1514 ARG cc_start: 0.7725 (ttp80) cc_final: 0.7189 (ttp80) REVERT: GY 1517 ASP cc_start: 0.7721 (p0) cc_final: 0.7039 (p0) REVERT: GY 1518 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: GY 1545 MET cc_start: 0.8525 (tpp) cc_final: 0.8304 (mmm) REVERT: HY 1527 ARG cc_start: 0.7747 (ttm-80) cc_final: 0.7280 (ttm110) REVERT: HY 1528 ASN cc_start: 0.8193 (t0) cc_final: 0.7827 (t0) REVERT: IY 1515 GLN cc_start: 0.8656 (mm-40) cc_final: 0.8369 (mm-40) REVERT: JY 1492 GLU cc_start: 0.8069 (tp30) cc_final: 0.7866 (tp30) REVERT: JY 1499 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7859 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.8039 (t0) REVERT: JY 1514 ARG cc_start: 0.7803 (ttp80) cc_final: 0.7554 (tmm-80) REVERT: KY 1505 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8430 (mt-10) REVERT: KY 1523 TYR cc_start: 0.8985 (t80) cc_final: 0.8760 (t80) REVERT: MY 1514 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7414 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.7752 (p0) cc_final: 0.7292 (p0) REVERT: MY 1518 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: NY 1528 ASN cc_start: 0.8149 (t0) cc_final: 0.7850 (t0) REVERT: NY 1538 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.7987 (mptp) REVERT: OY 1503 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.8155 (t0) REVERT: OY 1517 ASP cc_start: 0.8411 (p0) cc_final: 0.8176 (p0) REVERT: PY 1528 ASN cc_start: 0.8076 (t0) cc_final: 0.7334 (t0) REVERT: QY 1505 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7980 (mt-10) outliers start: 329 outliers final: 178 residues processed: 1118 average time/residue: 1.3460 time to fit residues: 1866.1265 Evaluate side-chains 987 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 767 time to evaluate : 5.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 83 ASN Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 319 SER Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 62 ASP Chi-restraints excluded: chain CX residue 93 ASN Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 94 HIS Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain GX residue 39 VAL Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 320 SER Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 283 ARG Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain JX residue 39 VAL Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 317 GLU Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 94 HIS Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 42 VAL Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 62 ASP Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 93 ASN Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 93 ASN Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 39 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 317 GLU Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 83 ASN Chi-restraints excluded: chain OX residue 91 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 320 SER Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 88 ILE Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain PX residue 324 GLU Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 264 ASP Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1561 VAL Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1502 SER Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1509 ILE Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1561 VAL Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1528 ASN Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1479 SER Chi-restraints excluded: chain JY residue 1497 CYS Chi-restraints excluded: chain JY residue 1503 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1561 VAL Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1497 CYS Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 432 optimal weight: 6.9990 chunk 455 optimal weight: 6.9990 chunk 415 optimal weight: 2.9990 chunk 442 optimal weight: 2.9990 chunk 266 optimal weight: 0.6980 chunk 192 optimal weight: 0.0970 chunk 347 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 400 optimal weight: 1.9990 chunk 418 optimal weight: 0.8980 chunk 441 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** JX 265 ASN ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** OX 91 ASN PX 83 ASN ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1549 ASN BY1583 GLN CY1484 ASN HY1484 ASN LY1484 ASN MY1484 ASN OY1583 GLN PY1484 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 41242 Z= 0.247 Angle : 0.619 11.212 55709 Z= 0.327 Chirality : 0.044 0.224 6375 Planarity : 0.004 0.049 7191 Dihedral : 6.449 71.475 5490 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 6.32 % Allowed : 34.35 % Favored : 59.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 4981 helix: 1.60 (0.12), residues: 2074 sheet: -2.11 (0.20), residues: 544 loop : -1.44 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPPX 58 HIS 0.007 0.001 HISIX 94 PHE 0.015 0.001 PHEIX 96 TYR 0.049 0.001 TYRCX 122 ARG 0.013 0.001 ARGLY1514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 800 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: AX 89 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9086 (p) REVERT: AX 107 MET cc_start: 0.8661 (ttm) cc_final: 0.8444 (ptm) REVERT: AX 120 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: AX 316 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7686 (m-70) REVERT: BX 49 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8521 (pp) REVERT: BX 120 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7761 (ttp80) REVERT: CX 120 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7698 (ttp-110) REVERT: CX 316 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7702 (m-70) REVERT: DX 92 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8363 (p) REVERT: DX 120 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7523 (ttp-110) REVERT: DX 277 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7970 (ttt-90) REVERT: EX 89 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8972 (m) REVERT: EX 94 HIS cc_start: 0.6453 (OUTLIER) cc_final: 0.6215 (p90) REVERT: EX 118 MET cc_start: 0.8197 (ttm) cc_final: 0.7891 (ttt) REVERT: FX 130 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.5928 (mmtm) REVERT: FX 273 ASP cc_start: 0.7869 (t0) cc_final: 0.6960 (t0) REVERT: FX 294 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6470 (mtp85) REVERT: FX 310 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8210 (mp) REVERT: GX 77 TYR cc_start: 0.8095 (t80) cc_final: 0.7851 (t80) REVERT: HX 49 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8563 (pp) REVERT: HX 120 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7694 (ttp-110) REVERT: HX 277 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8022 (ttt-90) REVERT: IX 89 VAL cc_start: 0.9313 (OUTLIER) cc_final: 0.9000 (m) REVERT: IX 277 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8121 (ttt-90) REVERT: IX 316 HIS cc_start: 0.7955 (OUTLIER) cc_final: 0.7707 (m-70) REVERT: JX 314 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7421 (pp30) REVERT: KX 87 SER cc_start: 0.8828 (OUTLIER) cc_final: 0.8471 (p) REVERT: KX 103 LYS cc_start: 0.8438 (mppt) cc_final: 0.8125 (mmtt) REVERT: KX 273 ASP cc_start: 0.8103 (t0) cc_final: 0.7728 (t0) REVERT: KX 316 HIS cc_start: 0.7886 (OUTLIER) cc_final: 0.7660 (m-70) REVERT: LX 49 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8651 (pp) REVERT: LX 89 VAL cc_start: 0.9298 (OUTLIER) cc_final: 0.9027 (m) REVERT: LX 316 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7595 (m-70) REVERT: NX 87 SER cc_start: 0.8864 (OUTLIER) cc_final: 0.8552 (p) REVERT: NX 103 LYS cc_start: 0.8507 (mppt) cc_final: 0.8235 (mmtt) REVERT: NX 120 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7476 (tmm160) REVERT: OX 69 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8958 (mt) REVERT: OX 273 ASP cc_start: 0.8101 (t0) cc_final: 0.7634 (t0) REVERT: OX 316 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7724 (m-70) REVERT: PX 316 HIS cc_start: 0.7938 (OUTLIER) cc_final: 0.7692 (m-70) REVERT: QX 89 VAL cc_start: 0.9292 (OUTLIER) cc_final: 0.8977 (m) REVERT: AY 1585 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7443 (pm20) REVERT: BY 1492 GLU cc_start: 0.8076 (tp30) cc_final: 0.7833 (tp30) REVERT: BY 1545 MET cc_start: 0.8307 (tpp) cc_final: 0.8009 (mmm) REVERT: BY 1585 GLU cc_start: 0.7989 (tp30) cc_final: 0.7714 (tp30) REVERT: CY 1503 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7994 (t0) REVERT: CY 1517 ASP cc_start: 0.8305 (p0) cc_final: 0.8060 (p0) REVERT: DY 1473 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8125 (tp30) REVERT: DY 1481 CYS cc_start: 0.6575 (p) cc_final: 0.6249 (p) REVERT: DY 1505 GLU cc_start: 0.8867 (OUTLIER) cc_final: 0.8548 (mt-10) REVERT: DY 1523 TYR cc_start: 0.8993 (t80) cc_final: 0.8646 (t80) REVERT: EY 1528 ASN cc_start: 0.8251 (p0) cc_final: 0.7505 (t0) REVERT: FY 1503 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.8061 (t0) REVERT: FY 1596 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7222 (mm-30) REVERT: GY 1503 ASP cc_start: 0.8268 (OUTLIER) cc_final: 0.8034 (t0) REVERT: GY 1514 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7343 (tmm-80) REVERT: GY 1517 ASP cc_start: 0.7733 (p0) cc_final: 0.7097 (p0) REVERT: GY 1518 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: GY 1545 MET cc_start: 0.8543 (tpp) cc_final: 0.8307 (mmm) REVERT: HY 1527 ARG cc_start: 0.7698 (ttm-80) cc_final: 0.7292 (ttm110) REVERT: HY 1528 ASN cc_start: 0.8223 (t0) cc_final: 0.7849 (t0) REVERT: IY 1481 CYS cc_start: 0.7056 (p) cc_final: 0.6680 (p) REVERT: IY 1596 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7292 (mt-10) REVERT: JY 1503 ASP cc_start: 0.8336 (m-30) cc_final: 0.8046 (t0) REVERT: KY 1496 GLN cc_start: 0.8172 (tm-30) cc_final: 0.7588 (tm130) REVERT: KY 1505 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8455 (mt-10) REVERT: MY 1514 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7409 (tmm-80) REVERT: MY 1517 ASP cc_start: 0.7761 (p0) cc_final: 0.7307 (p0) REVERT: MY 1518 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: NY 1528 ASN cc_start: 0.8178 (t0) cc_final: 0.7856 (t0) REVERT: NY 1538 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7900 (mptp) REVERT: NY 1596 GLU cc_start: 0.7457 (mt-10) cc_final: 0.7195 (mm-30) REVERT: OY 1503 ASP cc_start: 0.8357 (OUTLIER) cc_final: 0.8137 (t0) REVERT: OY 1517 ASP cc_start: 0.8418 (p0) cc_final: 0.8196 (p0) REVERT: QY 1505 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7999 (mt-10) outliers start: 287 outliers final: 181 residues processed: 1022 average time/residue: 1.3492 time to fit residues: 1708.8874 Evaluate side-chains 951 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 728 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 319 SER Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 62 ASP Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 310 LEU Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 49 LEU Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 94 HIS Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 317 GLU Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 49 LEU Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 93 ASN Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 320 SER Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 264 ASP Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 283 ARG Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 317 GLU Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 310 LEU Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 299 ASP Chi-restraints excluded: chain NX residue 317 GLU Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 69 LEU Chi-restraints excluded: chain OX residue 83 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 299 ASP Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 88 ILE Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 42 VAL Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 264 ASP Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1561 VAL Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1497 CYS Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1512 ILE Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain DY residue 1473 GLU Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1524 SER Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain DY residue 1585 GLU Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1509 ILE Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1503 ASP Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain MY residue 1473 GLU Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain MY residue 1555 THR Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1502 SER Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1520 ASP Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 290 optimal weight: 2.9990 chunk 468 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 325 optimal weight: 1.9990 chunk 491 optimal weight: 0.9990 chunk 452 optimal weight: 0.9990 chunk 391 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 302 optimal weight: 0.6980 chunk 239 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** KX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PX 83 ASN ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN BY1583 GLN CY1484 ASN HY1484 ASN LY1484 ASN MY1484 ASN OY1583 GLN PY1484 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 41242 Z= 0.249 Angle : 0.632 12.307 55709 Z= 0.334 Chirality : 0.044 0.217 6375 Planarity : 0.004 0.063 7191 Dihedral : 6.249 71.810 5480 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.84 % Allowed : 35.47 % Favored : 58.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 4981 helix: 1.56 (0.12), residues: 2074 sheet: -2.12 (0.20), residues: 544 loop : -1.41 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRPIX 58 HIS 0.007 0.001 HISIX 94 PHE 0.014 0.001 PHEQX 96 TYR 0.044 0.001 TYRCX 122 ARG 0.015 0.001 ARGDY1514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9962 Ramachandran restraints generated. 4981 Oldfield, 0 Emsley, 4981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 754 time to evaluate : 5.340 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: AX 89 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9042 (m) REVERT: AX 120 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7374 (ttp-170) REVERT: AX 316 HIS cc_start: 0.8005 (OUTLIER) cc_final: 0.7710 (m-70) REVERT: BX 49 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8522 (pp) REVERT: BX 83 ASN cc_start: 0.8906 (OUTLIER) cc_final: 0.8667 (t0) REVERT: BX 120 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7774 (ttp80) REVERT: CX 316 HIS cc_start: 0.7995 (OUTLIER) cc_final: 0.7697 (m-70) REVERT: DX 92 SER cc_start: 0.8606 (OUTLIER) cc_final: 0.8382 (p) REVERT: DX 120 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7511 (ttp-110) REVERT: DX 277 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7973 (ttt-90) REVERT: EX 89 VAL cc_start: 0.9237 (OUTLIER) cc_final: 0.8979 (m) REVERT: EX 118 MET cc_start: 0.8189 (ttm) cc_final: 0.7925 (ttt) REVERT: FX 130 LYS cc_start: 0.6798 (OUTLIER) cc_final: 0.5864 (mmtm) REVERT: FX 273 ASP cc_start: 0.7884 (t0) cc_final: 0.6874 (t0) REVERT: FX 294 ARG cc_start: 0.7225 (mtp85) cc_final: 0.6536 (mtp85) REVERT: FX 310 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8208 (mp) REVERT: HX 120 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7720 (ttp-110) REVERT: HX 277 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8065 (ttt-90) REVERT: IX 83 ASN cc_start: 0.8800 (OUTLIER) cc_final: 0.8236 (m-40) REVERT: IX 89 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8977 (m) REVERT: IX 277 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8156 (ttm-80) REVERT: IX 316 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7705 (m-70) REVERT: JX 314 GLN cc_start: 0.7650 (tm-30) cc_final: 0.7376 (pp30) REVERT: KX 87 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8479 (p) REVERT: KX 273 ASP cc_start: 0.8032 (t0) cc_final: 0.7769 (t0) REVERT: KX 316 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7664 (m-70) REVERT: LX 49 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8639 (pp) REVERT: LX 89 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9033 (m) REVERT: LX 316 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7595 (m-70) REVERT: NX 87 SER cc_start: 0.8868 (OUTLIER) cc_final: 0.8551 (p) REVERT: NX 103 LYS cc_start: 0.8495 (mppt) cc_final: 0.8219 (mmtt) REVERT: NX 120 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7500 (tmm160) REVERT: OX 273 ASP cc_start: 0.8103 (t0) cc_final: 0.7648 (t0) REVERT: OX 316 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7726 (m-70) REVERT: PX 316 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7661 (m-70) REVERT: QX 89 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8977 (m) REVERT: AY 1523 TYR cc_start: 0.8991 (t80) cc_final: 0.8777 (t80) REVERT: AY 1585 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7453 (pm20) REVERT: BY 1545 MET cc_start: 0.8315 (tpp) cc_final: 0.8003 (mmm) REVERT: BY 1585 GLU cc_start: 0.7993 (tp30) cc_final: 0.7758 (tp30) REVERT: CY 1503 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.8001 (t0) REVERT: CY 1517 ASP cc_start: 0.8308 (p0) cc_final: 0.8066 (p0) REVERT: CY 1572 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8265 (mm) REVERT: DY 1481 CYS cc_start: 0.6254 (p) cc_final: 0.5932 (p) REVERT: DY 1505 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8566 (mt-10) REVERT: EY 1523 TYR cc_start: 0.8823 (t80) cc_final: 0.8486 (t80) REVERT: EY 1528 ASN cc_start: 0.8241 (p0) cc_final: 0.7539 (t0) REVERT: FY 1503 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8052 (t0) REVERT: FY 1596 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7215 (mt-10) REVERT: GY 1503 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.8034 (t0) REVERT: GY 1514 ARG cc_start: 0.7724 (ttp80) cc_final: 0.7364 (tmm-80) REVERT: GY 1517 ASP cc_start: 0.7730 (p0) cc_final: 0.7114 (p0) REVERT: GY 1518 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: GY 1545 MET cc_start: 0.8550 (tpp) cc_final: 0.8324 (mmm) REVERT: HY 1527 ARG cc_start: 0.7692 (ttm-80) cc_final: 0.7284 (ttm110) REVERT: HY 1528 ASN cc_start: 0.8226 (t0) cc_final: 0.7850 (t0) REVERT: JY 1503 ASP cc_start: 0.8333 (m-30) cc_final: 0.8043 (t0) REVERT: KY 1496 GLN cc_start: 0.8067 (tm-30) cc_final: 0.7778 (tm130) REVERT: MY 1517 ASP cc_start: 0.7727 (p0) cc_final: 0.7273 (p0) REVERT: MY 1518 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: NY 1528 ASN cc_start: 0.8157 (t0) cc_final: 0.7829 (t0) REVERT: NY 1538 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8378 (mptp) REVERT: OY 1503 ASP cc_start: 0.8315 (OUTLIER) cc_final: 0.8055 (t0) REVERT: QY 1505 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8004 (mt-10) outliers start: 265 outliers final: 178 residues processed: 951 average time/residue: 1.3118 time to fit residues: 1556.1561 Evaluate side-chains 958 residues out of total 4539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 740 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain AX residue 42 VAL Chi-restraints excluded: chain AX residue 49 LEU Chi-restraints excluded: chain AX residue 89 VAL Chi-restraints excluded: chain AX residue 113 VAL Chi-restraints excluded: chain AX residue 120 ARG Chi-restraints excluded: chain AX residue 282 VAL Chi-restraints excluded: chain AX residue 316 HIS Chi-restraints excluded: chain AX residue 319 SER Chi-restraints excluded: chain BX residue 42 VAL Chi-restraints excluded: chain BX residue 49 LEU Chi-restraints excluded: chain BX residue 83 ASN Chi-restraints excluded: chain BX residue 113 VAL Chi-restraints excluded: chain BX residue 120 ARG Chi-restraints excluded: chain BX residue 270 SER Chi-restraints excluded: chain BX residue 282 VAL Chi-restraints excluded: chain BX residue 319 SER Chi-restraints excluded: chain CX residue 42 VAL Chi-restraints excluded: chain CX residue 62 ASP Chi-restraints excluded: chain CX residue 113 VAL Chi-restraints excluded: chain CX residue 120 ARG Chi-restraints excluded: chain CX residue 270 SER Chi-restraints excluded: chain CX residue 282 VAL Chi-restraints excluded: chain CX residue 310 LEU Chi-restraints excluded: chain CX residue 316 HIS Chi-restraints excluded: chain DX residue 42 VAL Chi-restraints excluded: chain DX residue 56 THR Chi-restraints excluded: chain DX residue 62 ASP Chi-restraints excluded: chain DX residue 92 SER Chi-restraints excluded: chain DX residue 113 VAL Chi-restraints excluded: chain DX residue 120 ARG Chi-restraints excluded: chain DX residue 264 ASP Chi-restraints excluded: chain DX residue 270 SER Chi-restraints excluded: chain DX residue 277 ARG Chi-restraints excluded: chain DX residue 282 VAL Chi-restraints excluded: chain DX residue 299 ASP Chi-restraints excluded: chain DX residue 317 GLU Chi-restraints excluded: chain EX residue 89 VAL Chi-restraints excluded: chain EX residue 113 VAL Chi-restraints excluded: chain EX residue 264 ASP Chi-restraints excluded: chain EX residue 282 VAL Chi-restraints excluded: chain EX residue 317 GLU Chi-restraints excluded: chain FX residue 42 VAL Chi-restraints excluded: chain FX residue 89 VAL Chi-restraints excluded: chain FX residue 93 ASN Chi-restraints excluded: chain FX residue 113 VAL Chi-restraints excluded: chain FX residue 120 ARG Chi-restraints excluded: chain FX residue 130 LYS Chi-restraints excluded: chain FX residue 282 VAL Chi-restraints excluded: chain FX residue 310 LEU Chi-restraints excluded: chain GX residue 42 VAL Chi-restraints excluded: chain GX residue 66 VAL Chi-restraints excluded: chain GX residue 113 VAL Chi-restraints excluded: chain GX residue 264 ASP Chi-restraints excluded: chain GX residue 282 VAL Chi-restraints excluded: chain GX residue 299 ASP Chi-restraints excluded: chain HX residue 42 VAL Chi-restraints excluded: chain HX residue 89 VAL Chi-restraints excluded: chain HX residue 113 VAL Chi-restraints excluded: chain HX residue 120 ARG Chi-restraints excluded: chain HX residue 264 ASP Chi-restraints excluded: chain HX residue 277 ARG Chi-restraints excluded: chain HX residue 282 VAL Chi-restraints excluded: chain HX residue 320 SER Chi-restraints excluded: chain IX residue 42 VAL Chi-restraints excluded: chain IX residue 83 ASN Chi-restraints excluded: chain IX residue 89 VAL Chi-restraints excluded: chain IX residue 113 VAL Chi-restraints excluded: chain IX residue 264 ASP Chi-restraints excluded: chain IX residue 277 ARG Chi-restraints excluded: chain IX residue 282 VAL Chi-restraints excluded: chain IX residue 283 ARG Chi-restraints excluded: chain IX residue 316 HIS Chi-restraints excluded: chain JX residue 42 VAL Chi-restraints excluded: chain JX residue 56 THR Chi-restraints excluded: chain JX residue 83 ASN Chi-restraints excluded: chain JX residue 89 VAL Chi-restraints excluded: chain JX residue 93 ASN Chi-restraints excluded: chain JX residue 113 VAL Chi-restraints excluded: chain JX residue 282 VAL Chi-restraints excluded: chain JX residue 317 GLU Chi-restraints excluded: chain KX residue 87 SER Chi-restraints excluded: chain KX residue 113 VAL Chi-restraints excluded: chain KX residue 270 SER Chi-restraints excluded: chain KX residue 282 VAL Chi-restraints excluded: chain KX residue 310 LEU Chi-restraints excluded: chain KX residue 316 HIS Chi-restraints excluded: chain LX residue 49 LEU Chi-restraints excluded: chain LX residue 89 VAL Chi-restraints excluded: chain LX residue 113 VAL Chi-restraints excluded: chain LX residue 264 ASP Chi-restraints excluded: chain LX residue 282 VAL Chi-restraints excluded: chain LX residue 316 HIS Chi-restraints excluded: chain MX residue 93 ASN Chi-restraints excluded: chain MX residue 94 HIS Chi-restraints excluded: chain MX residue 113 VAL Chi-restraints excluded: chain MX residue 282 VAL Chi-restraints excluded: chain NX residue 42 VAL Chi-restraints excluded: chain NX residue 87 SER Chi-restraints excluded: chain NX residue 89 VAL Chi-restraints excluded: chain NX residue 93 ASN Chi-restraints excluded: chain NX residue 113 VAL Chi-restraints excluded: chain NX residue 120 ARG Chi-restraints excluded: chain NX residue 264 ASP Chi-restraints excluded: chain NX residue 282 VAL Chi-restraints excluded: chain NX residue 317 GLU Chi-restraints excluded: chain OX residue 39 VAL Chi-restraints excluded: chain OX residue 42 VAL Chi-restraints excluded: chain OX residue 62 ASP Chi-restraints excluded: chain OX residue 83 ASN Chi-restraints excluded: chain OX residue 113 VAL Chi-restraints excluded: chain OX residue 120 ARG Chi-restraints excluded: chain OX residue 282 VAL Chi-restraints excluded: chain OX residue 316 HIS Chi-restraints excluded: chain OX residue 320 SER Chi-restraints excluded: chain PX residue 39 VAL Chi-restraints excluded: chain PX residue 83 ASN Chi-restraints excluded: chain PX residue 88 ILE Chi-restraints excluded: chain PX residue 94 HIS Chi-restraints excluded: chain PX residue 113 VAL Chi-restraints excluded: chain PX residue 282 VAL Chi-restraints excluded: chain PX residue 316 HIS Chi-restraints excluded: chain QX residue 49 LEU Chi-restraints excluded: chain QX residue 83 ASN Chi-restraints excluded: chain QX residue 89 VAL Chi-restraints excluded: chain QX residue 93 ASN Chi-restraints excluded: chain QX residue 113 VAL Chi-restraints excluded: chain QX residue 264 ASP Chi-restraints excluded: chain QX residue 282 VAL Chi-restraints excluded: chain QX residue 299 ASP Chi-restraints excluded: chain AY residue 1469 LEU Chi-restraints excluded: chain AY residue 1497 CYS Chi-restraints excluded: chain AY residue 1520 ASP Chi-restraints excluded: chain AY residue 1561 VAL Chi-restraints excluded: chain AY residue 1585 GLU Chi-restraints excluded: chain BY residue 1503 ASP Chi-restraints excluded: chain BY residue 1504 SER Chi-restraints excluded: chain BY residue 1520 ASP Chi-restraints excluded: chain BY residue 1524 SER Chi-restraints excluded: chain BY residue 1561 VAL Chi-restraints excluded: chain BY residue 1562 ASP Chi-restraints excluded: chain CY residue 1469 LEU Chi-restraints excluded: chain CY residue 1497 CYS Chi-restraints excluded: chain CY residue 1503 ASP Chi-restraints excluded: chain CY residue 1520 ASP Chi-restraints excluded: chain CY residue 1524 SER Chi-restraints excluded: chain CY residue 1562 ASP Chi-restraints excluded: chain CY residue 1572 ILE Chi-restraints excluded: chain DY residue 1502 SER Chi-restraints excluded: chain DY residue 1504 SER Chi-restraints excluded: chain DY residue 1505 GLU Chi-restraints excluded: chain DY residue 1509 ILE Chi-restraints excluded: chain DY residue 1520 ASP Chi-restraints excluded: chain DY residue 1526 LEU Chi-restraints excluded: chain DY residue 1562 ASP Chi-restraints excluded: chain EY residue 1469 LEU Chi-restraints excluded: chain EY residue 1497 CYS Chi-restraints excluded: chain EY residue 1504 SER Chi-restraints excluded: chain EY residue 1509 ILE Chi-restraints excluded: chain EY residue 1520 ASP Chi-restraints excluded: chain EY residue 1562 ASP Chi-restraints excluded: chain FY residue 1497 CYS Chi-restraints excluded: chain FY residue 1502 SER Chi-restraints excluded: chain FY residue 1503 ASP Chi-restraints excluded: chain FY residue 1504 SER Chi-restraints excluded: chain FY residue 1520 ASP Chi-restraints excluded: chain FY residue 1524 SER Chi-restraints excluded: chain FY residue 1562 ASP Chi-restraints excluded: chain GY residue 1497 CYS Chi-restraints excluded: chain GY residue 1503 ASP Chi-restraints excluded: chain GY residue 1504 SER Chi-restraints excluded: chain GY residue 1518 GLU Chi-restraints excluded: chain GY residue 1520 ASP Chi-restraints excluded: chain GY residue 1524 SER Chi-restraints excluded: chain GY residue 1562 ASP Chi-restraints excluded: chain HY residue 1497 CYS Chi-restraints excluded: chain HY residue 1520 ASP Chi-restraints excluded: chain HY residue 1562 ASP Chi-restraints excluded: chain IY residue 1504 SER Chi-restraints excluded: chain IY residue 1520 ASP Chi-restraints excluded: chain IY residue 1555 THR Chi-restraints excluded: chain IY residue 1562 ASP Chi-restraints excluded: chain JY residue 1520 ASP Chi-restraints excluded: chain JY residue 1562 ASP Chi-restraints excluded: chain JY residue 1580 ILE Chi-restraints excluded: chain KY residue 1469 LEU Chi-restraints excluded: chain KY residue 1520 ASP Chi-restraints excluded: chain KY residue 1562 ASP Chi-restraints excluded: chain LY residue 1497 CYS Chi-restraints excluded: chain LY residue 1502 SER Chi-restraints excluded: chain LY residue 1504 SER Chi-restraints excluded: chain LY residue 1520 ASP Chi-restraints excluded: chain LY residue 1561 VAL Chi-restraints excluded: chain LY residue 1562 ASP Chi-restraints excluded: chain MY residue 1497 CYS Chi-restraints excluded: chain MY residue 1504 SER Chi-restraints excluded: chain MY residue 1518 GLU Chi-restraints excluded: chain MY residue 1520 ASP Chi-restraints excluded: chain NY residue 1497 CYS Chi-restraints excluded: chain NY residue 1502 SER Chi-restraints excluded: chain NY residue 1504 SER Chi-restraints excluded: chain NY residue 1520 ASP Chi-restraints excluded: chain NY residue 1524 SER Chi-restraints excluded: chain NY residue 1538 LYS Chi-restraints excluded: chain NY residue 1562 ASP Chi-restraints excluded: chain OY residue 1497 CYS Chi-restraints excluded: chain OY residue 1503 ASP Chi-restraints excluded: chain OY residue 1504 SER Chi-restraints excluded: chain OY residue 1555 THR Chi-restraints excluded: chain PY residue 1503 ASP Chi-restraints excluded: chain PY residue 1520 ASP Chi-restraints excluded: chain PY residue 1524 SER Chi-restraints excluded: chain PY residue 1562 ASP Chi-restraints excluded: chain QY residue 1502 SER Chi-restraints excluded: chain QY residue 1504 SER Chi-restraints excluded: chain QY residue 1505 GLU Chi-restraints excluded: chain QY residue 1520 ASP Chi-restraints excluded: chain QY residue 1524 SER Chi-restraints excluded: chain QY residue 1562 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 493 random chunks: chunk 310 optimal weight: 6.9990 chunk 416 optimal weight: 0.8980 chunk 119 optimal weight: 7.9990 chunk 360 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 391 optimal weight: 0.7980 chunk 163 optimal weight: 0.7980 chunk 402 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AX 83 ASN ** AX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** BX 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BX 83 ASN ** BX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CX 83 ASN DX 83 ASN ** EX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** EX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** FX 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IX 83 ASN ** IX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** IX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** JX 83 ASN ** JX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** OX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** PX 83 ASN ** PX 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** QX 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AY1484 ASN CY1484 ASN ** DY1583 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HY1484 ASN LY1484 ASN MY1484 ASN PY1484 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.105828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091277 restraints weight = 84984.329| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.38 r_work: 0.3219 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 41242 Z= 0.299 Angle : 0.655 12.198 55709 Z= 0.347 Chirality : 0.045 0.222 6375 Planarity : 0.004 0.060 7191 Dihedral : 6.262 71.140 5478 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 5.84 % Allowed : 35.51 % Favored : 58.65 % 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: -0.37 (0.11), residues: 4981 helix: 1.51 (0.11), residues: 2074 sheet: -2.16 (0.20), residues: 544 loop : -1.39 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPQX 58 HIS 0.007 0.002 HISBX 94 PHE 0.015 0.002 PHEIX 96 TYR 0.047 0.002 TYRCX 122 ARG 0.015 0.001 ARGOY1514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24748.60 seconds wall clock time: 434 minutes 37.88 seconds (26077.88 seconds total)