Starting phenix.real_space_refine on Sun Mar 17 22:02:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tdz_10472/03_2024/6tdz_10472_trim_updated.pdb" } resolution = 3.14 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= 0.005 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: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 5 5.21 5 S 237 5.16 5 C 25856 2.51 5 N 6769 2.21 5 O 7687 1.98 5 H 41070 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ARG 202": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 223": "OD1" <-> "OD2" Residue "M ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 43": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 20": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 4": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 36": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 535": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 186": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 273": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 388": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 176": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 233": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 301": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 495": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 507": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 129": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 254": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 347": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 135": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 81638 Number of models: 1 Model: "" Number of chains: 32 Chain: "M" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 3778 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 14, 'TRANS': 228} Chain: "h" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 790 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "c" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 857 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain breaks: 1 Chain: "G" Number of atoms: 4898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 4898 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 5, 'TRANS': 297} Chain: "H" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2448 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "I" Number of atoms: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 1077 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "O" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "P" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "Q" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "R" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "S" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "T" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "U" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "V" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "W" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "X" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1185 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 3, 'TRANS': 77} Chain: "B" Number of atoms: 8292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 8292 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 504} Chain breaks: 1 Chain: "C" Number of atoms: 8353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 8353 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 508} Chain breaks: 1 Chain: "A" Number of atoms: 8302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 8302 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 506} Chain breaks: 1 Chain: "E" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "F" Number of atoms: 7408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7408 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 466} Chain: "D" Number of atoms: 7407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 7407 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 465} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "L" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "J" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 2596 Classifications: {'peptide': 170} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain: "N" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 802 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'TRT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 26.59, per 1000 atoms: 0.33 Number of scatterers: 81638 At special positions: 0 Unit cell: (160.65, 179.55, 234.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 237 16.00 P 14 15.00 Mg 5 11.99 O 7687 8.00 N 6769 7.00 C 25856 6.00 H 41070 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 53.01 Conformation dependent library (CDL) restraints added in 7.2 seconds 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 208 helices and 27 sheets defined 48.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.36 Creating SS restraints... Processing helix chain 'M' and resid 25 through 32 Processing helix chain 'M' and resid 49 through 62 Processing helix chain 'M' and resid 68 through 85 removed outlier: 3.682A pdb=" N PHE M 75 " --> pdb=" O VAL M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 102 No H-bonds generated for 'chain 'M' and resid 100 through 102' Processing helix chain 'M' and resid 105 through 117 Processing helix chain 'M' and resid 120 through 137 removed outlier: 5.019A pdb=" N GLU M 124 " --> pdb=" O ASP M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 169 removed outlier: 4.040A pdb=" N LYS M 161 " --> pdb=" O ALA M 157 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN M 162 " --> pdb=" O GLU M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 204 through 222 Processing helix chain 'M' and resid 240 through 245 Processing helix chain 'M' and resid 247 through 263 removed outlier: 3.881A pdb=" N ASP M 251 " --> pdb=" O GLY M 247 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP M 252 " --> pdb=" O SER M 248 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS M 258 " --> pdb=" O ALA M 254 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL M 259 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Processing helix chain 'h' and resid 282 through 292 Processing helix chain 'h' and resid 294 through 297 No H-bonds generated for 'chain 'h' and resid 294 through 297' Processing helix chain 'h' and resid 300 through 306 Processing helix chain 'h' and resid 310 through 327 Processing helix chain 'c' and resid 15 through 24 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 37 through 43 Processing helix chain 'c' and resid 79 through 87 Processing helix chain 'c' and resid 90 through 95 Processing helix chain 'G' and resid 4 through 41 removed outlier: 4.334A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ARG G 41 " --> pdb=" O GLN G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 56 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.537A pdb=" N GLU G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 98 Processing helix chain 'G' and resid 112 through 115 No H-bonds generated for 'chain 'G' and resid 112 through 115' Processing helix chain 'G' and resid 117 through 120 No H-bonds generated for 'chain 'G' and resid 117 through 120' Processing helix chain 'G' and resid 139 through 151 removed outlier: 3.930A pdb=" N THR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 192 Processing helix chain 'G' and resid 206 through 214 removed outlier: 4.039A pdb=" N GLY G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 293 removed outlier: 4.139A pdb=" N ILE G 248 " --> pdb=" O TYR G 244 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL G 249 " --> pdb=" O ALA G 245 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLN G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 27 through 30 Processing helix chain 'H' and resid 131 through 133 No H-bonds generated for 'chain 'H' and resid 131 through 133' Processing helix chain 'H' and resid 136 through 151 removed outlier: 3.688A pdb=" N LYS H 141 " --> pdb=" O GLU H 137 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU H 144 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU H 145 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 174 removed outlier: 3.810A pdb=" N ILE H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN H 160 " --> pdb=" O ALA H 156 " (cutoff:3.500A) Proline residue: H 170 - end of helix Processing helix chain 'I' and resid 10 through 24 Processing helix chain 'I' and resid 29 through 37 removed outlier: 4.326A pdb=" N ARG I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 33 through 46 removed outlier: 4.143A pdb=" N ILE O 37 " --> pdb=" O ALA O 34 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N GLY O 38 " --> pdb=" O ASN O 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY O 40 " --> pdb=" O ILE O 37 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY O 45 " --> pdb=" O ALA O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 66 Processing helix chain 'O' and resid 68 through 98 removed outlier: 4.879A pdb=" N ALA O 72 " --> pdb=" O ASN O 69 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU O 74 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU O 75 " --> pdb=" O ALA O 72 " (cutoff:3.500A) Proline residue: O 76 - end of helix removed outlier: 3.502A pdb=" N GLU O 86 " --> pdb=" O ALA O 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 36 No H-bonds generated for 'chain 'P' and resid 34 through 36' Processing helix chain 'P' and resid 38 through 45 removed outlier: 3.779A pdb=" N GLY P 45 " --> pdb=" O MET P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 66 removed outlier: 4.088A pdb=" N GLY P 52 " --> pdb=" O VAL P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 98 removed outlier: 4.593A pdb=" N ALA P 72 " --> pdb=" O ASN P 69 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU P 75 " --> pdb=" O ALA P 72 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.807A pdb=" N ILE P 79 " --> pdb=" O PRO P 76 " (cutoff:3.500A) Processing helix chain 'Q' and resid 34 through 45 removed outlier: 4.084A pdb=" N GLY Q 38 " --> pdb=" O ALA Q 34 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA Q 39 " --> pdb=" O ASN Q 35 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA Q 43 " --> pdb=" O ALA Q 39 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY Q 45 " --> pdb=" O MET Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 66 removed outlier: 3.865A pdb=" N GLY Q 52 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 101 removed outlier: 4.781A pdb=" N ALA Q 72 " --> pdb=" O ASN Q 69 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS Q 73 " --> pdb=" O MET Q 70 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU Q 74 " --> pdb=" O SER Q 71 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU Q 75 " --> pdb=" O ALA Q 72 " (cutoff:3.500A) Proline residue: Q 76 - end of helix removed outlier: 3.508A pdb=" N LEU Q 97 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N PHE Q 101 " --> pdb=" O LEU Q 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 35 No H-bonds generated for 'chain 'R' and resid 33 through 35' Processing helix chain 'R' and resid 37 through 46 removed outlier: 3.794A pdb=" N SER R 44 " --> pdb=" O GLY R 40 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY R 45 " --> pdb=" O MET R 41 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 66 removed outlier: 3.598A pdb=" N ILE R 51 " --> pdb=" O VAL R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 98 removed outlier: 4.604A pdb=" N ALA R 72 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU R 74 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU R 75 " --> pdb=" O ALA R 72 " (cutoff:3.500A) Proline residue: R 76 - end of helix removed outlier: 4.032A pdb=" N ILE R 95 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA R 96 " --> pdb=" O LEU R 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 34 through 45 removed outlier: 3.991A pdb=" N GLY S 38 " --> pdb=" O ASN S 35 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA S 39 " --> pdb=" O LEU S 36 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA S 43 " --> pdb=" O GLY S 40 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 66 removed outlier: 3.913A pdb=" N GLY S 52 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS S 56 " --> pdb=" O GLY S 52 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE S 57 " --> pdb=" O VAL S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 100 removed outlier: 4.474A pdb=" N ALA S 72 " --> pdb=" O ASN S 69 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU S 75 " --> pdb=" O ALA S 72 " (cutoff:3.500A) Proline residue: S 76 - end of helix removed outlier: 3.926A pdb=" N SER S 85 " --> pdb=" O PHE S 82 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLU S 86 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU S 88 " --> pdb=" O SER S 85 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LEU S 94 " --> pdb=" O PHE S 91 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE S 95 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU S 99 " --> pdb=" O ALA S 96 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU S 100 " --> pdb=" O LEU S 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 32 through 35 Processing helix chain 'T' and resid 38 through 43 Processing helix chain 'T' and resid 48 through 66 removed outlier: 4.019A pdb=" N ALA T 54 " --> pdb=" O ILE T 51 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N SER T 58 " --> pdb=" O MET T 55 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET T 61 " --> pdb=" O SER T 58 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA T 63 " --> pdb=" O TYR T 60 " (cutoff:3.500A) Processing helix chain 'T' and resid 68 through 100 removed outlier: 4.528A pdb=" N ALA T 72 " --> pdb=" O ASN T 69 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU T 74 " --> pdb=" O SER T 71 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU T 75 " --> pdb=" O ALA T 72 " (cutoff:3.500A) Proline residue: T 76 - end of helix removed outlier: 3.800A pdb=" N ILE T 95 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU T 97 " --> pdb=" O LEU T 94 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU T 100 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 32 through 36 Processing helix chain 'U' and resid 38 through 46 removed outlier: 4.245A pdb=" N GLY U 45 " --> pdb=" O MET U 41 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL U 46 " --> pdb=" O ALA U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 48 through 64 removed outlier: 3.534A pdb=" N SER U 58 " --> pdb=" O MET U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 98 removed outlier: 4.268A pdb=" N ALA U 72 " --> pdb=" O ASN U 69 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU U 75 " --> pdb=" O ALA U 72 " (cutoff:3.500A) Proline residue: U 76 - end of helix removed outlier: 4.207A pdb=" N LEU U 84 " --> pdb=" O GLY U 81 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N SER U 85 " --> pdb=" O PHE U 82 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 36 No H-bonds generated for 'chain 'V' and resid 34 through 36' Processing helix chain 'V' and resid 38 through 46 removed outlier: 4.163A pdb=" N GLY V 45 " --> pdb=" O MET V 41 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 66 Processing helix chain 'V' and resid 68 through 70 No H-bonds generated for 'chain 'V' and resid 68 through 70' Processing helix chain 'V' and resid 75 through 98 removed outlier: 4.247A pdb=" N ALA V 96 " --> pdb=" O THR V 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 34 through 45 removed outlier: 4.274A pdb=" N GLY W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ALA W 39 " --> pdb=" O ASN W 35 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLY W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY W 45 " --> pdb=" O MET W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 66 removed outlier: 3.555A pdb=" N CYS W 56 " --> pdb=" O GLY W 52 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER W 59 " --> pdb=" O MET W 55 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR W 60 " --> pdb=" O CYS W 56 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 98 removed outlier: 4.540A pdb=" N ALA W 72 " --> pdb=" O ASN W 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU W 74 " --> pdb=" O SER W 71 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU W 75 " --> pdb=" O ALA W 72 " (cutoff:3.500A) Proline residue: W 76 - end of helix removed outlier: 4.513A pdb=" N ILE W 79 " --> pdb=" O PRO W 76 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE W 95 " --> pdb=" O THR W 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 38 through 45 removed outlier: 3.680A pdb=" N ALA X 43 " --> pdb=" O ALA X 39 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY X 45 " --> pdb=" O MET X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 48 through 66 removed outlier: 4.225A pdb=" N ALA X 54 " --> pdb=" O ILE X 51 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER X 59 " --> pdb=" O CYS X 56 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N MET X 61 " --> pdb=" O SER X 58 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 101 removed outlier: 4.587A pdb=" N ALA X 72 " --> pdb=" O ASN X 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS X 73 " --> pdb=" O MET X 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU X 75 " --> pdb=" O ALA X 72 " (cutoff:3.500A) Proline residue: X 76 - end of helix removed outlier: 3.582A pdb=" N LEU X 97 " --> pdb=" O LEU X 94 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU X 100 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE X 101 " --> pdb=" O LEU X 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 153 No H-bonds generated for 'chain 'B' and resid 151 through 153' Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.604A pdb=" N LEU B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 201 removed outlier: 3.665A pdb=" N ILE B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 255 through 274 Proline residue: B 262 - end of helix removed outlier: 3.932A pdb=" N GLU B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 Processing helix chain 'B' and resid 306 through 308 No H-bonds generated for 'chain 'B' and resid 306 through 308' Processing helix chain 'B' and resid 311 through 323 removed outlier: 3.862A pdb=" N PHE B 314 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU B 321 " --> pdb=" O SER B 318 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU B 322 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 360 Processing helix chain 'B' and resid 369 through 372 No H-bonds generated for 'chain 'B' and resid 369 through 372' Processing helix chain 'B' and resid 396 through 418 removed outlier: 4.381A pdb=" N LYS B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU B 411 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 418 " --> pdb=" O LYS B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 440 Processing helix chain 'B' and resid 448 through 459 removed outlier: 3.851A pdb=" N ALA B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 458 " --> pdb=" O ALA B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 479 Processing helix chain 'B' and resid 483 through 486 No H-bonds generated for 'chain 'B' and resid 483 through 486' Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 514 through 540 Proline residue: B 518 - end of helix removed outlier: 4.310A pdb=" N GLN B 536 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 540 " --> pdb=" O GLN B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.847A pdb=" N ARG B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 166 through 171 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.643A pdb=" N ALA C 194 " --> pdb=" O LYS C 190 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N LYS C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 237 Processing helix chain 'C' and resid 255 through 274 Proline residue: C 262 - end of helix removed outlier: 3.740A pdb=" N GLU C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 removed outlier: 3.762A pdb=" N VAL C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 313 through 322 removed outlier: 3.745A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 358 Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 396 through 417 removed outlier: 3.776A pdb=" N VAL C 401 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS C 414 " --> pdb=" O GLY C 410 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 440 Processing helix chain 'C' and resid 448 through 459 removed outlier: 3.624A pdb=" N VAL C 453 " --> pdb=" O MET C 449 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 455 " --> pdb=" O ALA C 451 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 458 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 479 Processing helix chain 'C' and resid 483 through 487 Processing helix chain 'C' and resid 502 through 509 removed outlier: 4.017A pdb=" N ARG C 507 " --> pdb=" O TYR C 504 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE C 509 " --> pdb=" O ILE C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 534 Proline residue: C 518 - end of helix Processing helix chain 'C' and resid 536 through 541 Processing helix chain 'C' and resid 545 through 561 removed outlier: 3.516A pdb=" N ARG C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.822A pdb=" N ALA A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 202 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL A 204 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 237 Processing helix chain 'A' and resid 255 through 274 Proline residue: A 262 - end of helix removed outlier: 4.026A pdb=" N GLU A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 Processing helix chain 'A' and resid 306 through 308 No H-bonds generated for 'chain 'A' and resid 306 through 308' Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.566A pdb=" N HIS A 317 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 352 through 358 Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 396 through 415 removed outlier: 3.835A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 440 removed outlier: 3.551A pdb=" N ALA A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 459 removed outlier: 3.779A pdb=" N VAL A 453 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 458 " --> pdb=" O ALA A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 480 removed outlier: 4.601A pdb=" N LYS A 472 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 473 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 474 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 480 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 517 through 540 removed outlier: 5.142A pdb=" N ILE A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN A 536 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N SER A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 561 Processing helix chain 'E' and resid 49 through 52 No H-bonds generated for 'chain 'E' and resid 49 through 52' Processing helix chain 'E' and resid 149 through 153 Processing helix chain 'E' and resid 173 through 184 Processing helix chain 'E' and resid 201 through 213 Processing helix chain 'E' and resid 236 through 239 No H-bonds generated for 'chain 'E' and resid 236 through 239' Processing helix chain 'E' and resid 242 through 255 removed outlier: 3.739A pdb=" N TYR E 252 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE E 253 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 282 removed outlier: 3.813A pdb=" N ASN E 275 " --> pdb=" O PHE E 271 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA E 280 " --> pdb=" O SER E 276 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LEU E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 303 removed outlier: 3.775A pdb=" N LEU E 302 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 325 No H-bonds generated for 'chain 'E' and resid 323 through 325' Processing helix chain 'E' and resid 330 through 335 Processing helix chain 'E' and resid 347 through 351 Processing helix chain 'E' and resid 375 through 398 removed outlier: 3.544A pdb=" N THR E 389 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE E 397 " --> pdb=" O GLU E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.594A pdb=" N ILE E 413 " --> pdb=" O GLU E 409 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS E 422 " --> pdb=" O ARG E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 435 removed outlier: 4.285A pdb=" N VAL E 433 " --> pdb=" O VAL E 430 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR E 435 " --> pdb=" O GLU E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 455 removed outlier: 3.894A pdb=" N PHE E 451 " --> pdb=" O CYS E 447 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 467 No H-bonds generated for 'chain 'E' and resid 465 through 467' Processing helix chain 'E' and resid 473 through 500 Processing helix chain 'F' and resid 49 through 52 No H-bonds generated for 'chain 'F' and resid 49 through 52' Processing helix chain 'F' and resid 99 through 101 No H-bonds generated for 'chain 'F' and resid 99 through 101' Processing helix chain 'F' and resid 149 through 154 removed outlier: 3.574A pdb=" N ILE F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 Processing helix chain 'F' and resid 201 through 213 removed outlier: 3.578A pdb=" N MET F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 255 removed outlier: 4.087A pdb=" N ARG F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N GLN F 244 " --> pdb=" O ALA F 240 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR F 245 " --> pdb=" O ARG F 241 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE F 253 " --> pdb=" O MET F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 281 Processing helix chain 'F' and resid 295 through 303 removed outlier: 3.734A pdb=" N LEU F 302 " --> pdb=" O ASP F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 330 through 335 Processing helix chain 'F' and resid 347 through 351 Processing helix chain 'F' and resid 375 through 398 removed outlier: 3.542A pdb=" N ILE F 397 " --> pdb=" O GLU F 393 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 408 through 424 removed outlier: 3.688A pdb=" N LEU F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 435 No H-bonds generated for 'chain 'F' and resid 432 through 435' Processing helix chain 'F' and resid 444 through 456 Processing helix chain 'F' and resid 465 through 467 No H-bonds generated for 'chain 'F' and resid 465 through 467' Processing helix chain 'F' and resid 473 through 500 removed outlier: 3.668A pdb=" N LYS F 477 " --> pdb=" O LEU F 473 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N GLU F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 52 No H-bonds generated for 'chain 'D' and resid 49 through 52' Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 173 through 184 Processing helix chain 'D' and resid 201 through 213 Processing helix chain 'D' and resid 236 through 239 No H-bonds generated for 'chain 'D' and resid 236 through 239' Processing helix chain 'D' and resid 242 through 255 removed outlier: 3.630A pdb=" N TYR D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE D 253 " --> pdb=" O MET D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 282 Processing helix chain 'D' and resid 295 through 303 removed outlier: 3.908A pdb=" N LEU D 302 " --> pdb=" O ASP D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 330 through 335 Processing helix chain 'D' and resid 348 through 351 No H-bonds generated for 'chain 'D' and resid 348 through 351' Processing helix chain 'D' and resid 375 through 398 removed outlier: 3.575A pdb=" N ALA D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE D 397 " --> pdb=" O GLU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 408 through 424 Processing helix chain 'D' and resid 432 through 435 No H-bonds generated for 'chain 'D' and resid 432 through 435' Processing helix chain 'D' and resid 444 through 455 removed outlier: 3.729A pdb=" N SER D 449 " --> pdb=" O GLU D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 467 No H-bonds generated for 'chain 'D' and resid 465 through 467' Processing helix chain 'D' and resid 473 through 500 Processing helix chain 'K' and resid 40 through 47 Processing helix chain 'K' and resid 54 through 65 removed outlier: 3.635A pdb=" N ILE K 59 " --> pdb=" O ALA K 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL K 60 " --> pdb=" O GLY K 56 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS K 61 " --> pdb=" O GLU K 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 71 through 83 Processing helix chain 'K' and resid 97 through 109 Processing helix chain 'K' and resid 118 through 131 removed outlier: 3.888A pdb=" N TYR K 123 " --> pdb=" O GLU K 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 146 removed outlier: 3.570A pdb=" N VAL K 139 " --> pdb=" O ARG K 135 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 Processing helix chain 'L' and resid 40 through 47 Processing helix chain 'L' and resid 54 through 63 Processing helix chain 'L' and resid 71 through 83 Processing helix chain 'L' and resid 97 through 109 removed outlier: 4.461A pdb=" N LEU L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 118 through 131 Processing helix chain 'L' and resid 135 through 146 Processing helix chain 'L' and resid 153 through 168 removed outlier: 3.632A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 47 Processing helix chain 'J' and resid 54 through 64 Processing helix chain 'J' and resid 71 through 83 Processing helix chain 'J' and resid 97 through 109 removed outlier: 4.000A pdb=" N MET J 101 " --> pdb=" O LYS J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 131 removed outlier: 3.529A pdb=" N LEU J 128 " --> pdb=" O VAL J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 134 through 147 removed outlier: 3.660A pdb=" N TRP J 138 " --> pdb=" O PHE J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 153 through 168 Processing helix chain 'N' and resid 45 through 67 Processing sheet with id= A, first strand: chain 'M' and resid 176 through 183 Processing sheet with id= B, first strand: chain 'G' and resid 74 through 77 removed outlier: 6.245A pdb=" N SER G 169 " --> pdb=" O HIS G 165 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 106 through 109 removed outlier: 7.696A pdb=" N SER G 108 " --> pdb=" O ARG G 126 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N THR G 128 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 86 through 88 removed outlier: 7.605A pdb=" N LEU H 51 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS H 60 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 75 through 78 removed outlier: 4.237A pdb=" N ARG H 70 " --> pdb=" O ILE H 93 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N ILE H 93 " --> pdb=" O ARG H 70 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.596A pdb=" N THR B 41 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE B 35 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE B 39 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 80 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N ILE B 83 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N VAL B 71 " --> pdb=" O ILE B 83 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 57 through 59 Processing sheet with id= H, first strand: chain 'B' and resid 105 through 107 Processing sheet with id= I, first strand: chain 'B' and resid 181 through 183 Processing sheet with id= J, first strand: chain 'B' and resid 245 through 249 removed outlier: 6.391A pdb=" N VAL B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B 221 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ASP B 284 " --> pdb=" O ILE B 221 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 57 through 59 removed outlier: 3.516A pdb=" N GLY C 30 " --> pdb=" O VAL C 97 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA C 99 " --> pdb=" O LYS C 28 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LYS C 28 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C 41 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ILE C 35 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 39 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN C 73 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N ILE C 83 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL C 71 " --> pdb=" O ILE C 83 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 105 through 107 Processing sheet with id= M, first strand: chain 'C' and resid 182 through 184 Processing sheet with id= N, first strand: chain 'C' and resid 279 through 284 removed outlier: 6.479A pdb=" N LEU C 215 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N VAL C 282 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 217 " --> pdb=" O VAL C 282 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASP C 284 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 219 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.705A pdb=" N GLY A 30 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA A 99 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS A 28 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 41 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N ILE A 35 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 83 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL A 71 " --> pdb=" O ILE A 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 105 through 107 Processing sheet with id= Q, first strand: chain 'A' and resid 364 through 367 removed outlier: 7.077A pdb=" N LEU A 181 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N LEU A 367 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 183 " --> pdb=" O LEU A 367 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY A 184 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 245 through 249 Processing sheet with id= S, first strand: chain 'E' and resid 19 through 21 Processing sheet with id= T, first strand: chain 'E' and resid 29 through 33 removed outlier: 5.943A pdb=" N ILE E 72 " --> pdb=" O ILE E 60 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ILE E 60 " --> pdb=" O ILE E 72 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 341 through 344 removed outlier: 7.379A pdb=" N ILE E 163 " --> pdb=" O ILE E 314 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER E 316 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU E 165 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N GLN E 318 " --> pdb=" O LEU E 165 " (cutoff:3.500A) removed outlier: 8.213A pdb=" N GLY E 167 " --> pdb=" O GLN E 318 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N VAL E 320 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU E 263 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR E 191 " --> pdb=" O LEU E 262 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N PHE E 264 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL E 193 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP E 266 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 195 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 85 through 87 removed outlier: 6.699A pdb=" N ASP F 31 " --> pdb=" O GLN F 23 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE F 25 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ILE F 72 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE F 60 " --> pdb=" O ILE F 72 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 341 through 344 removed outlier: 8.347A pdb=" N ILE F 163 " --> pdb=" O ILE F 314 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 316 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU F 165 " --> pdb=" O SER F 316 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLN F 318 " --> pdb=" O LEU F 165 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 19 through 21 Processing sheet with id= Y, first strand: chain 'D' and resid 29 through 32 removed outlier: 6.191A pdb=" N ILE D 72 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ILE D 60 " --> pdb=" O ILE D 72 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 56 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'D' and resid 94 through 96 Processing sheet with id= AA, first strand: chain 'D' and resid 341 through 344 removed outlier: 7.387A pdb=" N ILE D 163 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER D 316 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N LEU D 165 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN D 318 " --> pdb=" O LEU D 165 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL D 261 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL D 317 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU D 263 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ALA D 319 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL D 265 " --> pdb=" O ALA D 319 " (cutoff:3.500A) 1716 hydrogen bonds defined for protein. 4146 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: 31.25 Time building geometry restraints manager: 55.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.00: 41002 1.00 - 1.21: 69 1.21 - 1.41: 16281 1.41 - 1.61: 24565 1.61 - 1.81: 408 Bond restraints: 82325 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.458 -0.070 1.00e-02 1.00e+04 4.84e+01 bond pdb=" C4 ATP D 601 " pdb=" C5 ATP D 601 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.69e+01 bond pdb=" C4 ATP A 601 " pdb=" C5 ATP A 601 " ideal model delta sigma weight residual 1.388 1.453 -0.065 1.00e-02 1.00e+04 4.16e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.470 -0.061 1.00e-02 1.00e+04 3.73e+01 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.313 0.061 1.00e-02 1.00e+04 3.71e+01 ... (remaining 82320 not shown) Histogram of bond angle deviations from ideal: 91.73 - 100.64: 149 100.64 - 109.54: 58444 109.54 - 118.45: 55910 118.45 - 127.35: 34448 127.35 - 136.26: 325 Bond angle restraints: 149276 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 120.23 19.64 1.00e+00 1.00e+00 3.86e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.48 19.39 1.00e+00 1.00e+00 3.76e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 121.97 17.90 1.00e+00 1.00e+00 3.21e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 121.93 14.90 1.00e+00 1.00e+00 2.22e+02 ... (remaining 149271 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 35034 16.30 - 32.59: 2701 32.59 - 48.89: 649 48.89 - 65.19: 268 65.19 - 81.48: 9 Dihedral angle restraints: 38661 sinusoidal: 21344 harmonic: 17317 Sorted by residual: dihedral pdb=" CA ASP F 266 " pdb=" C ASP F 266 " pdb=" N ASN F 267 " pdb=" CA ASN F 267 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA ASP A 284 " pdb=" C ASP A 284 " pdb=" N ASP A 285 " pdb=" CA ASP A 285 " ideal model delta harmonic sigma weight residual 180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA GLN A 442 " pdb=" C GLN A 442 " pdb=" N LYS A 443 " pdb=" CA LYS A 443 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 38658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 6495 0.224 - 0.448: 3 0.448 - 0.672: 0 0.672 - 0.896: 0 0.896 - 1.120: 1 Chirality restraints: 6499 Sorted by residual: chirality pdb=" CG LEU G 49 " pdb=" CB LEU G 49 " pdb=" CD1 LEU G 49 " pdb=" CD2 LEU G 49 " both_signs ideal model delta sigma weight residual False -2.59 -1.47 -1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CB VAL E 30 " pdb=" CA VAL E 30 " pdb=" CG1 VAL E 30 " pdb=" CG2 VAL E 30 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" C2' ATP D 601 " pdb=" C1' ATP D 601 " pdb=" C3' ATP D 601 " pdb=" O2' ATP D 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.42 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 6496 not shown) Planarity restraints: 12180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 111 " 0.059 9.50e-02 1.11e+02 4.74e-02 4.24e+01 pdb=" NE ARG L 111 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG L 111 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 111 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG L 111 " 0.087 2.00e-02 2.50e+03 pdb="HH11 ARG L 111 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG L 111 " -0.041 2.00e-02 2.50e+03 pdb="HH21 ARG L 111 " -0.083 2.00e-02 2.50e+03 pdb="HH22 ARG L 111 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 159 " 0.011 2.00e-02 2.50e+03 2.79e-02 2.33e+01 pdb=" CG TYR C 159 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR C 159 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 159 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 159 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR C 159 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 159 " -0.071 2.00e-02 2.50e+03 pdb=" OH TYR C 159 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 TYR C 159 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR C 159 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TYR C 159 " 0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR C 159 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 118 " -0.057 5.00e-02 4.00e+02 8.60e-02 1.18e+01 pdb=" N PRO A 119 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.047 5.00e-02 4.00e+02 ... (remaining 12177 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 4579 2.19 - 2.80: 178257 2.80 - 3.40: 224266 3.40 - 4.00: 302901 4.00 - 4.60: 483536 Nonbonded interactions: 1193539 Sorted by model distance: nonbonded pdb=" O ASP D 114 " pdb=" HH TYR L 33 " model vdw 1.593 1.850 nonbonded pdb=" OG SER G 205 " pdb=" HZ3 LYS G 209 " model vdw 1.606 1.850 nonbonded pdb="HE22 GLN A 295 " pdb=" OE1 GLU D 297 " model vdw 1.618 1.850 nonbonded pdb=" O LYS M 93 " pdb=" HG SER M 97 " model vdw 1.628 1.850 nonbonded pdb=" O CYS T 56 " pdb=" HG SER T 59 " model vdw 1.630 1.850 ... (remaining 1193534 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) selection = chain 'B' selection = (chain 'C' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ or name HA or name HB2 or name HB3 o \ r name HG2 or name HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name H \ Z1 or name HZ2 or name HZ3)) or resid 27 through 562 or resid 601 through 602)) } ncs_group { reference = (chain 'D' and resid 15 through 501) selection = (chain 'E' and resid 15 through 501) selection = (chain 'F' and (resid 15 through 173 or (resid 174 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 175 through 501)) } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 5.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.880 Extract box with map and model: 18.530 Check model and map are aligned: 0.890 Set scattering table: 0.550 Process input model: 211.760 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.530 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: 0.020 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 244.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.009 0.131 41255 Z= 0.609 Angle : 0.835 19.636 55909 Z= 0.485 Chirality : 0.051 1.120 6499 Planarity : 0.007 0.086 7138 Dihedral : 11.461 81.482 15294 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.10), residues: 5223 helix: -1.28 (0.08), residues: 2587 sheet: -2.59 (0.19), residues: 556 loop : -1.27 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 37 HIS 0.012 0.002 HIS E 63 PHE 0.032 0.003 PHE R 82 TYR 0.071 0.002 TYR C 159 ARG 0.026 0.003 ARG J 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 1315 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1315 time to evaluate : 5.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 SER cc_start: 0.8254 (m) cc_final: 0.8019 (p) REVERT: M 71 TYR cc_start: 0.8210 (m-80) cc_final: 0.7861 (m-80) REVERT: M 175 TYR cc_start: 0.7930 (m-80) cc_final: 0.7307 (m-10) REVERT: c 94 THR cc_start: 0.8130 (m) cc_final: 0.7913 (p) REVERT: H 165 LEU cc_start: 0.7473 (tp) cc_final: 0.7037 (mt) REVERT: H 166 GLU cc_start: 0.7245 (tt0) cc_final: 0.6981 (tt0) REVERT: O 55 MET cc_start: 0.8349 (ttm) cc_final: 0.7708 (ttm) REVERT: P 73 LYS cc_start: 0.9089 (mtpt) cc_final: 0.8655 (ttpp) REVERT: P 79 ILE cc_start: 0.8997 (mm) cc_final: 0.8580 (pt) REVERT: Q 25 ILE cc_start: 0.6891 (mt) cc_final: 0.6459 (mt) REVERT: Q 59 SER cc_start: 0.7480 (p) cc_final: 0.7222 (p) REVERT: R 37 ILE cc_start: 0.8596 (mt) cc_final: 0.7939 (mt) REVERT: S 41 MET cc_start: 0.6477 (mtp) cc_final: 0.6263 (mtp) REVERT: S 97 LEU cc_start: 0.8890 (mm) cc_final: 0.8517 (tp) REVERT: T 93 LEU cc_start: 0.9058 (tp) cc_final: 0.8811 (tp) REVERT: U 86 GLU cc_start: 0.7568 (tp30) cc_final: 0.7104 (tp30) REVERT: W 32 ASN cc_start: 0.8200 (m110) cc_final: 0.7579 (m110) REVERT: X 41 MET cc_start: 0.7635 (mtp) cc_final: 0.6623 (mtp) REVERT: B 497 MET cc_start: 0.7909 (mmm) cc_final: 0.7692 (mmt) REVERT: A 241 MET cc_start: 0.8240 (tpt) cc_final: 0.7768 (tpt) REVERT: A 346 SER cc_start: 0.7746 (m) cc_final: 0.7532 (p) REVERT: E 66 THR cc_start: 0.8203 (p) cc_final: 0.7975 (m) REVERT: E 141 ASP cc_start: 0.6564 (m-30) cc_final: 0.6291 (p0) REVERT: F 111 ASP cc_start: 0.7027 (m-30) cc_final: 0.6634 (m-30) REVERT: F 411 LYS cc_start: 0.7460 (ptpt) cc_final: 0.7200 (mtmm) REVERT: D 199 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7101 (mm-30) REVERT: K 95 GLU cc_start: 0.7892 (tt0) cc_final: 0.7559 (tt0) outliers start: 0 outliers final: 0 residues processed: 1315 average time/residue: 1.1905 time to fit residues: 2476.2610 Evaluate side-chains 732 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 732 time to evaluate : 4.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 439 optimal weight: 0.5980 chunk 394 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 266 optimal weight: 0.5980 chunk 210 optimal weight: 2.9990 chunk 408 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 303 optimal weight: 0.4980 chunk 473 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 197 ASN c 28 HIS H 88 GLN B 513 HIS C 489 GLN ** A 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 GLN F 24 GLN D 63 HIS J 96 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 41255 Z= 0.214 Angle : 0.551 7.713 55909 Z= 0.292 Chirality : 0.040 0.177 6499 Planarity : 0.005 0.080 7138 Dihedral : 5.679 80.582 5846 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.65 % Rotamer: Outliers : 1.32 % Allowed : 8.61 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % 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: -1.35 (0.11), residues: 5223 helix: -0.32 (0.09), residues: 2596 sheet: -2.21 (0.19), residues: 581 loop : -1.04 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 138 HIS 0.004 0.001 HIS c 28 PHE 0.020 0.001 PHE V 82 TYR 0.014 0.001 TYR A 474 ARG 0.006 0.000 ARG H 158 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 836 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 779 time to evaluate : 4.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 SER cc_start: 0.8270 (m) cc_final: 0.7946 (p) REVERT: M 114 ILE cc_start: 0.6637 (mt) cc_final: 0.6193 (mt) REVERT: c 94 THR cc_start: 0.8084 (m) cc_final: 0.7841 (p) REVERT: G 49 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8383 (mp) REVERT: G 138 SER cc_start: 0.6952 (p) cc_final: 0.6742 (p) REVERT: P 35 ASN cc_start: 0.8959 (t0) cc_final: 0.8717 (t0) REVERT: P 60 TYR cc_start: 0.8557 (t80) cc_final: 0.8138 (t80) REVERT: S 61 MET cc_start: 0.8088 (mtt) cc_final: 0.7766 (mtt) REVERT: S 97 LEU cc_start: 0.8879 (mm) cc_final: 0.8554 (tp) REVERT: T 80 LEU cc_start: 0.9022 (tp) cc_final: 0.8718 (mp) REVERT: U 41 MET cc_start: 0.6590 (mtp) cc_final: 0.6001 (mtp) REVERT: W 32 ASN cc_start: 0.8125 (m110) cc_final: 0.7498 (m110) REVERT: B 346 SER cc_start: 0.8757 (m) cc_final: 0.8480 (p) REVERT: C 327 MET cc_start: 0.8566 (mmm) cc_final: 0.8335 (mmm) REVERT: A 241 MET cc_start: 0.8204 (tpt) cc_final: 0.7672 (tpt) REVERT: E 141 ASP cc_start: 0.6647 (m-30) cc_final: 0.6307 (p0) REVERT: E 229 TYR cc_start: 0.8389 (m-80) cc_final: 0.7932 (m-80) REVERT: F 368 MET cc_start: 0.8704 (mmt) cc_final: 0.8205 (mmt) outliers start: 57 outliers final: 42 residues processed: 804 average time/residue: 1.1211 time to fit residues: 1485.7069 Evaluate side-chains 709 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 666 time to evaluate : 4.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain c residue 28 HIS Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain Q residue 28 GLU Chi-restraints excluded: chain R residue 55 MET Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 28 GLU Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain F residue 24 GLN Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 130 LYS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 262 optimal weight: 0.0170 chunk 146 optimal weight: 2.9990 chunk 393 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 473 optimal weight: 0.5980 chunk 512 optimal weight: 0.8980 chunk 422 optimal weight: 1.9990 chunk 470 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 380 optimal weight: 3.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 197 ASN c 28 HIS ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN C 356 ASN C 395 ASN A 441 ASN D 458 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 41255 Z= 0.269 Angle : 0.533 6.483 55909 Z= 0.279 Chirality : 0.040 0.197 6499 Planarity : 0.004 0.083 7138 Dihedral : 5.664 80.471 5846 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 1.25 % Allowed : 10.03 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % 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: -0.79 (0.12), residues: 5223 helix: 0.16 (0.10), residues: 2602 sheet: -1.79 (0.20), residues: 585 loop : -0.86 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 113 HIS 0.004 0.001 HIS G 227 PHE 0.017 0.001 PHE G 223 TYR 0.015 0.001 TYR A 159 ARG 0.008 0.000 ARG G 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 753 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 699 time to evaluate : 5.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 SER cc_start: 0.8362 (m) cc_final: 0.8050 (p) REVERT: h 325 VAL cc_start: 0.8207 (m) cc_final: 0.7962 (p) REVERT: c 94 THR cc_start: 0.8105 (m) cc_final: 0.7887 (p) REVERT: G 49 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8533 (mp) REVERT: S 79 ILE cc_start: 0.8783 (mm) cc_final: 0.8522 (pt) REVERT: S 97 LEU cc_start: 0.8902 (mm) cc_final: 0.8605 (tp) REVERT: T 70 MET cc_start: 0.7505 (mmm) cc_final: 0.7224 (mmm) REVERT: T 80 LEU cc_start: 0.9025 (tp) cc_final: 0.8769 (mp) REVERT: U 28 GLU cc_start: 0.7818 (mp0) cc_final: 0.7571 (mp0) REVERT: U 41 MET cc_start: 0.6515 (mtp) cc_final: 0.6141 (mtt) REVERT: U 79 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8416 (pt) REVERT: W 32 ASN cc_start: 0.8144 (m110) cc_final: 0.7556 (m110) REVERT: W 56 CYS cc_start: 0.8766 (t) cc_final: 0.8409 (t) REVERT: B 284 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: C 497 MET cc_start: 0.8756 (mmt) cc_final: 0.8481 (mmt) REVERT: A 241 MET cc_start: 0.8221 (tpt) cc_final: 0.7744 (tpt) REVERT: E 141 ASP cc_start: 0.6691 (m-30) cc_final: 0.6331 (p0) REVERT: E 211 MET cc_start: 0.8030 (mtt) cc_final: 0.7804 (mtt) REVERT: F 368 MET cc_start: 0.8760 (mmt) cc_final: 0.8466 (mmt) REVERT: L 34 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: J 114 ILE cc_start: 0.8468 (mt) cc_final: 0.8224 (mm) outliers start: 54 outliers final: 36 residues processed: 728 average time/residue: 1.0654 time to fit residues: 1255.3239 Evaluate side-chains 683 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 643 time to evaluate : 4.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 468 optimal weight: 1.9990 chunk 356 optimal weight: 1.9990 chunk 245 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 475 optimal weight: 2.9990 chunk 503 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 450 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN F 24 GLN F 128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 41255 Z= 0.306 Angle : 0.548 9.252 55909 Z= 0.287 Chirality : 0.041 0.174 6499 Planarity : 0.004 0.077 7138 Dihedral : 5.875 88.680 5846 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 10.75 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 5223 helix: 0.38 (0.10), residues: 2601 sheet: -1.71 (0.20), residues: 568 loop : -0.68 (0.14), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.007 0.001 HIS F 377 PHE 0.018 0.001 PHE U 82 TYR 0.017 0.001 TYR P 60 ARG 0.004 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 767 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 687 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 SER cc_start: 0.8471 (m) cc_final: 0.8194 (p) REVERT: I 46 TYR cc_start: 0.8461 (p90) cc_final: 0.7959 (p90) REVERT: O 55 MET cc_start: 0.7952 (ttm) cc_final: 0.7709 (ttm) REVERT: P 73 LYS cc_start: 0.9130 (mtpp) cc_final: 0.8836 (ttpp) REVERT: S 79 ILE cc_start: 0.8774 (mm) cc_final: 0.8526 (pt) REVERT: S 97 LEU cc_start: 0.8939 (mm) cc_final: 0.8670 (tp) REVERT: T 80 LEU cc_start: 0.8986 (tp) cc_final: 0.8756 (mp) REVERT: W 32 ASN cc_start: 0.8230 (m110) cc_final: 0.7628 (m110) REVERT: W 56 CYS cc_start: 0.8838 (t) cc_final: 0.8513 (t) REVERT: B 179 ARG cc_start: 0.8183 (ptt-90) cc_final: 0.7775 (ptt90) REVERT: B 284 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7484 (m-30) REVERT: B 430 MET cc_start: 0.8114 (mmm) cc_final: 0.7753 (mmt) REVERT: C 88 ILE cc_start: 0.8706 (mp) cc_final: 0.8158 (mt) REVERT: C 398 MET cc_start: 0.8572 (tpt) cc_final: 0.8273 (tpt) REVERT: C 497 MET cc_start: 0.8860 (mmt) cc_final: 0.8548 (mmt) REVERT: A 241 MET cc_start: 0.8313 (tpt) cc_final: 0.7790 (tpt) REVERT: E 211 MET cc_start: 0.8204 (mtt) cc_final: 0.7955 (mtt) REVERT: E 424 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: F 368 MET cc_start: 0.8870 (mmt) cc_final: 0.8625 (mmt) REVERT: K 109 ASP cc_start: 0.7828 (t0) cc_final: 0.7566 (t0) REVERT: J 114 ILE cc_start: 0.8556 (mt) cc_final: 0.8317 (mm) outliers start: 80 outliers final: 59 residues processed: 729 average time/residue: 1.0963 time to fit residues: 1305.9278 Evaluate side-chains 692 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 631 time to evaluate : 4.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain E residue 424 MET Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 233 ASN Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 419 optimal weight: 0.7980 chunk 285 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 374 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 429 optimal weight: 0.9990 chunk 348 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 257 optimal weight: 1.9990 chunk 452 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN G 140 GLN ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 87 GLN F 267 ASN F 395 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 41255 Z= 0.277 Angle : 0.518 6.394 55909 Z= 0.271 Chirality : 0.040 0.170 6499 Planarity : 0.004 0.073 7138 Dihedral : 5.866 87.213 5846 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.22 % Favored : 96.76 % Rotamer: Outliers : 1.83 % Allowed : 11.40 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 5223 helix: 0.54 (0.11), residues: 2593 sheet: -1.65 (0.21), residues: 554 loop : -0.61 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.006 0.001 HIS F 377 PHE 0.016 0.001 PHE G 223 TYR 0.016 0.001 TYR P 60 ARG 0.004 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 736 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 657 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 48 SER cc_start: 0.8489 (m) cc_final: 0.8260 (p) REVERT: h 326 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7636 (mm-30) REVERT: G 137 MET cc_start: 0.6870 (mpp) cc_final: 0.6609 (mpp) REVERT: H 160 GLN cc_start: 0.6363 (mp10) cc_final: 0.6079 (mp10) REVERT: I 46 TYR cc_start: 0.8477 (p90) cc_final: 0.7990 (p90) REVERT: O 55 MET cc_start: 0.8101 (ttm) cc_final: 0.7861 (ttm) REVERT: P 73 LYS cc_start: 0.9103 (mtpp) cc_final: 0.8756 (ttpp) REVERT: S 79 ILE cc_start: 0.8773 (mm) cc_final: 0.8530 (pt) REVERT: S 90 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8213 (mt) REVERT: S 97 LEU cc_start: 0.8945 (mm) cc_final: 0.8694 (tp) REVERT: T 80 LEU cc_start: 0.9011 (tp) cc_final: 0.8771 (mp) REVERT: U 79 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8417 (pt) REVERT: W 32 ASN cc_start: 0.8242 (m110) cc_final: 0.7892 (m110) REVERT: W 56 CYS cc_start: 0.8874 (t) cc_final: 0.8557 (t) REVERT: B 179 ARG cc_start: 0.8166 (ptt-90) cc_final: 0.7789 (ptt90) REVERT: B 284 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: B 289 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8131 (tt0) REVERT: C 316 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8917 (tt) REVERT: C 497 MET cc_start: 0.8843 (mmt) cc_final: 0.8607 (mmt) REVERT: A 241 MET cc_start: 0.8326 (tpt) cc_final: 0.7805 (tpt) REVERT: E 211 MET cc_start: 0.8122 (mtt) cc_final: 0.7872 (mtt) REVERT: E 486 GLU cc_start: 0.7686 (tp30) cc_final: 0.7425 (tp30) REVERT: K 109 ASP cc_start: 0.7927 (t0) cc_final: 0.7678 (t0) REVERT: J 114 ILE cc_start: 0.8545 (mt) cc_final: 0.8321 (mm) outliers start: 79 outliers final: 58 residues processed: 699 average time/residue: 1.1103 time to fit residues: 1265.9594 Evaluate side-chains 691 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 628 time to evaluate : 4.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 150 GLU Chi-restraints excluded: chain M residue 164 GLU Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain T residue 85 SER Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 480 ASN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 403 ILE Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 45 GLU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 169 optimal weight: 1.9990 chunk 453 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 295 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 504 optimal weight: 0.8980 chunk 418 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 489 GLN ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 503 ASN F 395 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 41255 Z= 0.317 Angle : 0.537 7.014 55909 Z= 0.281 Chirality : 0.041 0.206 6499 Planarity : 0.004 0.093 7138 Dihedral : 6.088 88.203 5846 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.52 % Favored : 96.46 % Rotamer: Outliers : 1.97 % Allowed : 11.84 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.12), residues: 5223 helix: 0.62 (0.11), residues: 2608 sheet: -1.57 (0.21), residues: 572 loop : -0.55 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.009 0.001 HIS F 377 PHE 0.016 0.001 PHE H 57 TYR 0.017 0.002 TYR B 263 ARG 0.012 0.000 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 726 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 641 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 326 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7714 (mm-30) REVERT: I 46 TYR cc_start: 0.8497 (p90) cc_final: 0.7996 (p90) REVERT: P 73 LYS cc_start: 0.9134 (mtpp) cc_final: 0.8780 (ttpp) REVERT: R 73 LYS cc_start: 0.8408 (mtpt) cc_final: 0.8181 (mtmt) REVERT: S 79 ILE cc_start: 0.8821 (mm) cc_final: 0.8577 (pt) REVERT: S 90 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8263 (mt) REVERT: S 97 LEU cc_start: 0.8952 (mm) cc_final: 0.8732 (tp) REVERT: T 80 LEU cc_start: 0.8996 (tp) cc_final: 0.8765 (mp) REVERT: W 32 ASN cc_start: 0.8291 (m110) cc_final: 0.7954 (m110) REVERT: X 82 PHE cc_start: 0.8468 (t80) cc_final: 0.8253 (t80) REVERT: B 179 ARG cc_start: 0.8214 (ptt-90) cc_final: 0.7774 (ptt90) REVERT: B 273 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.8128 (ttp80) REVERT: B 284 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: B 289 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: C 316 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8994 (tt) REVERT: A 241 MET cc_start: 0.8333 (tpt) cc_final: 0.7842 (tpt) REVERT: E 211 MET cc_start: 0.8137 (mtt) cc_final: 0.7924 (mtt) REVERT: E 440 TYR cc_start: 0.8368 (m-80) cc_final: 0.8152 (m-80) REVERT: K 72 GLN cc_start: 0.7417 (pt0) cc_final: 0.7201 (tt0) REVERT: K 109 ASP cc_start: 0.7959 (t0) cc_final: 0.7703 (t0) REVERT: J 114 ILE cc_start: 0.8568 (mt) cc_final: 0.8344 (mm) outliers start: 85 outliers final: 65 residues processed: 686 average time/residue: 1.0600 time to fit residues: 1189.4475 Evaluate side-chains 691 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 621 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 174 ILE Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain Q residue 95 ILE Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 41 MET Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 85 SER Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 486 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 368 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 424 optimal weight: 1.9990 chunk 281 optimal weight: 1.9990 chunk 502 optimal weight: 2.9990 chunk 314 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 32 ASN U 35 ASN A 356 ASN F 395 GLN D 458 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 41255 Z= 0.383 Angle : 0.558 9.818 55909 Z= 0.292 Chirality : 0.042 0.165 6499 Planarity : 0.004 0.048 7138 Dihedral : 6.225 82.113 5846 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.34 % Rotamer: Outliers : 1.88 % Allowed : 12.47 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.12), residues: 5223 helix: 0.58 (0.11), residues: 2609 sheet: -1.49 (0.21), residues: 570 loop : -0.56 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.012 0.001 HIS F 377 PHE 0.023 0.001 PHE S 103 TYR 0.018 0.002 TYR J 52 ARG 0.005 0.001 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 715 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 634 time to evaluate : 4.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: h 326 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7585 (mm-30) REVERT: I 46 TYR cc_start: 0.8529 (p90) cc_final: 0.8036 (p90) REVERT: P 73 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8827 (ttpp) REVERT: R 73 LYS cc_start: 0.8388 (mtpt) cc_final: 0.8138 (mtmt) REVERT: S 79 ILE cc_start: 0.8858 (mm) cc_final: 0.8625 (pt) REVERT: S 90 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8269 (mt) REVERT: S 97 LEU cc_start: 0.8936 (mm) cc_final: 0.8714 (tp) REVERT: T 80 LEU cc_start: 0.9025 (tp) cc_final: 0.8779 (mp) REVERT: U 73 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7894 (mttt) REVERT: W 32 ASN cc_start: 0.8292 (m110) cc_final: 0.7959 (m110) REVERT: B 273 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.7837 (mtm110) REVERT: B 284 ASP cc_start: 0.8080 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: B 289 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: A 241 MET cc_start: 0.8371 (tpt) cc_final: 0.7901 (tpt) REVERT: A 396 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8743 (ptmt) REVERT: E 211 MET cc_start: 0.8144 (mtt) cc_final: 0.7936 (mtt) REVERT: J 96 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8315 (t160) REVERT: J 114 ILE cc_start: 0.8561 (mt) cc_final: 0.8345 (mm) outliers start: 81 outliers final: 63 residues processed: 680 average time/residue: 1.0726 time to fit residues: 1199.0369 Evaluate side-chains 669 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 600 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 32 ASN Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 59 SER Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 79 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain E residue 65 ASP Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 199 GLU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 70 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 152 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 310 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 299 optimal weight: 0.1980 chunk 151 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 319 optimal weight: 1.9990 chunk 342 optimal weight: 0.6980 chunk 248 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 394 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 234 ASN ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 ASN E 273 GLN F 63 HIS K 96 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.5253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 41255 Z= 0.190 Angle : 0.502 7.583 55909 Z= 0.260 Chirality : 0.039 0.168 6499 Planarity : 0.004 0.046 7138 Dihedral : 5.939 87.943 5846 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.06 % Favored : 96.92 % Rotamer: Outliers : 1.72 % Allowed : 13.07 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % 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: 0.00 (0.12), residues: 5223 helix: 0.78 (0.11), residues: 2602 sheet: -1.47 (0.21), residues: 562 loop : -0.43 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 10 HIS 0.006 0.001 HIS F 377 PHE 0.016 0.001 PHE F 428 TYR 0.014 0.001 TYR J 52 ARG 0.004 0.000 ARG J 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 696 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 622 time to evaluate : 4.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 ASP cc_start: 0.7540 (m-30) cc_final: 0.7253 (m-30) REVERT: h 326 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7643 (mm-30) REVERT: I 46 TYR cc_start: 0.8492 (p90) cc_final: 0.7982 (p90) REVERT: P 73 LYS cc_start: 0.9154 (mtpp) cc_final: 0.8826 (ttpp) REVERT: Q 91 PHE cc_start: 0.8044 (m-80) cc_final: 0.7695 (m-80) REVERT: R 73 LYS cc_start: 0.8338 (mtpt) cc_final: 0.8057 (mtmt) REVERT: S 79 ILE cc_start: 0.8865 (mm) cc_final: 0.8647 (pt) REVERT: S 97 LEU cc_start: 0.8905 (mm) cc_final: 0.8688 (tp) REVERT: T 80 LEU cc_start: 0.9011 (tp) cc_final: 0.8772 (mp) REVERT: U 73 LYS cc_start: 0.8413 (mtpt) cc_final: 0.7899 (mttt) REVERT: V 80 LEU cc_start: 0.8585 (tt) cc_final: 0.8348 (mt) REVERT: W 32 ASN cc_start: 0.8297 (m110) cc_final: 0.7969 (m110) REVERT: B 284 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7373 (m-30) REVERT: B 289 GLN cc_start: 0.8970 (OUTLIER) cc_final: 0.8133 (tt0) REVERT: B 327 MET cc_start: 0.9048 (mmm) cc_final: 0.8795 (mmm) REVERT: A 241 MET cc_start: 0.8328 (tpt) cc_final: 0.7635 (tpt) REVERT: A 396 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8767 (ptmt) REVERT: K 109 ASP cc_start: 0.8004 (t0) cc_final: 0.7752 (t0) REVERT: J 96 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8250 (t160) REVERT: J 114 ILE cc_start: 0.8548 (mt) cc_final: 0.8334 (mm) outliers start: 74 outliers final: 57 residues processed: 661 average time/residue: 1.0473 time to fit residues: 1125.8466 Evaluate side-chains 671 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 610 time to evaluate : 4.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 59 SER Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain S residue 90 LEU Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 284 ASP Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 103 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 456 optimal weight: 0.5980 chunk 481 optimal weight: 1.9990 chunk 438 optimal weight: 1.9990 chunk 467 optimal weight: 4.9990 chunk 480 optimal weight: 0.8980 chunk 281 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 367 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 422 optimal weight: 1.9990 chunk 442 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 501 ASN F 395 GLN L 96 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41255 Z= 0.227 Angle : 0.502 6.753 55909 Z= 0.260 Chirality : 0.039 0.162 6499 Planarity : 0.004 0.048 7138 Dihedral : 5.856 89.805 5846 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.67 % Rotamer: Outliers : 1.49 % Allowed : 13.42 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % 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: 0.11 (0.12), residues: 5223 helix: 0.87 (0.11), residues: 2604 sheet: -1.41 (0.21), residues: 561 loop : -0.37 (0.14), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.006 0.001 HIS F 377 PHE 0.015 0.001 PHE h 287 TYR 0.018 0.001 TYR Q 77 ARG 0.004 0.000 ARG D 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 693 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 629 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 ASP cc_start: 0.7510 (m-30) cc_final: 0.7224 (m-30) REVERT: h 326 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7744 (mm-30) REVERT: P 73 LYS cc_start: 0.9160 (mtpp) cc_final: 0.8828 (ttpp) REVERT: R 70 MET cc_start: 0.8743 (tpp) cc_final: 0.8384 (tpt) REVERT: R 73 LYS cc_start: 0.8326 (mtpt) cc_final: 0.7998 (mtmt) REVERT: S 79 ILE cc_start: 0.8862 (mm) cc_final: 0.8654 (pt) REVERT: S 97 LEU cc_start: 0.8913 (mm) cc_final: 0.8696 (tp) REVERT: T 80 LEU cc_start: 0.9013 (tp) cc_final: 0.8780 (mp) REVERT: U 73 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7899 (mttt) REVERT: V 80 LEU cc_start: 0.8587 (tt) cc_final: 0.8361 (mt) REVERT: W 32 ASN cc_start: 0.8314 (m110) cc_final: 0.7989 (m110) REVERT: B 179 ARG cc_start: 0.8043 (ptt-90) cc_final: 0.7706 (ptt90) REVERT: B 289 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: C 470 TYR cc_start: 0.8776 (m-10) cc_final: 0.8380 (m-10) REVERT: A 241 MET cc_start: 0.8315 (tpt) cc_final: 0.7765 (tpt) REVERT: A 396 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8735 (ptmt) REVERT: E 486 GLU cc_start: 0.7729 (tp30) cc_final: 0.7397 (tp30) REVERT: K 109 ASP cc_start: 0.8020 (t0) cc_final: 0.7773 (t0) REVERT: J 96 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8215 (t160) REVERT: J 114 ILE cc_start: 0.8540 (mt) cc_final: 0.8327 (mm) outliers start: 64 outliers final: 57 residues processed: 663 average time/residue: 1.0754 time to fit residues: 1165.2056 Evaluate side-chains 677 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 617 time to evaluate : 4.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain Q residue 90 LEU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 466 optimal weight: 0.9990 chunk 307 optimal weight: 0.6980 chunk 494 optimal weight: 0.4980 chunk 302 optimal weight: 1.9990 chunk 234 optimal weight: 0.9980 chunk 343 optimal weight: 1.9990 chunk 519 optimal weight: 4.9990 chunk 477 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 ASN C 501 ASN F 395 GLN L 96 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 41255 Z= 0.228 Angle : 0.502 6.899 55909 Z= 0.260 Chirality : 0.040 0.162 6499 Planarity : 0.004 0.056 7138 Dihedral : 5.819 89.182 5846 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.12 % Favored : 96.86 % Rotamer: Outliers : 1.51 % Allowed : 13.56 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.12), residues: 5223 helix: 0.88 (0.11), residues: 2620 sheet: -1.42 (0.21), residues: 563 loop : -0.31 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 10 HIS 0.006 0.001 HIS F 377 PHE 0.022 0.001 PHE Q 57 TYR 0.027 0.001 TYR Q 77 ARG 0.012 0.000 ARG C 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10446 Ramachandran restraints generated. 5223 Oldfield, 0 Emsley, 5223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 191 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Residue THR 174 is missing expected H atoms. Skipping. Evaluate side-chains 690 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 625 time to evaluate : 5.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 74 ASP cc_start: 0.7492 (m-30) cc_final: 0.7206 (m-30) REVERT: h 326 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7762 (mm-30) REVERT: I 46 TYR cc_start: 0.8490 (p90) cc_final: 0.7992 (p90) REVERT: P 73 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8823 (ttpp) REVERT: R 70 MET cc_start: 0.8757 (tpp) cc_final: 0.8390 (tpt) REVERT: R 73 LYS cc_start: 0.8305 (mtpt) cc_final: 0.8014 (mtmt) REVERT: S 79 ILE cc_start: 0.8851 (mm) cc_final: 0.8643 (pt) REVERT: S 97 LEU cc_start: 0.8915 (mm) cc_final: 0.8697 (tp) REVERT: T 55 MET cc_start: 0.8325 (ttm) cc_final: 0.8123 (ttt) REVERT: T 80 LEU cc_start: 0.9011 (tp) cc_final: 0.8767 (mp) REVERT: U 73 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7890 (mttt) REVERT: V 80 LEU cc_start: 0.8590 (tt) cc_final: 0.8370 (mt) REVERT: W 32 ASN cc_start: 0.8324 (m110) cc_final: 0.7995 (m110) REVERT: B 179 ARG cc_start: 0.8071 (ptt-90) cc_final: 0.7736 (ptt90) REVERT: B 289 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: C 470 TYR cc_start: 0.8813 (m-10) cc_final: 0.8441 (m-10) REVERT: A 241 MET cc_start: 0.8315 (tpt) cc_final: 0.7625 (tpt) REVERT: A 396 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8757 (ptmt) REVERT: E 486 GLU cc_start: 0.7783 (tp30) cc_final: 0.7443 (tp30) REVERT: K 109 ASP cc_start: 0.8028 (t0) cc_final: 0.7782 (t0) REVERT: J 96 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8213 (t160) REVERT: J 114 ILE cc_start: 0.8511 (mt) cc_final: 0.8305 (mm) REVERT: N 31 ASP cc_start: 0.7672 (m-30) cc_final: 0.7465 (m-30) outliers start: 65 outliers final: 58 residues processed: 660 average time/residue: 1.0840 time to fit residues: 1171.7413 Evaluate side-chains 678 residues out of total 4307 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 617 time to evaluate : 4.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 127 ARG Chi-restraints excluded: chain M residue 211 THR Chi-restraints excluded: chain M residue 250 VAL Chi-restraints excluded: chain h residue 308 HIS Chi-restraints excluded: chain c residue 83 VAL Chi-restraints excluded: chain G residue 27 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 115 ASP Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 136 HIS Chi-restraints excluded: chain H residue 143 LEU Chi-restraints excluded: chain H residue 169 GLU Chi-restraints excluded: chain O residue 41 MET Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 99 GLU Chi-restraints excluded: chain R residue 82 PHE Chi-restraints excluded: chain S residue 82 PHE Chi-restraints excluded: chain T residue 74 LEU Chi-restraints excluded: chain T residue 82 PHE Chi-restraints excluded: chain U residue 79 ILE Chi-restraints excluded: chain V residue 82 PHE Chi-restraints excluded: chain V residue 98 LEU Chi-restraints excluded: chain W residue 82 PHE Chi-restraints excluded: chain X residue 25 ILE Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 273 ARG Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 512 ASN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 376 GLN Chi-restraints excluded: chain A residue 396 LYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain E residue 212 MET Chi-restraints excluded: chain F residue 71 CYS Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 225 CYS Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 120 SER Chi-restraints excluded: chain L residue 34 GLU Chi-restraints excluded: chain L residue 111 ARG Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 103 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 521 random chunks: chunk 253 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 440 optimal weight: 0.9980 chunk 126 optimal weight: 3.9990 chunk 381 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 413 optimal weight: 1.9990 chunk 173 optimal weight: 0.0470 chunk 425 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 ASN F 395 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.085373 restraints weight = 185544.280| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.14 r_work: 0.2885 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 41255 Z= 0.246 Angle : 0.503 6.213 55909 Z= 0.261 Chirality : 0.040 0.173 6499 Planarity : 0.004 0.048 7138 Dihedral : 5.815 88.341 5846 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.48 % Favored : 96.50 % Rotamer: Outliers : 1.65 % Allowed : 13.56 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.84 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.12), residues: 5223 helix: 0.90 (0.11), residues: 2621 sheet: -1.37 (0.21), residues: 568 loop : -0.31 (0.14), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 10 HIS 0.007 0.001 HIS F 377 PHE 0.015 0.001 PHE Q 57 TYR 0.014 0.001 TYR J 52 ARG 0.009 0.000 ARG C 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22006.23 seconds wall clock time: 380 minutes 53.64 seconds (22853.64 seconds total)