Starting phenix.real_space_refine on Mon Mar 18 23:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8foy_29355/03_2024/8foy_29355.pdb" } resolution = 2.9 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= 0.003 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 528 5.16 5 C 56400 2.51 5 N 15264 2.21 5 O 17880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ASP 4": "OD1" <-> "OD2" Residue "D GLU 24": "OE1" <-> "OE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ASP 146": "OD1" <-> "OD2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 418": "NH1" <-> "NH2" Residue "D ARG 488": "NH1" <-> "NH2" Residue "A ASP 4": "OD1" <-> "OD2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ASP 146": "OD1" <-> "OD2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 488": "NH1" <-> "NH2" Residue "B ASP 4": "OD1" <-> "OD2" Residue "B GLU 24": "OE1" <-> "OE2" Residue "B TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B ASP 146": "OD1" <-> "OD2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 488": "NH1" <-> "NH2" Residue "C ASP 4": "OD1" <-> "OD2" Residue "C GLU 24": "OE1" <-> "OE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C ASP 146": "OD1" <-> "OD2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C GLU 325": "OE1" <-> "OE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 418": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "E ASP 4": "OD1" <-> "OD2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 146": "OD1" <-> "OD2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 418": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "F ASP 4": "OD1" <-> "OD2" Residue "F GLU 24": "OE1" <-> "OE2" Residue "F TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F ASP 146": "OD1" <-> "OD2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 418": "NH1" <-> "NH2" Residue "F ARG 488": "NH1" <-> "NH2" Residue "G ASP 4": "OD1" <-> "OD2" Residue "G GLU 24": "OE1" <-> "OE2" Residue "G TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G ASP 243": "OD1" <-> "OD2" Residue "G GLU 325": "OE1" <-> "OE2" Residue "G TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 418": "NH1" <-> "NH2" Residue "G ARG 488": "NH1" <-> "NH2" Residue "H ASP 4": "OD1" <-> "OD2" Residue "H GLU 24": "OE1" <-> "OE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H ASP 146": "OD1" <-> "OD2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 418": "NH1" <-> "NH2" Residue "H ARG 488": "NH1" <-> "NH2" Residue "I ASP 4": "OD1" <-> "OD2" Residue "I GLU 24": "OE1" <-> "OE2" Residue "I TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I ASP 146": "OD1" <-> "OD2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I ASP 243": "OD1" <-> "OD2" Residue "I GLU 325": "OE1" <-> "OE2" Residue "I TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 418": "NH1" <-> "NH2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "J ASP 4": "OD1" <-> "OD2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J ASP 146": "OD1" <-> "OD2" Residue "J GLU 215": "OE1" <-> "OE2" Residue "J ASP 243": "OD1" <-> "OD2" Residue "J GLU 325": "OE1" <-> "OE2" Residue "J TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 418": "NH1" <-> "NH2" Residue "J ARG 488": "NH1" <-> "NH2" Residue "K ASP 4": "OD1" <-> "OD2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 134": "OD1" <-> "OD2" Residue "K ASP 146": "OD1" <-> "OD2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 418": "NH1" <-> "NH2" Residue "K ARG 488": "NH1" <-> "NH2" Residue "L ASP 4": "OD1" <-> "OD2" Residue "L GLU 24": "OE1" <-> "OE2" Residue "L TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L ASP 146": "OD1" <-> "OD2" Residue "L GLU 215": "OE1" <-> "OE2" Residue "L ASP 243": "OD1" <-> "OD2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 418": "NH1" <-> "NH2" Residue "L ARG 488": "NH1" <-> "NH2" Residue "M ASP 4": "OD1" <-> "OD2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 134": "OD1" <-> "OD2" Residue "M ASP 146": "OD1" <-> "OD2" Residue "M GLU 215": "OE1" <-> "OE2" Residue "M ASP 243": "OD1" <-> "OD2" Residue "M GLU 325": "OE1" <-> "OE2" Residue "M TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 418": "NH1" <-> "NH2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "N ASP 4": "OD1" <-> "OD2" Residue "N GLU 24": "OE1" <-> "OE2" Residue "N TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 134": "OD1" <-> "OD2" Residue "N ASP 146": "OD1" <-> "OD2" Residue "N GLU 215": "OE1" <-> "OE2" Residue "N ASP 243": "OD1" <-> "OD2" Residue "N GLU 325": "OE1" <-> "OE2" Residue "N TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 418": "NH1" <-> "NH2" Residue "N ARG 488": "NH1" <-> "NH2" Residue "O ASP 4": "OD1" <-> "OD2" Residue "O GLU 24": "OE1" <-> "OE2" Residue "O TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 134": "OD1" <-> "OD2" Residue "O ASP 146": "OD1" <-> "OD2" Residue "O GLU 215": "OE1" <-> "OE2" Residue "O ASP 243": "OD1" <-> "OD2" Residue "O GLU 325": "OE1" <-> "OE2" Residue "O TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 418": "NH1" <-> "NH2" Residue "O ARG 488": "NH1" <-> "NH2" Residue "P ASP 4": "OD1" <-> "OD2" Residue "P GLU 24": "OE1" <-> "OE2" Residue "P TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 134": "OD1" <-> "OD2" Residue "P ASP 146": "OD1" <-> "OD2" Residue "P GLU 215": "OE1" <-> "OE2" Residue "P ASP 243": "OD1" <-> "OD2" Residue "P GLU 325": "OE1" <-> "OE2" Residue "P TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 418": "NH1" <-> "NH2" Residue "P ARG 488": "NH1" <-> "NH2" Residue "Q ASP 4": "OD1" <-> "OD2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 134": "OD1" <-> "OD2" Residue "Q ASP 146": "OD1" <-> "OD2" Residue "Q GLU 215": "OE1" <-> "OE2" Residue "Q ASP 243": "OD1" <-> "OD2" Residue "Q GLU 325": "OE1" <-> "OE2" Residue "Q TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 418": "NH1" <-> "NH2" Residue "Q ARG 488": "NH1" <-> "NH2" Residue "R ASP 4": "OD1" <-> "OD2" Residue "R GLU 24": "OE1" <-> "OE2" Residue "R TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 134": "OD1" <-> "OD2" Residue "R ASP 146": "OD1" <-> "OD2" Residue "R GLU 215": "OE1" <-> "OE2" Residue "R ASP 243": "OD1" <-> "OD2" Residue "R GLU 325": "OE1" <-> "OE2" Residue "R TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 418": "NH1" <-> "NH2" Residue "R ARG 488": "NH1" <-> "NH2" Residue "S ASP 4": "OD1" <-> "OD2" Residue "S GLU 24": "OE1" <-> "OE2" Residue "S TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 134": "OD1" <-> "OD2" Residue "S ASP 146": "OD1" <-> "OD2" Residue "S GLU 215": "OE1" <-> "OE2" Residue "S ASP 243": "OD1" <-> "OD2" Residue "S GLU 325": "OE1" <-> "OE2" Residue "S TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 418": "NH1" <-> "NH2" Residue "S ARG 488": "NH1" <-> "NH2" Residue "T ASP 4": "OD1" <-> "OD2" Residue "T GLU 24": "OE1" <-> "OE2" Residue "T TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 134": "OD1" <-> "OD2" Residue "T ASP 146": "OD1" <-> "OD2" Residue "T GLU 215": "OE1" <-> "OE2" Residue "T ASP 243": "OD1" <-> "OD2" Residue "T GLU 325": "OE1" <-> "OE2" Residue "T TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 418": "NH1" <-> "NH2" Residue "T ARG 488": "NH1" <-> "NH2" Residue "U ASP 4": "OD1" <-> "OD2" Residue "U GLU 24": "OE1" <-> "OE2" Residue "U TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 134": "OD1" <-> "OD2" Residue "U ASP 146": "OD1" <-> "OD2" Residue "U GLU 215": "OE1" <-> "OE2" Residue "U ASP 243": "OD1" <-> "OD2" Residue "U GLU 325": "OE1" <-> "OE2" Residue "U TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 418": "NH1" <-> "NH2" Residue "U ARG 488": "NH1" <-> "NH2" Residue "V ASP 4": "OD1" <-> "OD2" Residue "V GLU 24": "OE1" <-> "OE2" Residue "V TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 134": "OD1" <-> "OD2" Residue "V ASP 146": "OD1" <-> "OD2" Residue "V GLU 215": "OE1" <-> "OE2" Residue "V ASP 243": "OD1" <-> "OD2" Residue "V GLU 325": "OE1" <-> "OE2" Residue "V TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 418": "NH1" <-> "NH2" Residue "V ARG 488": "NH1" <-> "NH2" Residue "W ASP 4": "OD1" <-> "OD2" Residue "W GLU 24": "OE1" <-> "OE2" Residue "W TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 134": "OD1" <-> "OD2" Residue "W ASP 146": "OD1" <-> "OD2" Residue "W GLU 215": "OE1" <-> "OE2" Residue "W ASP 243": "OD1" <-> "OD2" Residue "W GLU 325": "OE1" <-> "OE2" Residue "W TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 418": "NH1" <-> "NH2" Residue "W ARG 488": "NH1" <-> "NH2" Residue "X ASP 4": "OD1" <-> "OD2" Residue "X GLU 24": "OE1" <-> "OE2" Residue "X TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 134": "OD1" <-> "OD2" Residue "X ASP 146": "OD1" <-> "OD2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X ASP 243": "OD1" <-> "OD2" Residue "X GLU 325": "OE1" <-> "OE2" Residue "X TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 418": "NH1" <-> "NH2" Residue "X ARG 488": "NH1" <-> "NH2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90072 Number of models: 1 Model: "" Number of chains: 24 Chain: "D" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "A" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "B" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "C" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "E" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "F" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "G" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "H" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "I" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "J" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "K" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "L" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "M" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "N" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "O" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "P" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "Q" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "R" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "S" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "T" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "U" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "V" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "W" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Chain: "X" Number of atoms: 3753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3753 Classifications: {'peptide': 500} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 474} Time building chain proxies: 37.63, per 1000 atoms: 0.42 Number of scatterers: 90072 At special positions: 0 Unit cell: (234.52, 234.52, 174.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 528 16.00 O 17880 8.00 N 15264 7.00 C 56400 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=144, symmetry=0 Simple disulfide: pdb=" SG CYS D 14 " - pdb=" SG CYS C 244 " distance=2.88 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 73 " - pdb=" SG CYS D 320 " distance=2.04 Simple disulfide: pdb=" SG CYS D 75 " - pdb=" SG CYS D 300 " distance=2.04 Simple disulfide: pdb=" SG CYS D 216 " - pdb=" SG CYS V 327 " distance=0.56 Simple disulfide: pdb=" SG CYS D 217 " - pdb=" SG CYS D 249 " distance=2.03 Simple disulfide: pdb=" SG CYS D 244 " - pdb=" SG CYS B 14 " distance=2.88 Simple disulfide: pdb=" SG CYS D 327 " - pdb=" SG CYS H 216 " distance=0.56 Simple disulfide: pdb=" SG CYS D 467 " - pdb=" SG CYS Q 501 " distance=0.97 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 244 " distance=2.88 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS A 73 " - pdb=" SG CYS A 320 " distance=2.04 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 300 " distance=2.04 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 249 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS F 216 " distance=0.56 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS K 467 " distance=0.97 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 73 " - pdb=" SG CYS B 320 " distance=2.04 Simple disulfide: pdb=" SG CYS B 75 " - pdb=" SG CYS B 300 " distance=2.04 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS U 327 " distance=0.56 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 249 " distance=2.03 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS G 216 " distance=0.56 Simple disulfide: pdb=" SG CYS B 501 " - pdb=" SG CYS L 467 " distance=0.97 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 73 " - pdb=" SG CYS C 320 " distance=2.04 Simple disulfide: pdb=" SG CYS C 75 " - pdb=" SG CYS C 300 " distance=2.04 Simple disulfide: pdb=" SG CYS C 216 " - pdb=" SG CYS W 327 " distance=0.56 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS R 501 " distance=0.97 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 244 " distance=2.88 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 303 " distance=2.03 Simple disulfide: pdb=" SG CYS E 73 " - pdb=" SG CYS E 320 " distance=2.04 Simple disulfide: pdb=" SG CYS E 75 " - pdb=" SG CYS E 300 " distance=2.04 Simple disulfide: pdb=" SG CYS E 217 " - pdb=" SG CYS E 249 " distance=2.03 Simple disulfide: pdb=" SG CYS E 327 " - pdb=" SG CYS J 216 " distance=0.56 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS O 467 " distance=0.97 Simple disulfide: pdb=" SG CYS F 14 " - pdb=" SG CYS G 244 " distance=2.88 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 303 " distance=2.03 Simple disulfide: pdb=" SG CYS F 73 " - pdb=" SG CYS F 320 " distance=2.04 Simple disulfide: pdb=" SG CYS F 75 " - pdb=" SG CYS F 300 " distance=2.04 Simple disulfide: pdb=" SG CYS F 217 " - pdb=" SG CYS F 249 " distance=2.03 Simple disulfide: pdb=" SG CYS F 327 " - pdb=" SG CYS K 216 " distance=0.56 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS P 467 " distance=0.97 Simple disulfide: pdb=" SG CYS G 14 " - pdb=" SG CYS H 244 " distance=2.88 Simple disulfide: pdb=" SG CYS G 26 " - pdb=" SG CYS G 303 " distance=2.03 Simple disulfide: pdb=" SG CYS G 73 " - pdb=" SG CYS G 320 " distance=2.04 Simple disulfide: pdb=" SG CYS G 75 " - pdb=" SG CYS G 300 " distance=2.04 Simple disulfide: pdb=" SG CYS G 217 " - pdb=" SG CYS G 249 " distance=2.03 Simple disulfide: pdb=" SG CYS G 327 " - pdb=" SG CYS L 216 " distance=0.56 Simple disulfide: pdb=" SG CYS G 467 " - pdb=" SG CYS U 501 " distance=0.97 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 303 " distance=2.03 Simple disulfide: pdb=" SG CYS H 73 " - pdb=" SG CYS H 320 " distance=2.04 Simple disulfide: pdb=" SG CYS H 75 " - pdb=" SG CYS H 300 " distance=2.04 Simple disulfide: pdb=" SG CYS H 217 " - pdb=" SG CYS H 249 " distance=2.03 Simple disulfide: pdb=" SG CYS H 467 " - pdb=" SG CYS V 501 " distance=0.97 Simple disulfide: pdb=" SG CYS I 14 " - pdb=" SG CYS J 244 " distance=2.88 Simple disulfide: pdb=" SG CYS I 26 " - pdb=" SG CYS I 303 " distance=2.03 Simple disulfide: pdb=" SG CYS I 73 " - pdb=" SG CYS I 320 " distance=2.03 Simple disulfide: pdb=" SG CYS I 75 " - pdb=" SG CYS I 300 " distance=2.04 Simple disulfide: pdb=" SG CYS I 217 " - pdb=" SG CYS I 249 " distance=2.03 Simple disulfide: pdb=" SG CYS I 327 " - pdb=" SG CYS N 216 " distance=0.56 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS S 467 " distance=0.97 Simple disulfide: pdb=" SG CYS J 14 " - pdb=" SG CYS K 244 " distance=2.88 Simple disulfide: pdb=" SG CYS J 26 " - pdb=" SG CYS J 303 " distance=2.03 Simple disulfide: pdb=" SG CYS J 73 " - pdb=" SG CYS J 320 " distance=2.04 Simple disulfide: pdb=" SG CYS J 75 " - pdb=" SG CYS J 300 " distance=2.04 Simple disulfide: pdb=" SG CYS J 217 " - pdb=" SG CYS J 249 " distance=2.03 Simple disulfide: pdb=" SG CYS J 327 " - pdb=" SG CYS O 216 " distance=0.56 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS T 467 " distance=0.97 Simple disulfide: pdb=" SG CYS K 14 " - pdb=" SG CYS L 244 " distance=2.88 Simple disulfide: pdb=" SG CYS K 26 " - pdb=" SG CYS K 303 " distance=2.03 Simple disulfide: pdb=" SG CYS K 73 " - pdb=" SG CYS K 320 " distance=2.04 Simple disulfide: pdb=" SG CYS K 75 " - pdb=" SG CYS K 300 " distance=2.04 Simple disulfide: pdb=" SG CYS K 217 " - pdb=" SG CYS K 249 " distance=2.03 Simple disulfide: pdb=" SG CYS K 327 " - pdb=" SG CYS P 216 " distance=0.56 Simple disulfide: pdb=" SG CYS L 26 " - pdb=" SG CYS L 303 " distance=2.03 Simple disulfide: pdb=" SG CYS L 73 " - pdb=" SG CYS L 320 " distance=2.04 Simple disulfide: pdb=" SG CYS L 75 " - pdb=" SG CYS L 300 " distance=2.04 Simple disulfide: pdb=" SG CYS L 217 " - pdb=" SG CYS L 249 " distance=2.03 Simple disulfide: pdb=" SG CYS M 14 " - pdb=" SG CYS N 244 " distance=2.88 Simple disulfide: pdb=" SG CYS M 26 " - pdb=" SG CYS M 303 " distance=2.03 Simple disulfide: pdb=" SG CYS M 73 " - pdb=" SG CYS M 320 " distance=2.04 Simple disulfide: pdb=" SG CYS M 75 " - pdb=" SG CYS M 300 " distance=2.04 Simple disulfide: pdb=" SG CYS M 217 " - pdb=" SG CYS M 249 " distance=2.03 Simple disulfide: pdb=" SG CYS M 327 " - pdb=" SG CYS R 216 " distance=0.56 Simple disulfide: pdb=" SG CYS M 501 " - pdb=" SG CYS W 467 " distance=0.97 Simple disulfide: pdb=" SG CYS N 14 " - pdb=" SG CYS O 244 " distance=2.88 Simple disulfide: pdb=" SG CYS N 26 " - pdb=" SG CYS N 303 " distance=2.03 Simple disulfide: pdb=" SG CYS N 73 " - pdb=" SG CYS N 320 " distance=2.04 Simple disulfide: pdb=" SG CYS N 75 " - pdb=" SG CYS N 300 " distance=2.04 Simple disulfide: pdb=" SG CYS N 217 " - pdb=" SG CYS N 249 " distance=2.03 Simple disulfide: pdb=" SG CYS N 327 " - pdb=" SG CYS S 216 " distance=0.56 Simple disulfide: pdb=" SG CYS N 501 " - pdb=" SG CYS X 467 " distance=0.97 Simple disulfide: pdb=" SG CYS O 14 " - pdb=" SG CYS P 244 " distance=2.88 Simple disulfide: pdb=" SG CYS O 26 " - pdb=" SG CYS O 303 " distance=2.03 Simple disulfide: pdb=" SG CYS O 73 " - pdb=" SG CYS O 320 " distance=2.04 Simple disulfide: pdb=" SG CYS O 75 " - pdb=" SG CYS O 300 " distance=2.04 Simple disulfide: pdb=" SG CYS O 217 " - pdb=" SG CYS O 249 " distance=2.03 Simple disulfide: pdb=" SG CYS O 327 " - pdb=" SG CYS T 216 " distance=0.56 Simple disulfide: pdb=" SG CYS P 26 " - pdb=" SG CYS P 303 " distance=2.03 Simple disulfide: pdb=" SG CYS P 73 " - pdb=" SG CYS P 320 " distance=2.04 Simple disulfide: pdb=" SG CYS P 75 " - pdb=" SG CYS P 300 " distance=2.04 Simple disulfide: pdb=" SG CYS P 217 " - pdb=" SG CYS P 249 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 14 " - pdb=" SG CYS R 244 " distance=2.88 Simple disulfide: pdb=" SG CYS Q 26 " - pdb=" SG CYS Q 303 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 73 " - pdb=" SG CYS Q 320 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 75 " - pdb=" SG CYS Q 300 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 217 " - pdb=" SG CYS Q 249 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 327 " - pdb=" SG CYS V 216 " distance=0.56 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS S 244 " distance=2.88 Simple disulfide: pdb=" SG CYS R 26 " - pdb=" SG CYS R 303 " distance=2.03 Simple disulfide: pdb=" SG CYS R 73 " - pdb=" SG CYS R 320 " distance=2.03 Simple disulfide: pdb=" SG CYS R 75 " - pdb=" SG CYS R 300 " distance=2.04 Simple disulfide: pdb=" SG CYS R 217 " - pdb=" SG CYS R 249 " distance=2.03 Simple disulfide: pdb=" SG CYS R 327 " - pdb=" SG CYS W 216 " distance=0.56 Simple disulfide: pdb=" SG CYS S 14 " - pdb=" SG CYS T 244 " distance=2.88 Simple disulfide: pdb=" SG CYS S 26 " - pdb=" SG CYS S 303 " distance=2.03 Simple disulfide: pdb=" SG CYS S 73 " - pdb=" SG CYS S 320 " distance=2.04 Simple disulfide: pdb=" SG CYS S 75 " - pdb=" SG CYS S 300 " distance=2.04 Simple disulfide: pdb=" SG CYS S 217 " - pdb=" SG CYS S 249 " distance=2.03 Simple disulfide: pdb=" SG CYS S 327 " - pdb=" SG CYS X 216 " distance=0.56 Simple disulfide: pdb=" SG CYS T 26 " - pdb=" SG CYS T 303 " distance=2.03 Simple disulfide: pdb=" SG CYS T 73 " - pdb=" SG CYS T 320 " distance=2.04 Simple disulfide: pdb=" SG CYS T 75 " - pdb=" SG CYS T 300 " distance=2.04 Simple disulfide: pdb=" SG CYS T 217 " - pdb=" SG CYS T 249 " distance=2.03 Simple disulfide: pdb=" SG CYS U 14 " - pdb=" SG CYS V 244 " distance=2.88 Simple disulfide: pdb=" SG CYS U 26 " - pdb=" SG CYS U 303 " distance=2.03 Simple disulfide: pdb=" SG CYS U 73 " - pdb=" SG CYS U 320 " distance=2.04 Simple disulfide: pdb=" SG CYS U 75 " - pdb=" SG CYS U 300 " distance=2.04 Simple disulfide: pdb=" SG CYS U 217 " - pdb=" SG CYS U 249 " distance=2.03 Simple disulfide: pdb=" SG CYS V 14 " - pdb=" SG CYS W 244 " distance=2.88 Simple disulfide: pdb=" SG CYS V 26 " - pdb=" SG CYS V 303 " distance=2.03 Simple disulfide: pdb=" SG CYS V 73 " - pdb=" SG CYS V 320 " distance=2.03 Simple disulfide: pdb=" SG CYS V 75 " - pdb=" SG CYS V 300 " distance=2.04 Simple disulfide: pdb=" SG CYS V 217 " - pdb=" SG CYS V 249 " distance=2.03 Simple disulfide: pdb=" SG CYS W 14 " - pdb=" SG CYS X 244 " distance=2.88 Simple disulfide: pdb=" SG CYS W 26 " - pdb=" SG CYS W 303 " distance=2.03 Simple disulfide: pdb=" SG CYS W 73 " - pdb=" SG CYS W 320 " distance=2.03 Simple disulfide: pdb=" SG CYS W 75 " - pdb=" SG CYS W 300 " distance=2.04 Simple disulfide: pdb=" SG CYS W 217 " - pdb=" SG CYS W 249 " distance=2.03 Simple disulfide: pdb=" SG CYS X 26 " - pdb=" SG CYS X 303 " distance=2.03 Simple disulfide: pdb=" SG CYS X 73 " - pdb=" SG CYS X 320 " distance=2.04 Simple disulfide: pdb=" SG CYS X 75 " - pdb=" SG CYS X 300 " distance=2.04 Simple disulfide: pdb=" SG CYS X 217 " - pdb=" SG CYS X 249 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.96 Conformation dependent library (CDL) restraints added in 13.1 seconds 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21936 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 144 sheets defined 30.6% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.84 Creating SS restraints... Processing helix chain 'D' and resid 53 through 59 Processing helix chain 'D' and resid 62 through 75 Processing helix chain 'D' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA D 121 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 143 Processing helix chain 'D' and resid 166 through 170 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 227 through 242 Processing helix chain 'D' and resid 260 through 267 Processing helix chain 'D' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE D 315 " --> pdb=" O GLN D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 342 Processing helix chain 'D' and resid 384 through 403 Processing helix chain 'D' and resid 404 through 406 No H-bonds generated for 'chain 'D' and resid 404 through 406' Processing helix chain 'D' and resid 425 through 440 Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA A 121 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 227 through 242 Processing helix chain 'A' and resid 260 through 267 Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 384 through 403 Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 425 through 440 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 62 through 75 Processing helix chain 'B' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA B 121 " --> pdb=" O ALA B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 166 through 170 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 227 through 242 Processing helix chain 'B' and resid 260 through 267 Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE B 315 " --> pdb=" O GLN B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 384 through 403 Processing helix chain 'B' and resid 404 through 406 No H-bonds generated for 'chain 'B' and resid 404 through 406' Processing helix chain 'B' and resid 425 through 440 Processing helix chain 'B' and resid 450 through 454 Processing helix chain 'C' and resid 53 through 59 Processing helix chain 'C' and resid 62 through 75 Processing helix chain 'C' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA C 121 " --> pdb=" O ALA C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 227 through 242 Processing helix chain 'C' and resid 260 through 267 Processing helix chain 'C' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 384 through 403 Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 425 through 440 Processing helix chain 'C' and resid 450 through 454 Processing helix chain 'E' and resid 53 through 59 Processing helix chain 'E' and resid 62 through 75 Processing helix chain 'E' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA E 121 " --> pdb=" O ALA E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 143 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 227 through 242 Processing helix chain 'E' and resid 260 through 267 Processing helix chain 'E' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE E 315 " --> pdb=" O GLN E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 342 Processing helix chain 'E' and resid 384 through 403 Processing helix chain 'E' and resid 404 through 406 No H-bonds generated for 'chain 'E' and resid 404 through 406' Processing helix chain 'E' and resid 425 through 440 Processing helix chain 'E' and resid 450 through 454 Processing helix chain 'F' and resid 53 through 59 Processing helix chain 'F' and resid 62 through 75 Processing helix chain 'F' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA F 121 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 143 Processing helix chain 'F' and resid 166 through 170 Processing helix chain 'F' and resid 208 through 213 Processing helix chain 'F' and resid 227 through 242 Processing helix chain 'F' and resid 260 through 267 Processing helix chain 'F' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 removed outlier: 3.954A pdb=" N PHE F 315 " --> pdb=" O GLN F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 342 Processing helix chain 'F' and resid 384 through 403 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 425 through 440 Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'G' and resid 53 through 59 Processing helix chain 'G' and resid 62 through 75 Processing helix chain 'G' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA G 121 " --> pdb=" O ALA G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 143 Processing helix chain 'G' and resid 166 through 170 Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 227 through 242 Processing helix chain 'G' and resid 260 through 267 Processing helix chain 'G' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR G 290 " --> pdb=" O LEU G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE G 315 " --> pdb=" O GLN G 311 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 342 Processing helix chain 'G' and resid 384 through 403 Processing helix chain 'G' and resid 404 through 406 No H-bonds generated for 'chain 'G' and resid 404 through 406' Processing helix chain 'G' and resid 425 through 440 Processing helix chain 'G' and resid 450 through 454 Processing helix chain 'H' and resid 53 through 59 Processing helix chain 'H' and resid 62 through 75 Processing helix chain 'H' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA H 121 " --> pdb=" O ALA H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 143 Processing helix chain 'H' and resid 166 through 170 Processing helix chain 'H' and resid 208 through 213 Processing helix chain 'H' and resid 227 through 242 Processing helix chain 'H' and resid 260 through 267 Processing helix chain 'H' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR H 290 " --> pdb=" O LEU H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE H 315 " --> pdb=" O GLN H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 342 Processing helix chain 'H' and resid 384 through 403 Processing helix chain 'H' and resid 404 through 406 No H-bonds generated for 'chain 'H' and resid 404 through 406' Processing helix chain 'H' and resid 425 through 440 Processing helix chain 'H' and resid 450 through 454 Processing helix chain 'I' and resid 53 through 59 Processing helix chain 'I' and resid 62 through 75 Processing helix chain 'I' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA I 121 " --> pdb=" O ALA I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 143 Processing helix chain 'I' and resid 166 through 170 Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 227 through 242 Processing helix chain 'I' and resid 260 through 267 Processing helix chain 'I' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR I 290 " --> pdb=" O LEU I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE I 315 " --> pdb=" O GLN I 311 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 342 Processing helix chain 'I' and resid 384 through 403 Processing helix chain 'I' and resid 404 through 406 No H-bonds generated for 'chain 'I' and resid 404 through 406' Processing helix chain 'I' and resid 425 through 440 Processing helix chain 'I' and resid 450 through 454 Processing helix chain 'J' and resid 53 through 59 Processing helix chain 'J' and resid 62 through 75 Processing helix chain 'J' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA J 121 " --> pdb=" O ALA J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 143 Processing helix chain 'J' and resid 166 through 170 Processing helix chain 'J' and resid 208 through 213 Processing helix chain 'J' and resid 227 through 242 Processing helix chain 'J' and resid 260 through 267 Processing helix chain 'J' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR J 290 " --> pdb=" O LEU J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE J 315 " --> pdb=" O GLN J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 342 Processing helix chain 'J' and resid 384 through 403 Processing helix chain 'J' and resid 404 through 406 No H-bonds generated for 'chain 'J' and resid 404 through 406' Processing helix chain 'J' and resid 425 through 440 Processing helix chain 'J' and resid 450 through 454 Processing helix chain 'K' and resid 53 through 59 Processing helix chain 'K' and resid 62 through 75 Processing helix chain 'K' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA K 121 " --> pdb=" O ALA K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 143 Processing helix chain 'K' and resid 166 through 170 Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 227 through 242 Processing helix chain 'K' and resid 260 through 267 Processing helix chain 'K' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR K 290 " --> pdb=" O LEU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 311 through 316 removed outlier: 3.954A pdb=" N PHE K 315 " --> pdb=" O GLN K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 342 Processing helix chain 'K' and resid 384 through 403 Processing helix chain 'K' and resid 404 through 406 No H-bonds generated for 'chain 'K' and resid 404 through 406' Processing helix chain 'K' and resid 425 through 440 Processing helix chain 'K' and resid 450 through 454 Processing helix chain 'L' and resid 53 through 59 Processing helix chain 'L' and resid 62 through 75 Processing helix chain 'L' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA L 121 " --> pdb=" O ALA L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 143 Processing helix chain 'L' and resid 166 through 170 Processing helix chain 'L' and resid 208 through 213 Processing helix chain 'L' and resid 227 through 242 Processing helix chain 'L' and resid 260 through 267 Processing helix chain 'L' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR L 290 " --> pdb=" O LEU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE L 315 " --> pdb=" O GLN L 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 342 Processing helix chain 'L' and resid 384 through 403 Processing helix chain 'L' and resid 404 through 406 No H-bonds generated for 'chain 'L' and resid 404 through 406' Processing helix chain 'L' and resid 425 through 440 Processing helix chain 'L' and resid 450 through 454 Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 62 through 75 Processing helix chain 'M' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA M 121 " --> pdb=" O ALA M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 131 through 143 Processing helix chain 'M' and resid 166 through 170 Processing helix chain 'M' and resid 208 through 213 Processing helix chain 'M' and resid 227 through 242 Processing helix chain 'M' and resid 260 through 267 Processing helix chain 'M' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR M 290 " --> pdb=" O LEU M 286 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 316 removed outlier: 3.954A pdb=" N PHE M 315 " --> pdb=" O GLN M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 342 Processing helix chain 'M' and resid 384 through 403 Processing helix chain 'M' and resid 404 through 406 No H-bonds generated for 'chain 'M' and resid 404 through 406' Processing helix chain 'M' and resid 425 through 440 Processing helix chain 'M' and resid 450 through 454 Processing helix chain 'N' and resid 53 through 59 Processing helix chain 'N' and resid 62 through 75 Processing helix chain 'N' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA N 121 " --> pdb=" O ALA N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 131 through 143 Processing helix chain 'N' and resid 166 through 170 Processing helix chain 'N' and resid 208 through 213 Processing helix chain 'N' and resid 227 through 242 Processing helix chain 'N' and resid 260 through 267 Processing helix chain 'N' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR N 290 " --> pdb=" O LEU N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE N 315 " --> pdb=" O GLN N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 342 Processing helix chain 'N' and resid 384 through 403 Processing helix chain 'N' and resid 404 through 406 No H-bonds generated for 'chain 'N' and resid 404 through 406' Processing helix chain 'N' and resid 425 through 440 Processing helix chain 'N' and resid 450 through 454 Processing helix chain 'O' and resid 53 through 59 Processing helix chain 'O' and resid 62 through 75 Processing helix chain 'O' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA O 121 " --> pdb=" O ALA O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 143 Processing helix chain 'O' and resid 166 through 170 Processing helix chain 'O' and resid 208 through 213 Processing helix chain 'O' and resid 227 through 242 Processing helix chain 'O' and resid 260 through 267 Processing helix chain 'O' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR O 290 " --> pdb=" O LEU O 286 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE O 315 " --> pdb=" O GLN O 311 " (cutoff:3.500A) Processing helix chain 'O' and resid 332 through 342 Processing helix chain 'O' and resid 384 through 403 Processing helix chain 'O' and resid 404 through 406 No H-bonds generated for 'chain 'O' and resid 404 through 406' Processing helix chain 'O' and resid 425 through 440 Processing helix chain 'O' and resid 450 through 454 Processing helix chain 'P' and resid 53 through 59 Processing helix chain 'P' and resid 62 through 75 Processing helix chain 'P' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA P 121 " --> pdb=" O ALA P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 143 Processing helix chain 'P' and resid 166 through 170 Processing helix chain 'P' and resid 208 through 213 Processing helix chain 'P' and resid 227 through 242 Processing helix chain 'P' and resid 260 through 267 Processing helix chain 'P' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR P 290 " --> pdb=" O LEU P 286 " (cutoff:3.500A) Processing helix chain 'P' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE P 315 " --> pdb=" O GLN P 311 " (cutoff:3.500A) Processing helix chain 'P' and resid 332 through 342 Processing helix chain 'P' and resid 384 through 403 Processing helix chain 'P' and resid 404 through 406 No H-bonds generated for 'chain 'P' and resid 404 through 406' Processing helix chain 'P' and resid 425 through 440 Processing helix chain 'P' and resid 450 through 454 Processing helix chain 'Q' and resid 53 through 59 Processing helix chain 'Q' and resid 62 through 75 Processing helix chain 'Q' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA Q 121 " --> pdb=" O ALA Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 131 through 143 Processing helix chain 'Q' and resid 166 through 170 Processing helix chain 'Q' and resid 208 through 213 Processing helix chain 'Q' and resid 227 through 242 Processing helix chain 'Q' and resid 260 through 267 Processing helix chain 'Q' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR Q 290 " --> pdb=" O LEU Q 286 " (cutoff:3.500A) Processing helix chain 'Q' and resid 311 through 316 removed outlier: 3.954A pdb=" N PHE Q 315 " --> pdb=" O GLN Q 311 " (cutoff:3.500A) Processing helix chain 'Q' and resid 332 through 342 Processing helix chain 'Q' and resid 384 through 403 Processing helix chain 'Q' and resid 404 through 406 No H-bonds generated for 'chain 'Q' and resid 404 through 406' Processing helix chain 'Q' and resid 425 through 440 Processing helix chain 'Q' and resid 450 through 454 Processing helix chain 'R' and resid 53 through 59 Processing helix chain 'R' and resid 62 through 75 Processing helix chain 'R' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA R 121 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 143 Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 208 through 213 Processing helix chain 'R' and resid 227 through 242 Processing helix chain 'R' and resid 260 through 267 Processing helix chain 'R' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE R 315 " --> pdb=" O GLN R 311 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 342 Processing helix chain 'R' and resid 384 through 403 Processing helix chain 'R' and resid 404 through 406 No H-bonds generated for 'chain 'R' and resid 404 through 406' Processing helix chain 'R' and resid 425 through 440 Processing helix chain 'R' and resid 450 through 454 Processing helix chain 'S' and resid 53 through 59 Processing helix chain 'S' and resid 62 through 75 Processing helix chain 'S' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA S 121 " --> pdb=" O ALA S 118 " (cutoff:3.500A) Processing helix chain 'S' and resid 131 through 143 Processing helix chain 'S' and resid 166 through 170 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 227 through 242 Processing helix chain 'S' and resid 260 through 267 Processing helix chain 'S' and resid 286 through 303 removed outlier: 3.675A pdb=" N THR S 290 " --> pdb=" O LEU S 286 " (cutoff:3.500A) Processing helix chain 'S' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE S 315 " --> pdb=" O GLN S 311 " (cutoff:3.500A) Processing helix chain 'S' and resid 332 through 342 Processing helix chain 'S' and resid 384 through 403 Processing helix chain 'S' and resid 404 through 406 No H-bonds generated for 'chain 'S' and resid 404 through 406' Processing helix chain 'S' and resid 425 through 440 Processing helix chain 'S' and resid 450 through 454 Processing helix chain 'T' and resid 53 through 59 Processing helix chain 'T' and resid 62 through 75 Processing helix chain 'T' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA T 121 " --> pdb=" O ALA T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 143 Processing helix chain 'T' and resid 166 through 170 Processing helix chain 'T' and resid 208 through 213 Processing helix chain 'T' and resid 227 through 242 Processing helix chain 'T' and resid 260 through 267 Processing helix chain 'T' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR T 290 " --> pdb=" O LEU T 286 " (cutoff:3.500A) Processing helix chain 'T' and resid 311 through 316 removed outlier: 3.954A pdb=" N PHE T 315 " --> pdb=" O GLN T 311 " (cutoff:3.500A) Processing helix chain 'T' and resid 332 through 342 Processing helix chain 'T' and resid 384 through 403 Processing helix chain 'T' and resid 404 through 406 No H-bonds generated for 'chain 'T' and resid 404 through 406' Processing helix chain 'T' and resid 425 through 440 Processing helix chain 'T' and resid 450 through 454 Processing helix chain 'U' and resid 53 through 59 Processing helix chain 'U' and resid 62 through 75 Processing helix chain 'U' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA U 121 " --> pdb=" O ALA U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 143 Processing helix chain 'U' and resid 166 through 170 Processing helix chain 'U' and resid 208 through 213 Processing helix chain 'U' and resid 227 through 242 Processing helix chain 'U' and resid 260 through 267 Processing helix chain 'U' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR U 290 " --> pdb=" O LEU U 286 " (cutoff:3.500A) Processing helix chain 'U' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE U 315 " --> pdb=" O GLN U 311 " (cutoff:3.500A) Processing helix chain 'U' and resid 332 through 342 Processing helix chain 'U' and resid 384 through 403 Processing helix chain 'U' and resid 404 through 406 No H-bonds generated for 'chain 'U' and resid 404 through 406' Processing helix chain 'U' and resid 425 through 440 Processing helix chain 'U' and resid 450 through 454 Processing helix chain 'V' and resid 53 through 59 Processing helix chain 'V' and resid 62 through 75 Processing helix chain 'V' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA V 121 " --> pdb=" O ALA V 118 " (cutoff:3.500A) Processing helix chain 'V' and resid 131 through 143 Processing helix chain 'V' and resid 166 through 170 Processing helix chain 'V' and resid 208 through 213 Processing helix chain 'V' and resid 227 through 242 Processing helix chain 'V' and resid 260 through 267 Processing helix chain 'V' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR V 290 " --> pdb=" O LEU V 286 " (cutoff:3.500A) Processing helix chain 'V' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE V 315 " --> pdb=" O GLN V 311 " (cutoff:3.500A) Processing helix chain 'V' and resid 332 through 342 Processing helix chain 'V' and resid 384 through 403 Processing helix chain 'V' and resid 404 through 406 No H-bonds generated for 'chain 'V' and resid 404 through 406' Processing helix chain 'V' and resid 425 through 440 Processing helix chain 'V' and resid 450 through 454 Processing helix chain 'W' and resid 53 through 59 Processing helix chain 'W' and resid 62 through 75 Processing helix chain 'W' and resid 117 through 121 removed outlier: 3.561A pdb=" N ALA W 121 " --> pdb=" O ALA W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 143 Processing helix chain 'W' and resid 166 through 170 Processing helix chain 'W' and resid 208 through 213 Processing helix chain 'W' and resid 227 through 242 Processing helix chain 'W' and resid 260 through 267 Processing helix chain 'W' and resid 286 through 303 removed outlier: 3.673A pdb=" N THR W 290 " --> pdb=" O LEU W 286 " (cutoff:3.500A) Processing helix chain 'W' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE W 315 " --> pdb=" O GLN W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 342 Processing helix chain 'W' and resid 384 through 403 Processing helix chain 'W' and resid 404 through 406 No H-bonds generated for 'chain 'W' and resid 404 through 406' Processing helix chain 'W' and resid 425 through 440 Processing helix chain 'W' and resid 450 through 454 Processing helix chain 'X' and resid 53 through 59 Processing helix chain 'X' and resid 62 through 75 Processing helix chain 'X' and resid 117 through 121 removed outlier: 3.562A pdb=" N ALA X 121 " --> pdb=" O ALA X 118 " (cutoff:3.500A) Processing helix chain 'X' and resid 131 through 143 Processing helix chain 'X' and resid 166 through 170 Processing helix chain 'X' and resid 208 through 213 Processing helix chain 'X' and resid 227 through 242 Processing helix chain 'X' and resid 260 through 267 Processing helix chain 'X' and resid 286 through 303 removed outlier: 3.674A pdb=" N THR X 290 " --> pdb=" O LEU X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 311 through 316 removed outlier: 3.953A pdb=" N PHE X 315 " --> pdb=" O GLN X 311 " (cutoff:3.500A) Processing helix chain 'X' and resid 332 through 342 Processing helix chain 'X' and resid 384 through 403 Processing helix chain 'X' and resid 404 through 406 No H-bonds generated for 'chain 'X' and resid 404 through 406' Processing helix chain 'X' and resid 425 through 440 Processing helix chain 'X' and resid 450 through 454 Processing sheet with id= 1, first strand: chain 'D' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL D 81 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 32 " --> pdb=" O LEU D 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE D 256 " --> pdb=" O LEU D 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL D 255 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL D 345 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG D 276 " --> pdb=" O VAL D 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER D 347 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA D 278 " --> pdb=" O SER D 347 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'D' and resid 149 through 154 Processing sheet with id= 3, first strand: chain 'D' and resid 109 through 113 Processing sheet with id= 4, first strand: chain 'D' and resid 323 through 324 Processing sheet with id= 5, first strand: chain 'D' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA D 409 " --> pdb=" O THR D 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'D' and resid 455 through 459 Processing sheet with id= 7, first strand: chain 'A' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL A 81 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 32 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE A 256 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 255 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A 345 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG A 276 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER A 347 " --> pdb=" O ARG A 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA A 278 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 149 through 154 Processing sheet with id= 9, first strand: chain 'A' and resid 109 through 113 Processing sheet with id= 10, first strand: chain 'A' and resid 323 through 324 Processing sheet with id= 11, first strand: chain 'A' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA A 409 " --> pdb=" O THR A 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'A' and resid 455 through 459 Processing sheet with id= 13, first strand: chain 'B' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL B 81 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY B 32 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE B 256 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL B 255 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL B 345 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 276 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER B 347 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA B 278 " --> pdb=" O SER B 347 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 149 through 154 Processing sheet with id= 15, first strand: chain 'B' and resid 109 through 113 Processing sheet with id= 16, first strand: chain 'B' and resid 323 through 324 Processing sheet with id= 17, first strand: chain 'B' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA B 409 " --> pdb=" O THR B 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'B' and resid 455 through 459 Processing sheet with id= 19, first strand: chain 'C' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL C 81 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY C 32 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE C 256 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 255 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL C 345 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG C 276 " --> pdb=" O VAL C 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER C 347 " --> pdb=" O ARG C 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA C 278 " --> pdb=" O SER C 347 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'C' and resid 149 through 154 Processing sheet with id= 21, first strand: chain 'C' and resid 109 through 113 Processing sheet with id= 22, first strand: chain 'C' and resid 323 through 324 Processing sheet with id= 23, first strand: chain 'C' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA C 409 " --> pdb=" O THR C 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'C' and resid 455 through 459 Processing sheet with id= 25, first strand: chain 'E' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL E 81 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY E 32 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE E 256 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 255 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL E 345 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG E 276 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N SER E 347 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA E 278 " --> pdb=" O SER E 347 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'E' and resid 149 through 154 Processing sheet with id= 27, first strand: chain 'E' and resid 109 through 113 Processing sheet with id= 28, first strand: chain 'E' and resid 323 through 324 Processing sheet with id= 29, first strand: chain 'E' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA E 409 " --> pdb=" O THR E 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 29 Processing sheet with id= 30, first strand: chain 'E' and resid 455 through 459 Processing sheet with id= 31, first strand: chain 'F' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL F 81 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY F 32 " --> pdb=" O LEU F 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE F 256 " --> pdb=" O LEU F 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 255 " --> pdb=" O SER F 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL F 345 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG F 276 " --> pdb=" O VAL F 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER F 347 " --> pdb=" O ARG F 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA F 278 " --> pdb=" O SER F 347 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'F' and resid 149 through 154 Processing sheet with id= 33, first strand: chain 'F' and resid 109 through 113 Processing sheet with id= 34, first strand: chain 'F' and resid 323 through 324 Processing sheet with id= 35, first strand: chain 'F' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA F 409 " --> pdb=" O THR F 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 35 Processing sheet with id= 36, first strand: chain 'F' and resid 455 through 459 Processing sheet with id= 37, first strand: chain 'G' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL G 81 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY G 32 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE G 256 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL G 255 " --> pdb=" O SER G 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL G 345 " --> pdb=" O LEU G 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG G 276 " --> pdb=" O VAL G 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER G 347 " --> pdb=" O ARG G 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA G 278 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 149 through 154 Processing sheet with id= 39, first strand: chain 'G' and resid 109 through 113 Processing sheet with id= 40, first strand: chain 'G' and resid 323 through 324 Processing sheet with id= 41, first strand: chain 'G' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA G 409 " --> pdb=" O THR G 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 41 Processing sheet with id= 42, first strand: chain 'G' and resid 455 through 459 Processing sheet with id= 43, first strand: chain 'H' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL H 81 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY H 32 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE H 256 " --> pdb=" O LEU H 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL H 255 " --> pdb=" O SER H 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL H 345 " --> pdb=" O LEU H 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG H 276 " --> pdb=" O VAL H 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER H 347 " --> pdb=" O ARG H 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA H 278 " --> pdb=" O SER H 347 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'H' and resid 149 through 154 Processing sheet with id= 45, first strand: chain 'H' and resid 109 through 113 Processing sheet with id= 46, first strand: chain 'H' and resid 323 through 324 Processing sheet with id= 47, first strand: chain 'H' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA H 409 " --> pdb=" O THR H 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 47 Processing sheet with id= 48, first strand: chain 'H' and resid 455 through 459 Processing sheet with id= 49, first strand: chain 'I' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL I 81 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY I 32 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE I 256 " --> pdb=" O LEU I 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL I 255 " --> pdb=" O SER I 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL I 345 " --> pdb=" O LEU I 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG I 276 " --> pdb=" O VAL I 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER I 347 " --> pdb=" O ARG I 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA I 278 " --> pdb=" O SER I 347 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'I' and resid 149 through 154 Processing sheet with id= 51, first strand: chain 'I' and resid 109 through 113 Processing sheet with id= 52, first strand: chain 'I' and resid 323 through 324 Processing sheet with id= 53, first strand: chain 'I' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA I 409 " --> pdb=" O THR I 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 53 Processing sheet with id= 54, first strand: chain 'I' and resid 455 through 459 Processing sheet with id= 55, first strand: chain 'J' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL J 81 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY J 32 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE J 256 " --> pdb=" O LEU J 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL J 255 " --> pdb=" O SER J 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL J 345 " --> pdb=" O LEU J 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG J 276 " --> pdb=" O VAL J 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER J 347 " --> pdb=" O ARG J 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA J 278 " --> pdb=" O SER J 347 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'J' and resid 149 through 154 Processing sheet with id= 57, first strand: chain 'J' and resid 109 through 113 Processing sheet with id= 58, first strand: chain 'J' and resid 323 through 324 Processing sheet with id= 59, first strand: chain 'J' and resid 409 through 410 removed outlier: 5.916A pdb=" N ALA J 409 " --> pdb=" O THR J 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'J' and resid 455 through 459 Processing sheet with id= 61, first strand: chain 'K' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL K 81 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY K 32 " --> pdb=" O LEU K 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE K 256 " --> pdb=" O LEU K 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL K 255 " --> pdb=" O SER K 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL K 345 " --> pdb=" O LEU K 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG K 276 " --> pdb=" O VAL K 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER K 347 " --> pdb=" O ARG K 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA K 278 " --> pdb=" O SER K 347 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'K' and resid 149 through 154 Processing sheet with id= 63, first strand: chain 'K' and resid 109 through 113 Processing sheet with id= 64, first strand: chain 'K' and resid 323 through 324 Processing sheet with id= 65, first strand: chain 'K' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA K 409 " --> pdb=" O THR K 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'K' and resid 455 through 459 Processing sheet with id= 67, first strand: chain 'L' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL L 81 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY L 32 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE L 256 " --> pdb=" O LEU L 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 255 " --> pdb=" O SER L 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL L 345 " --> pdb=" O LEU L 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG L 276 " --> pdb=" O VAL L 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER L 347 " --> pdb=" O ARG L 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA L 278 " --> pdb=" O SER L 347 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'L' and resid 149 through 154 Processing sheet with id= 69, first strand: chain 'L' and resid 109 through 113 Processing sheet with id= 70, first strand: chain 'L' and resid 323 through 324 Processing sheet with id= 71, first strand: chain 'L' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA L 409 " --> pdb=" O THR L 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'L' and resid 455 through 459 Processing sheet with id= 73, first strand: chain 'M' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL M 81 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY M 32 " --> pdb=" O LEU M 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE M 256 " --> pdb=" O LEU M 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL M 255 " --> pdb=" O SER M 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL M 345 " --> pdb=" O LEU M 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG M 276 " --> pdb=" O VAL M 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER M 347 " --> pdb=" O ARG M 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA M 278 " --> pdb=" O SER M 347 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'M' and resid 149 through 154 Processing sheet with id= 75, first strand: chain 'M' and resid 109 through 113 Processing sheet with id= 76, first strand: chain 'M' and resid 323 through 324 Processing sheet with id= 77, first strand: chain 'M' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA M 409 " --> pdb=" O THR M 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 77 Processing sheet with id= 78, first strand: chain 'M' and resid 455 through 459 Processing sheet with id= 79, first strand: chain 'N' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL N 81 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY N 32 " --> pdb=" O LEU N 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE N 256 " --> pdb=" O LEU N 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL N 255 " --> pdb=" O SER N 275 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL N 345 " --> pdb=" O LEU N 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG N 276 " --> pdb=" O VAL N 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER N 347 " --> pdb=" O ARG N 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA N 278 " --> pdb=" O SER N 347 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'N' and resid 149 through 154 Processing sheet with id= 81, first strand: chain 'N' and resid 109 through 113 Processing sheet with id= 82, first strand: chain 'N' and resid 323 through 324 Processing sheet with id= 83, first strand: chain 'N' and resid 409 through 410 removed outlier: 5.916A pdb=" N ALA N 409 " --> pdb=" O THR N 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'N' and resid 455 through 459 Processing sheet with id= 85, first strand: chain 'O' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL O 81 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY O 32 " --> pdb=" O LEU O 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE O 256 " --> pdb=" O LEU O 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL O 255 " --> pdb=" O SER O 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL O 345 " --> pdb=" O LEU O 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG O 276 " --> pdb=" O VAL O 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER O 347 " --> pdb=" O ARG O 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA O 278 " --> pdb=" O SER O 347 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'O' and resid 149 through 154 Processing sheet with id= 87, first strand: chain 'O' and resid 109 through 113 Processing sheet with id= 88, first strand: chain 'O' and resid 323 through 324 Processing sheet with id= 89, first strand: chain 'O' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA O 409 " --> pdb=" O THR O 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 89 Processing sheet with id= 90, first strand: chain 'O' and resid 455 through 459 Processing sheet with id= 91, first strand: chain 'P' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL P 81 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY P 32 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE P 256 " --> pdb=" O LEU P 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL P 255 " --> pdb=" O SER P 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL P 345 " --> pdb=" O LEU P 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG P 276 " --> pdb=" O VAL P 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER P 347 " --> pdb=" O ARG P 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA P 278 " --> pdb=" O SER P 347 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'P' and resid 149 through 154 Processing sheet with id= 93, first strand: chain 'P' and resid 109 through 113 Processing sheet with id= 94, first strand: chain 'P' and resid 323 through 324 Processing sheet with id= 95, first strand: chain 'P' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA P 409 " --> pdb=" O THR P 424 " (cutoff:3.500A) No H-bonds generated for sheet with id= 95 Processing sheet with id= 96, first strand: chain 'P' and resid 455 through 459 Processing sheet with id= 97, first strand: chain 'Q' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL Q 81 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY Q 32 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE Q 256 " --> pdb=" O LEU Q 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Q 255 " --> pdb=" O SER Q 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL Q 345 " --> pdb=" O LEU Q 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG Q 276 " --> pdb=" O VAL Q 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER Q 347 " --> pdb=" O ARG Q 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA Q 278 " --> pdb=" O SER Q 347 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'Q' and resid 149 through 154 Processing sheet with id= 99, first strand: chain 'Q' and resid 109 through 113 Processing sheet with id=100, first strand: chain 'Q' and resid 323 through 324 Processing sheet with id=101, first strand: chain 'Q' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA Q 409 " --> pdb=" O THR Q 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=101 Processing sheet with id=102, first strand: chain 'Q' and resid 455 through 459 Processing sheet with id=103, first strand: chain 'R' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL R 81 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY R 32 " --> pdb=" O LEU R 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE R 256 " --> pdb=" O LEU R 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL R 255 " --> pdb=" O SER R 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL R 345 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG R 276 " --> pdb=" O VAL R 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER R 347 " --> pdb=" O ARG R 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA R 278 " --> pdb=" O SER R 347 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'R' and resid 149 through 154 Processing sheet with id=105, first strand: chain 'R' and resid 109 through 113 Processing sheet with id=106, first strand: chain 'R' and resid 323 through 324 Processing sheet with id=107, first strand: chain 'R' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA R 409 " --> pdb=" O THR R 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=107 Processing sheet with id=108, first strand: chain 'R' and resid 455 through 459 Processing sheet with id=109, first strand: chain 'S' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL S 81 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY S 32 " --> pdb=" O LEU S 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE S 256 " --> pdb=" O LEU S 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL S 255 " --> pdb=" O SER S 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL S 345 " --> pdb=" O LEU S 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG S 276 " --> pdb=" O VAL S 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER S 347 " --> pdb=" O ARG S 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA S 278 " --> pdb=" O SER S 347 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'S' and resid 149 through 154 Processing sheet with id=111, first strand: chain 'S' and resid 109 through 113 Processing sheet with id=112, first strand: chain 'S' and resid 323 through 324 Processing sheet with id=113, first strand: chain 'S' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA S 409 " --> pdb=" O THR S 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=113 Processing sheet with id=114, first strand: chain 'S' and resid 455 through 459 Processing sheet with id=115, first strand: chain 'T' and resid 46 through 48 removed outlier: 4.093A pdb=" N VAL T 81 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY T 32 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE T 256 " --> pdb=" O LEU T 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL T 255 " --> pdb=" O SER T 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL T 345 " --> pdb=" O LEU T 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG T 276 " --> pdb=" O VAL T 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER T 347 " --> pdb=" O ARG T 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA T 278 " --> pdb=" O SER T 347 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'T' and resid 149 through 154 Processing sheet with id=117, first strand: chain 'T' and resid 109 through 113 Processing sheet with id=118, first strand: chain 'T' and resid 323 through 324 Processing sheet with id=119, first strand: chain 'T' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA T 409 " --> pdb=" O THR T 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=119 Processing sheet with id=120, first strand: chain 'T' and resid 455 through 459 Processing sheet with id=121, first strand: chain 'U' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL U 81 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY U 32 " --> pdb=" O LEU U 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE U 256 " --> pdb=" O LEU U 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL U 255 " --> pdb=" O SER U 275 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL U 345 " --> pdb=" O LEU U 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG U 276 " --> pdb=" O VAL U 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER U 347 " --> pdb=" O ARG U 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA U 278 " --> pdb=" O SER U 347 " (cutoff:3.500A) Processing sheet with id=122, first strand: chain 'U' and resid 149 through 154 Processing sheet with id=123, first strand: chain 'U' and resid 109 through 113 Processing sheet with id=124, first strand: chain 'U' and resid 323 through 324 Processing sheet with id=125, first strand: chain 'U' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA U 409 " --> pdb=" O THR U 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=125 Processing sheet with id=126, first strand: chain 'U' and resid 455 through 459 Processing sheet with id=127, first strand: chain 'V' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL V 81 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY V 32 " --> pdb=" O LEU V 84 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N PHE V 256 " --> pdb=" O LEU V 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL V 255 " --> pdb=" O SER V 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL V 345 " --> pdb=" O LEU V 274 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG V 276 " --> pdb=" O VAL V 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER V 347 " --> pdb=" O ARG V 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA V 278 " --> pdb=" O SER V 347 " (cutoff:3.500A) Processing sheet with id=128, first strand: chain 'V' and resid 149 through 154 Processing sheet with id=129, first strand: chain 'V' and resid 109 through 113 Processing sheet with id=130, first strand: chain 'V' and resid 323 through 324 Processing sheet with id=131, first strand: chain 'V' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA V 409 " --> pdb=" O THR V 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=131 Processing sheet with id=132, first strand: chain 'V' and resid 455 through 459 Processing sheet with id=133, first strand: chain 'W' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL W 81 " --> pdb=" O VAL W 48 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY W 32 " --> pdb=" O LEU W 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE W 256 " --> pdb=" O LEU W 223 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL W 255 " --> pdb=" O SER W 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL W 345 " --> pdb=" O LEU W 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG W 276 " --> pdb=" O VAL W 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER W 347 " --> pdb=" O ARG W 276 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA W 278 " --> pdb=" O SER W 347 " (cutoff:3.500A) Processing sheet with id=134, first strand: chain 'W' and resid 149 through 154 Processing sheet with id=135, first strand: chain 'W' and resid 109 through 113 Processing sheet with id=136, first strand: chain 'W' and resid 323 through 324 Processing sheet with id=137, first strand: chain 'W' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA W 409 " --> pdb=" O THR W 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=137 Processing sheet with id=138, first strand: chain 'W' and resid 455 through 459 Processing sheet with id=139, first strand: chain 'X' and resid 46 through 48 removed outlier: 4.094A pdb=" N VAL X 81 " --> pdb=" O VAL X 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY X 32 " --> pdb=" O LEU X 84 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHE X 256 " --> pdb=" O LEU X 223 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL X 255 " --> pdb=" O SER X 275 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL X 345 " --> pdb=" O LEU X 274 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG X 276 " --> pdb=" O VAL X 345 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER X 347 " --> pdb=" O ARG X 276 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ALA X 278 " --> pdb=" O SER X 347 " (cutoff:3.500A) Processing sheet with id=140, first strand: chain 'X' and resid 149 through 154 Processing sheet with id=141, first strand: chain 'X' and resid 109 through 113 Processing sheet with id=142, first strand: chain 'X' and resid 323 through 324 Processing sheet with id=143, first strand: chain 'X' and resid 409 through 410 removed outlier: 5.915A pdb=" N ALA X 409 " --> pdb=" O THR X 424 " (cutoff:3.500A) No H-bonds generated for sheet with id=143 Processing sheet with id=144, first strand: chain 'X' and resid 455 through 459 3312 hydrogen bonds defined for protein. 9288 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: 48.84 Time building geometry restraints manager: 30.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 30431 1.34 - 1.46: 20837 1.46 - 1.58: 39956 1.58 - 1.70: 0 1.70 - 1.82: 672 Bond restraints: 91896 Sorted by residual: bond pdb=" C TYR Q 370 " pdb=" N LEU Q 371 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.73e-02 3.34e+03 6.18e+00 bond pdb=" C TYR V 370 " pdb=" N LEU V 371 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.73e-02 3.34e+03 6.11e+00 bond pdb=" C TYR S 370 " pdb=" N LEU S 371 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.73e-02 3.34e+03 6.09e+00 bond pdb=" C TYR K 370 " pdb=" N LEU K 371 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.73e-02 3.34e+03 6.07e+00 bond pdb=" C TYR W 370 " pdb=" N LEU W 371 " ideal model delta sigma weight residual 1.331 1.288 0.043 1.73e-02 3.34e+03 6.07e+00 ... (remaining 91891 not shown) Histogram of bond angle deviations from ideal: 99.85 - 106.69: 2897 106.69 - 113.53: 50749 113.53 - 120.37: 33503 120.37 - 127.21: 37369 127.21 - 134.05: 1002 Bond angle restraints: 125520 Sorted by residual: angle pdb=" N ASN L 414 " pdb=" CA ASN L 414 " pdb=" C ASN L 414 " ideal model delta sigma weight residual 114.31 108.73 5.58 1.29e+00 6.01e-01 1.87e+01 angle pdb=" N ASN R 414 " pdb=" CA ASN R 414 " pdb=" C ASN R 414 " ideal model delta sigma weight residual 114.31 108.74 5.57 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N ASN S 414 " pdb=" CA ASN S 414 " pdb=" C ASN S 414 " ideal model delta sigma weight residual 114.31 108.75 5.56 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N ASN P 414 " pdb=" CA ASN P 414 " pdb=" C ASN P 414 " ideal model delta sigma weight residual 114.31 108.75 5.56 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N ASN C 414 " pdb=" CA ASN C 414 " pdb=" C ASN C 414 " ideal model delta sigma weight residual 114.31 108.75 5.56 1.29e+00 6.01e-01 1.86e+01 ... (remaining 125515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 50462 16.28 - 32.56: 3400 32.56 - 48.85: 514 48.85 - 65.13: 248 65.13 - 81.41: 144 Dihedral angle restraints: 54768 sinusoidal: 20448 harmonic: 34320 Sorted by residual: dihedral pdb=" CA ASN W 376 " pdb=" C ASN W 376 " pdb=" N ARG W 377 " pdb=" CA ARG W 377 " ideal model delta harmonic sigma weight residual 180.00 129.83 50.17 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASN Q 376 " pdb=" C ASN Q 376 " pdb=" N ARG Q 377 " pdb=" CA ARG Q 377 " ideal model delta harmonic sigma weight residual 180.00 129.83 50.17 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA ASN R 376 " pdb=" C ASN R 376 " pdb=" N ARG R 377 " pdb=" CA ARG R 377 " ideal model delta harmonic sigma weight residual 180.00 129.84 50.16 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 54765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 7518 0.032 - 0.065: 4674 0.065 - 0.097: 1399 0.097 - 0.129: 869 0.129 - 0.161: 60 Chirality restraints: 14520 Sorted by residual: chirality pdb=" CA CYS A 249 " pdb=" N CYS A 249 " pdb=" C CYS A 249 " pdb=" CB CYS A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA CYS K 249 " pdb=" N CYS K 249 " pdb=" C CYS K 249 " pdb=" CB CYS K 249 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CA CYS W 249 " pdb=" N CYS W 249 " pdb=" C CYS W 249 " pdb=" CB CYS W 249 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 14517 not shown) Planarity restraints: 16632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 376 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C ASN E 376 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN E 376 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG E 377 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 376 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ASN G 376 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN G 376 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG G 377 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 376 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASN A 376 " -0.030 2.00e-02 2.50e+03 pdb=" O ASN A 376 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 377 " 0.010 2.00e-02 2.50e+03 ... (remaining 16629 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.59: 36 1.59 - 2.42: 600 2.42 - 3.25: 95991 3.25 - 4.07: 242409 4.07 - 4.90: 462071 Warning: very small nonbonded interaction distances. Nonbonded interactions: 801107 Sorted by model distance: nonbonded pdb=" O ASN O 20 " pdb=" ND2 ASN P 379 " model vdw 0.765 2.520 nonbonded pdb=" O ASN D 20 " pdb=" ND2 ASN C 379 " model vdw 0.765 2.520 nonbonded pdb=" O ASN F 20 " pdb=" ND2 ASN G 379 " model vdw 0.765 2.520 nonbonded pdb=" O ASN R 20 " pdb=" ND2 ASN S 379 " model vdw 0.765 2.520 nonbonded pdb=" O ASN K 20 " pdb=" ND2 ASN L 379 " model vdw 0.765 2.520 ... (remaining 801102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = 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: 9.270 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 29.650 Check model and map are aligned: 1.050 Set scattering table: 0.640 Process input model: 207.280 Find NCS groups from input model: 5.000 Set up NCS constraints: 0.710 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 265.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 0.051 91896 Z= 0.566 Angle : 0.796 7.879 125520 Z= 0.450 Chirality : 0.048 0.161 14520 Planarity : 0.004 0.042 16632 Dihedral : 12.113 81.411 32400 Min Nonbonded Distance : 0.765 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.04 % Favored : 90.76 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.06 (0.07), residues: 11952 helix: -0.99 (0.08), residues: 3600 sheet: -1.66 (0.10), residues: 2040 loop : -1.43 (0.08), residues: 6312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP G 237 HIS 0.003 0.001 HIS F 475 PHE 0.021 0.002 PHE I 194 TYR 0.024 0.002 TYR H 176 ARG 0.005 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1747 time to evaluate : 7.863 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: D 188 GLU cc_start: 0.7742 (tt0) cc_final: 0.7405 (tt0) REVERT: D 488 ARG cc_start: 0.8069 (ttp-170) cc_final: 0.7758 (ttm170) REVERT: A 51 GLU cc_start: 0.8080 (tt0) cc_final: 0.7878 (tm-30) REVERT: A 375 LYS cc_start: 0.8624 (mttm) cc_final: 0.6783 (tmtt) REVERT: A 377 ARG cc_start: 0.7047 (ttp-170) cc_final: 0.6261 (ttt-90) REVERT: A 418 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7251 (mpp-170) REVERT: A 466 LYS cc_start: 0.8495 (mtmt) cc_final: 0.8219 (mmpt) REVERT: A 488 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: C 173 SER cc_start: 0.8336 (t) cc_final: 0.8084 (m) REVERT: C 375 LYS cc_start: 0.8236 (mttm) cc_final: 0.7825 (mttp) REVERT: E 375 LYS cc_start: 0.8483 (mttm) cc_final: 0.6681 (tmtt) REVERT: E 466 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7161 (tmtt) REVERT: F 466 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7944 (tmtt) REVERT: G 27 LYS cc_start: 0.8220 (mtpp) cc_final: 0.8011 (mtmt) REVERT: G 362 TYR cc_start: 0.9135 (p90) cc_final: 0.8794 (p90) REVERT: H 427 ARG cc_start: 0.8059 (ttp-110) cc_final: 0.7515 (ttm-80) REVERT: H 435 LYS cc_start: 0.8319 (tttm) cc_final: 0.8106 (tppt) REVERT: I 215 GLU cc_start: 0.7463 (mm-30) cc_final: 0.6394 (tm-30) REVERT: I 319 SER cc_start: 0.8614 (p) cc_final: 0.8371 (t) REVERT: J 375 LYS cc_start: 0.8296 (mttm) cc_final: 0.7430 (mmtt) REVERT: J 439 ASP cc_start: 0.7913 (m-30) cc_final: 0.7704 (m-30) REVERT: J 447 GLU cc_start: 0.7682 (tp30) cc_final: 0.7342 (tt0) REVERT: K 146 ASP cc_start: 0.7883 (m-30) cc_final: 0.7660 (m-30) REVERT: K 447 GLU cc_start: 0.8026 (tp30) cc_final: 0.7671 (mm-30) REVERT: L 427 ARG cc_start: 0.7630 (ttp-110) cc_final: 0.7421 (ttm-80) REVERT: M 377 ARG cc_start: 0.6839 (ttp-170) cc_final: 0.5122 (tpt170) REVERT: M 439 ASP cc_start: 0.7919 (m-30) cc_final: 0.7693 (m-30) REVERT: M 452 ASN cc_start: 0.8473 (m-40) cc_final: 0.8255 (m-40) REVERT: N 173 SER cc_start: 0.8068 (t) cc_final: 0.7863 (m) REVERT: O 404 GLN cc_start: 0.8638 (pt0) cc_final: 0.8368 (pt0) REVERT: P 319 SER cc_start: 0.8825 (p) cc_final: 0.8599 (m) REVERT: P 353 SER cc_start: 0.8618 (t) cc_final: 0.8239 (m) REVERT: P 439 ASP cc_start: 0.7811 (m-30) cc_final: 0.7604 (m-30) REVERT: Q 134 ASP cc_start: 0.8455 (m-30) cc_final: 0.8191 (m-30) REVERT: Q 372 ARG cc_start: 0.7747 (ptp-110) cc_final: 0.7183 (ptp90) REVERT: Q 375 LYS cc_start: 0.8483 (mttm) cc_final: 0.6319 (tmtt) REVERT: Q 377 ARG cc_start: 0.7029 (ttp-170) cc_final: 0.6256 (ttp80) REVERT: R 173 SER cc_start: 0.8313 (t) cc_final: 0.7706 (p) REVERT: R 439 ASP cc_start: 0.7937 (m-30) cc_final: 0.7706 (m-30) REVERT: S 351 THR cc_start: 0.8619 (p) cc_final: 0.8328 (p) REVERT: T 454 ASP cc_start: 0.8108 (m-30) cc_final: 0.7812 (m-30) REVERT: U 418 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7203 (mpp-170) REVERT: V 94 LYS cc_start: 0.8938 (mttt) cc_final: 0.8693 (mttt) REVERT: V 375 LYS cc_start: 0.8480 (mttm) cc_final: 0.7049 (mmtt) REVERT: V 479 ARG cc_start: 0.8530 (ttt-90) cc_final: 0.8079 (tmt170) REVERT: V 488 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7918 (ttp-170) REVERT: W 499 ASP cc_start: 0.7933 (m-30) cc_final: 0.7726 (m-30) REVERT: X 134 ASP cc_start: 0.8411 (m-30) cc_final: 0.8200 (m-30) REVERT: X 479 ARG cc_start: 0.8471 (ttt-90) cc_final: 0.8256 (ttt-90) outliers start: 0 outliers final: 4 residues processed: 1747 average time/residue: 1.6721 time to fit residues: 3960.5945 Evaluate side-chains 803 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 799 time to evaluate : 7.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain R residue 37 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1013 optimal weight: 0.9980 chunk 909 optimal weight: 5.9990 chunk 504 optimal weight: 0.3980 chunk 310 optimal weight: 5.9990 chunk 613 optimal weight: 0.7980 chunk 485 optimal weight: 8.9990 chunk 940 optimal weight: 6.9990 chunk 363 optimal weight: 2.9990 chunk 571 optimal weight: 2.9990 chunk 700 optimal weight: 5.9990 chunk 1089 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 GLN D 340 GLN D 357 ASN D 369 ASN D 438 GLN D 492 ASN ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN A 340 GLN A 357 ASN A 369 ASN A 492 ASN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 311 GLN B 340 GLN B 357 ASN B 369 ASN B 404 GLN B 490 ASN B 492 ASN C 20 ASN C 311 GLN C 340 GLN C 355 GLN C 357 ASN C 369 ASN C 450 ASN C 456 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 291 ASN E 311 GLN E 340 GLN E 357 ASN E 369 ASN E 450 ASN E 456 GLN E 490 ASN E 492 ASN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 311 GLN F 340 GLN F 357 ASN F 369 ASN F 490 ASN F 492 ASN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 ASN G 311 GLN G 340 GLN G 357 ASN G 369 ASN ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 492 ASN H 20 ASN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 311 GLN H 340 GLN H 357 ASN H 369 ASN H 490 ASN ** I 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 311 GLN I 340 GLN I 357 ASN I 369 ASN I 492 ASN ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 GLN J 60 GLN J 311 GLN J 340 GLN J 357 ASN J 369 ASN J 490 ASN J 492 ASN ** K 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 GLN K 252 HIS K 291 ASN K 311 GLN K 340 GLN K 357 ASN K 369 ASN K 438 GLN K 450 ASN K 464 GLN K 492 ASN L 20 ASN L 291 ASN L 311 GLN L 340 GLN L 355 GLN L 357 ASN L 369 ASN L 438 GLN L 450 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 311 GLN M 340 GLN M 357 ASN M 369 ASN M 438 GLN M 492 ASN ** N 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 GLN N 311 GLN N 340 GLN N 357 ASN N 369 ASN N 404 GLN N 450 ASN N 492 ASN ** O 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 GLN O 164 ASN O 252 HIS O 257 ASN O 305 ASN O 311 GLN O 340 GLN O 357 ASN O 369 ASN O 404 GLN O 450 ASN O 492 ASN P 20 ASN P 112 GLN P 311 GLN P 340 GLN P 357 ASN P 369 ASN ** Q 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 GLN Q 340 GLN Q 357 ASN Q 369 ASN Q 416 ASN Q 450 ASN Q 492 ASN ** R 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 33 GLN R 311 GLN R 340 GLN R 355 GLN R 357 ASN R 369 ASN R 490 ASN R 492 ASN ** S 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 252 HIS S 309 ASN S 311 GLN S 340 GLN S 357 ASN S 369 ASN S 404 GLN S 438 GLN S 490 ASN S 492 ASN T 20 ASN T 311 GLN T 340 GLN T 357 ASN T 369 ASN T 450 ASN T 490 ASN T 492 ASN U 252 HIS U 311 GLN U 340 GLN U 355 GLN U 357 ASN U 369 ASN U 456 GLN U 492 ASN V 20 ASN ** V 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 311 GLN V 340 GLN V 355 GLN V 357 ASN V 369 ASN V 456 GLN ** W 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 252 HIS W 311 GLN W 340 GLN W 357 ASN W 369 ASN W 416 ASN W 464 GLN W 492 ASN X 20 ASN X 196 GLN ** X 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 309 ASN X 311 GLN X 340 GLN X 357 ASN X 369 ASN X 404 GLN X 450 ASN X 464 GLN X 490 ASN Total number of N/Q/H flips: 187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 91896 Z= 0.222 Angle : 0.579 7.837 125520 Z= 0.305 Chirality : 0.043 0.167 14520 Planarity : 0.004 0.041 16632 Dihedral : 5.239 57.383 12896 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.71 % Allowed : 10.09 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.88 (0.08), residues: 11952 helix: 0.35 (0.09), residues: 3600 sheet: -0.96 (0.11), residues: 2040 loop : -0.96 (0.08), residues: 6312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 331 HIS 0.005 0.001 HIS O 252 PHE 0.024 0.002 PHE E 194 TYR 0.016 0.001 TYR T 97 ARG 0.007 0.001 ARG G 418 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1083 time to evaluate : 7.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 453 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (mm-30) REVERT: D 499 ASP cc_start: 0.6070 (OUTLIER) cc_final: 0.5521 (m-30) REVERT: A 198 THR cc_start: 0.8332 (OUTLIER) cc_final: 0.8088 (t) REVERT: A 207 ASN cc_start: 0.8828 (t0) cc_final: 0.8572 (t0) REVERT: A 418 ARG cc_start: 0.7914 (mmm-85) cc_final: 0.7206 (mpp-170) REVERT: C 51 GLU cc_start: 0.7994 (tt0) cc_final: 0.7645 (mt-10) REVERT: C 435 LYS cc_start: 0.8684 (tttm) cc_final: 0.8438 (tttm) REVERT: E 27 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8412 (mtpp) REVERT: E 117 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8360 (tm-30) REVERT: E 215 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7092 (mm-30) REVERT: E 418 ARG cc_start: 0.3599 (mpt180) cc_final: 0.3233 (mpp-170) REVERT: E 456 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8261 (mm-40) REVERT: E 466 LYS cc_start: 0.8015 (mtmt) cc_final: 0.7327 (tmtt) REVERT: F 76 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.4696 (pmtt) REVERT: F 163 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8219 (mpt90) REVERT: F 466 LYS cc_start: 0.8434 (mtmt) cc_final: 0.8156 (mmmt) REVERT: G 27 LYS cc_start: 0.8276 (mtpp) cc_final: 0.8040 (mttm) REVERT: G 117 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: G 119 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: G 232 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: G 452 ASN cc_start: 0.8958 (m-40) cc_final: 0.8666 (m-40) REVERT: H 108 ASP cc_start: 0.7948 (m-30) cc_final: 0.7647 (m-30) REVERT: H 232 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7703 (mt-10) REVERT: H 427 ARG cc_start: 0.8211 (ttp-110) cc_final: 0.7530 (ttm-80) REVERT: H 488 ARG cc_start: 0.8155 (ttm-80) cc_final: 0.7913 (ttm170) REVERT: I 167 THR cc_start: 0.8312 (m) cc_final: 0.8008 (p) REVERT: I 435 LYS cc_start: 0.8244 (tppt) cc_final: 0.7935 (tttt) REVERT: J 56 GLU cc_start: 0.7590 (mp0) cc_final: 0.7378 (mp0) REVERT: J 447 GLU cc_start: 0.7880 (tp30) cc_final: 0.7530 (tt0) REVERT: K 198 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7817 (p) REVERT: K 323 MET cc_start: 0.8406 (ptm) cc_final: 0.8197 (ptt) REVERT: K 466 LYS cc_start: 0.8062 (mtmt) cc_final: 0.7696 (mtmm) REVERT: L 87 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7834 (tt0) REVERT: L 427 ARG cc_start: 0.8093 (ttp-110) cc_final: 0.7632 (ttm-80) REVERT: L 488 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7885 (ttp-170) REVERT: M 146 ASP cc_start: 0.7755 (m-30) cc_final: 0.7511 (m-30) REVERT: M 173 SER cc_start: 0.8377 (t) cc_final: 0.8061 (p) REVERT: M 377 ARG cc_start: 0.6589 (ttp-170) cc_final: 0.6215 (ttp80) REVERT: N 418 ARG cc_start: 0.7882 (mtt-85) cc_final: 0.7634 (mtt-85) REVERT: O 46 THR cc_start: 0.8547 (p) cc_final: 0.8296 (t) REVERT: O 94 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8564 (mttt) REVERT: O 384 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7294 (m-30) REVERT: O 435 LYS cc_start: 0.8555 (tttm) cc_final: 0.8168 (tptm) REVERT: O 439 ASP cc_start: 0.8162 (m-30) cc_final: 0.7960 (m-30) REVERT: O 493 MET cc_start: 0.8124 (mtp) cc_final: 0.7912 (mtm) REVERT: P 198 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7732 (t) REVERT: P 353 SER cc_start: 0.8684 (t) cc_final: 0.8334 (m) REVERT: P 375 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7590 (mttt) REVERT: P 377 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7361 (mtp-110) REVERT: Q 34 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8492 (ptm) REVERT: Q 51 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7131 (tm-30) REVERT: Q 76 LYS cc_start: 0.4994 (OUTLIER) cc_final: 0.4249 (pmtt) REVERT: Q 106 THR cc_start: 0.9006 (p) cc_final: 0.8125 (p) REVERT: Q 377 ARG cc_start: 0.6867 (ttp-170) cc_final: 0.6357 (ttp80) REVERT: Q 425 ASN cc_start: 0.8994 (OUTLIER) cc_final: 0.8595 (p0) REVERT: Q 428 LEU cc_start: 0.8813 (mt) cc_final: 0.8588 (mt) REVERT: Q 453 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7791 (tm-30) REVERT: R 51 GLU cc_start: 0.7468 (pm20) cc_final: 0.7050 (pm20) REVERT: R 173 SER cc_start: 0.8717 (t) cc_final: 0.8108 (p) REVERT: S 198 THR cc_start: 0.8050 (OUTLIER) cc_final: 0.7819 (p) REVERT: S 418 ARG cc_start: 0.7728 (mmt90) cc_final: 0.7459 (mmt180) REVERT: T 188 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: T 198 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7911 (p) REVERT: T 232 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: T 374 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.7022 (mt-10) REVERT: T 439 ASP cc_start: 0.7826 (m-30) cc_final: 0.7498 (m-30) REVERT: U 377 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.3696 (mtt-85) REVERT: U 418 ARG cc_start: 0.7511 (mmm-85) cc_final: 0.7064 (mpp-170) REVERT: U 479 ARG cc_start: 0.8619 (ttt-90) cc_final: 0.8413 (ttt-90) REVERT: X 27 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7946 (mttt) outliers start: 263 outliers final: 60 residues processed: 1264 average time/residue: 1.5986 time to fit residues: 2789.1602 Evaluate side-chains 821 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 734 time to evaluate : 7.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 456 GLN Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 320 CYS Chi-restraints excluded: chain G residue 117 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 198 THR Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 449 ASP Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 269 ASP Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain O residue 94 LYS Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 323 MET Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 198 THR Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain P residue 377 ARG Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain Q residue 8 ASP Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 34 MET Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 425 ASN Chi-restraints excluded: chain Q residue 453 GLU Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ASP Chi-restraints excluded: chain S residue 54 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 131 THR Chi-restraints excluded: chain S residue 198 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 374 GLU Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 188 GLU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 198 THR Chi-restraints excluded: chain T residue 232 GLU Chi-restraints excluded: chain T residue 374 GLU Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 37 ASP Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 191 THR Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 387 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 605 optimal weight: 0.0050 chunk 338 optimal weight: 10.0000 chunk 906 optimal weight: 4.9990 chunk 742 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 1091 optimal weight: 9.9990 chunk 1179 optimal weight: 0.4980 chunk 972 optimal weight: 9.9990 chunk 1082 optimal weight: 1.9990 chunk 372 optimal weight: 9.9990 chunk 875 optimal weight: 9.9990 overall best weight: 1.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 20 ASN D 490 ASN A 20 ASN ** A 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 379 ASN A 490 ASN B 20 ASN B 305 ASN B 404 GLN C 33 GLN C 379 ASN C 456 GLN E 20 ASN E 252 HIS E 414 ASN F 20 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN G 112 GLN ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN H 304 ASN H 450 ASN I 20 ASN I 490 ASN ** J 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 GLN J 252 HIS K 20 ASN ** K 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 GLN K 450 ASN K 490 ASN L 196 GLN L 252 HIS L 450 ASN L 492 ASN ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 ASN M 355 GLN M 357 ASN M 490 ASN N 20 ASN ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 342 ASN O 20 ASN O 164 ASN O 450 ASN O 490 ASN P 196 GLN P 450 ASN P 490 ASN P 492 ASN Q 20 ASN ** Q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 416 ASN Q 490 ASN R 20 ASN R 252 HIS S 20 ASN S 203 ASN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 456 GLN V 252 HIS V 379 ASN W 20 ASN W 33 GLN W 379 ASN X 178 ASN ** X 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 379 ASN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 91896 Z= 0.210 Angle : 0.541 8.246 125520 Z= 0.283 Chirality : 0.042 0.159 14520 Planarity : 0.004 0.045 16632 Dihedral : 4.927 54.740 12888 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.07 % Allowed : 12.81 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.38 (0.08), residues: 11952 helix: 0.81 (0.09), residues: 3600 sheet: -0.57 (0.11), residues: 2088 loop : -0.72 (0.08), residues: 6264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 237 HIS 0.003 0.001 HIS T 252 PHE 0.019 0.001 PHE E 194 TYR 0.019 0.001 TYR T 176 ARG 0.011 0.000 ARG F 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 901 time to evaluate : 8.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 453 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7812 (mm-30) REVERT: D 499 ASP cc_start: 0.5939 (OUTLIER) cc_final: 0.5367 (m-30) REVERT: A 108 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: A 207 ASN cc_start: 0.8798 (t0) cc_final: 0.8588 (t0) REVERT: A 418 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7202 (mpp-170) REVERT: A 439 ASP cc_start: 0.7934 (m-30) cc_final: 0.7601 (m-30) REVERT: A 466 LYS cc_start: 0.8503 (mtmt) cc_final: 0.8093 (mmpt) REVERT: C 51 GLU cc_start: 0.7938 (tt0) cc_final: 0.7613 (mt-10) REVERT: C 419 THR cc_start: 0.9187 (m) cc_final: 0.8982 (p) REVERT: E 27 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8508 (mtpp) REVERT: E 49 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7850 (p) REVERT: E 215 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7336 (mm-30) REVERT: E 249 CYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4309 (m) REVERT: E 328 THR cc_start: 0.8877 (m) cc_final: 0.8525 (p) REVERT: E 466 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7494 (tmtt) REVERT: G 27 LYS cc_start: 0.8256 (mtpp) cc_final: 0.8020 (mttm) REVERT: G 36 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: G 232 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: G 323 MET cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (ptt) REVERT: G 452 ASN cc_start: 0.9078 (m-40) cc_final: 0.8780 (m-40) REVERT: G 456 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.7667 (mm-40) REVERT: H 56 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: H 108 ASP cc_start: 0.7951 (m-30) cc_final: 0.7635 (m-30) REVERT: H 232 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7715 (mt-10) REVERT: H 414 ASN cc_start: 0.8409 (m-40) cc_final: 0.8204 (m-40) REVERT: I 24 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7466 (tp30) REVERT: I 76 LYS cc_start: 0.6881 (OUTLIER) cc_final: 0.6620 (pttm) REVERT: I 319 SER cc_start: 0.8231 (p) cc_final: 0.7824 (t) REVERT: I 435 LYS cc_start: 0.8371 (tppt) cc_final: 0.8098 (tttt) REVERT: I 481 ARG cc_start: 0.8690 (mtp85) cc_final: 0.7086 (mmp-170) REVERT: J 52 LEU cc_start: 0.8197 (mp) cc_final: 0.7854 (mm) REVERT: J 56 GLU cc_start: 0.7689 (mp0) cc_final: 0.7377 (mp0) REVERT: J 188 GLU cc_start: 0.7661 (mp0) cc_final: 0.7438 (mm-30) REVERT: K 87 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7542 (mt-10) REVERT: K 323 MET cc_start: 0.8599 (ptm) cc_final: 0.8340 (ptt) REVERT: K 375 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7867 (mtmm) REVERT: L 198 THR cc_start: 0.7769 (OUTLIER) cc_final: 0.7513 (p) REVERT: L 427 ARG cc_start: 0.8119 (ttp-110) cc_final: 0.7573 (ttm-80) REVERT: M 173 SER cc_start: 0.8617 (t) cc_final: 0.8260 (p) REVERT: M 313 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: M 377 ARG cc_start: 0.6379 (ttp-170) cc_final: 0.5987 (tmt170) REVERT: M 468 VAL cc_start: 0.8266 (t) cc_final: 0.8016 (p) REVERT: N 452 ASN cc_start: 0.8441 (m110) cc_final: 0.8205 (m-40) REVERT: O 24 GLU cc_start: 0.7876 (tp30) cc_final: 0.7649 (tp30) REVERT: O 46 THR cc_start: 0.8592 (p) cc_final: 0.8372 (t) REVERT: O 384 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7111 (m-30) REVERT: P 184 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8095 (p) REVERT: P 353 SER cc_start: 0.8608 (t) cc_final: 0.8269 (m) REVERT: P 375 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7639 (mttt) REVERT: Q 452 ASN cc_start: 0.8744 (m110) cc_final: 0.8341 (m-40) REVERT: R 51 GLU cc_start: 0.7522 (pm20) cc_final: 0.7131 (pm20) REVERT: R 173 SER cc_start: 0.8759 (t) cc_final: 0.8182 (p) REVERT: R 413 LYS cc_start: 0.8752 (pttm) cc_final: 0.8392 (ptpt) REVERT: R 488 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7419 (ttp-170) REVERT: S 55 ILE cc_start: 0.8913 (mp) cc_final: 0.8669 (mp) REVERT: S 188 GLU cc_start: 0.8089 (mp0) cc_final: 0.7654 (mp0) REVERT: S 384 ASP cc_start: 0.7792 (m-30) cc_final: 0.7566 (m-30) REVERT: S 418 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7630 (mtt-85) REVERT: T 45 VAL cc_start: 0.9211 (m) cc_final: 0.8981 (t) REVERT: T 188 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: U 249 CYS cc_start: 0.5589 (OUTLIER) cc_final: 0.5283 (m) REVERT: U 377 ARG cc_start: 0.5293 (OUTLIER) cc_final: 0.4114 (mtt-85) REVERT: U 418 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7192 (mpp-170) REVERT: V 374 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6852 (mt-10) REVERT: X 379 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8082 (t0) outliers start: 298 outliers final: 110 residues processed: 1110 average time/residue: 1.5985 time to fit residues: 2432.2305 Evaluate side-chains 856 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 723 time to evaluate : 7.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 4 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 249 CYS Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 37 ASP Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 375 LYS Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 313 GLN Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 351 THR Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 193 THR Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain Q residue 8 ASP Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain R residue 37 ASP Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 384 ASP Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain T residue 188 GLU Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 449 ASP Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 374 GLU Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 197 THR Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain X residue 167 THR Chi-restraints excluded: chain X residue 178 ASN Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 379 ASN Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1078 optimal weight: 5.9990 chunk 820 optimal weight: 10.0000 chunk 566 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 521 optimal weight: 10.0000 chunk 733 optimal weight: 6.9990 chunk 1095 optimal weight: 9.9990 chunk 1159 optimal weight: 8.9990 chunk 572 optimal weight: 8.9990 chunk 1038 optimal weight: 8.9990 chunk 312 optimal weight: 0.8980 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 ASN E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 450 ASN G 438 GLN ** H 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 304 ASN H 438 GLN J 60 GLN J 355 GLN L 214 ASN L 257 ASN M 20 ASN ** M 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 112 GLN ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 164 ASN O 450 ASN ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 464 GLN Q 416 ASN ** R 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 355 GLN S 464 GLN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 456 GLN W 490 ASN ** X 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 91896 Z= 0.433 Angle : 0.642 9.524 125520 Z= 0.336 Chirality : 0.045 0.238 14520 Planarity : 0.004 0.046 16632 Dihedral : 5.459 56.989 12888 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.56 % Favored : 92.43 % Rotamer: Outliers : 3.90 % Allowed : 13.52 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.08), residues: 11952 helix: 0.78 (0.09), residues: 3456 sheet: -0.45 (0.11), residues: 2088 loop : -0.73 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 237 HIS 0.005 0.001 HIS T 252 PHE 0.019 0.002 PHE D 194 TYR 0.038 0.002 TYR T 176 ARG 0.009 0.001 ARG J 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 741 time to evaluate : 8.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: D 188 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: D 453 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7876 (mm-30) REVERT: D 499 ASP cc_start: 0.5926 (OUTLIER) cc_final: 0.5289 (m-30) REVERT: A 108 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7918 (m-30) REVERT: A 207 ASN cc_start: 0.8870 (t0) cc_final: 0.8666 (t0) REVERT: A 418 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.6946 (mpp-170) REVERT: A 466 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8045 (mmpt) REVERT: C 13 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9054 (mp) REVERT: C 24 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7585 (mm-30) REVERT: C 51 GLU cc_start: 0.7888 (tt0) cc_final: 0.7584 (mt-10) REVERT: E 27 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8452 (mtpp) REVERT: E 34 MET cc_start: 0.9262 (ptt) cc_final: 0.8726 (ptt) REVERT: E 439 ASP cc_start: 0.8454 (t0) cc_final: 0.8085 (m-30) REVERT: E 450 ASN cc_start: 0.8061 (t0) cc_final: 0.7739 (t0) REVERT: E 453 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7525 (pt0) REVERT: F 163 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8440 (mpt90) REVERT: G 27 LYS cc_start: 0.8279 (mtpp) cc_final: 0.7963 (mtmt) REVERT: G 232 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7415 (tt0) REVERT: G 323 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8546 (ptt) REVERT: G 456 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.7647 (mm-40) REVERT: H 56 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: H 196 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8646 (tp40) REVERT: H 488 ARG cc_start: 0.8563 (ttm-80) cc_final: 0.7967 (ttt-90) REVERT: I 76 LYS cc_start: 0.7065 (OUTLIER) cc_final: 0.6864 (pttm) REVERT: I 323 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8472 (ptp) REVERT: I 435 LYS cc_start: 0.8437 (tppt) cc_final: 0.8120 (tttt) REVERT: I 466 LYS cc_start: 0.5620 (OUTLIER) cc_final: 0.4647 (mmpt) REVERT: I 481 ARG cc_start: 0.8779 (mtp85) cc_final: 0.7107 (mmp-170) REVERT: J 27 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8161 (mtpt) REVERT: J 52 LEU cc_start: 0.8260 (mp) cc_final: 0.7911 (mm) REVERT: J 56 GLU cc_start: 0.7758 (mp0) cc_final: 0.7471 (mp0) REVERT: J 188 GLU cc_start: 0.7846 (mp0) cc_final: 0.7645 (mm-30) REVERT: J 453 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7648 (tm-30) REVERT: K 87 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7727 (mt-10) REVERT: L 87 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: L 427 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7582 (ttm-80) REVERT: M 173 SER cc_start: 0.8859 (t) cc_final: 0.8576 (p) REVERT: M 377 ARG cc_start: 0.6617 (ttp-170) cc_final: 0.6337 (tmt170) REVERT: N 313 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7980 (mp10) REVERT: N 418 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7909 (mtt-85) REVERT: N 427 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7781 (ttp80) REVERT: N 452 ASN cc_start: 0.8529 (m110) cc_final: 0.8204 (m-40) REVERT: O 24 GLU cc_start: 0.7840 (tp30) cc_final: 0.7640 (tp30) REVERT: O 384 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: P 119 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: P 215 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7223 (mt-10) REVERT: P 353 SER cc_start: 0.8829 (t) cc_final: 0.8392 (m) REVERT: P 375 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7657 (mttt) REVERT: P 377 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7491 (mtp-110) REVERT: P 456 GLN cc_start: 0.8892 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: Q 76 LYS cc_start: 0.5115 (OUTLIER) cc_final: 0.4594 (pmtt) REVERT: Q 377 ARG cc_start: 0.4585 (OUTLIER) cc_final: 0.3128 (mtp85) REVERT: Q 452 ASN cc_start: 0.8763 (m110) cc_final: 0.8435 (m-40) REVERT: Q 453 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: R 51 GLU cc_start: 0.7569 (pm20) cc_final: 0.7270 (pm20) REVERT: R 117 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: R 119 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7602 (mt-10) REVERT: R 173 SER cc_start: 0.8852 (t) cc_final: 0.8364 (p) REVERT: R 323 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.8057 (ptt) REVERT: R 413 LYS cc_start: 0.8904 (pttm) cc_final: 0.8453 (ptpt) REVERT: R 488 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7605 (ttp-170) REVERT: S 188 GLU cc_start: 0.8219 (mp0) cc_final: 0.7504 (mp0) REVERT: S 384 ASP cc_start: 0.7824 (m-30) cc_final: 0.7600 (m-30) REVERT: T 188 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: T 232 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7133 (mm-30) REVERT: T 418 ARG cc_start: 0.8285 (mtt-85) cc_final: 0.8045 (mtt90) REVERT: T 435 LYS cc_start: 0.8191 (tttm) cc_final: 0.7719 (tptt) REVERT: T 439 ASP cc_start: 0.8412 (m-30) cc_final: 0.8113 (m-30) REVERT: U 377 ARG cc_start: 0.5408 (OUTLIER) cc_final: 0.3848 (mtt-85) REVERT: U 418 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7120 (mpp-170) REVERT: W 24 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.6268 (tt0) REVERT: W 488 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7952 (ttt90) outliers start: 379 outliers final: 188 residues processed: 1036 average time/residue: 1.5489 time to fit residues: 2221.3962 Evaluate side-chains 875 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 654 time to evaluate : 7.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 319 SER Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 228 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 414 ASN Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 413 LYS Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain G residue 462 GLU Chi-restraints excluded: chain H residue 36 ASP Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 196 GLN Chi-restraints excluded: chain H residue 198 THR Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 76 LYS Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 466 LYS Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 271 SER Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 374 GLU Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 184 SER Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 462 GLU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 184 SER Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 313 GLN Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 115 MET Chi-restraints excluded: chain O residue 144 SER Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 314 THR Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 384 ASP Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 458 LEU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 215 GLU Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 375 LYS Chi-restraints excluded: chain P residue 377 ARG Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain Q residue 8 ASP Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 453 GLU Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 117 GLU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 384 ASP Chi-restraints excluded: chain R residue 408 LEU Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 188 GLU Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 197 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 211 THR Chi-restraints excluded: chain U residue 228 THR Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 51 GLU Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 298 SER Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 319 SER Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 966 optimal weight: 9.9990 chunk 658 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 863 optimal weight: 0.9980 chunk 478 optimal weight: 0.9990 chunk 989 optimal weight: 0.9990 chunk 801 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 592 optimal weight: 7.9990 chunk 1041 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 GLN C 309 ASN E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN ** H 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 ASN H 492 ASN I 414 ASN J 60 GLN J 355 GLN K 416 ASN N 414 ASN O 464 GLN Q 416 ASN ** R 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 355 GLN R 379 ASN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 196 GLN U 456 GLN V 20 ASN ** X 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 379 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 91896 Z= 0.178 Angle : 0.524 7.048 125520 Z= 0.274 Chirality : 0.041 0.176 14520 Planarity : 0.004 0.036 16632 Dihedral : 4.942 55.380 12888 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.11 % Allowed : 15.07 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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 (0.08), residues: 11952 helix: 0.97 (0.09), residues: 3600 sheet: -0.27 (0.12), residues: 2088 loop : -0.57 (0.08), residues: 6264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP T 331 HIS 0.005 0.000 HIS G 252 PHE 0.018 0.001 PHE D 194 TYR 0.019 0.001 TYR S 114 ARG 0.008 0.000 ARG I 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1122 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 820 time to evaluate : 8.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 117 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (tt0) REVERT: D 198 THR cc_start: 0.8309 (OUTLIER) cc_final: 0.8044 (t) REVERT: D 453 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7856 (mm-30) REVERT: D 499 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5380 (m-30) REVERT: A 108 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: A 418 ARG cc_start: 0.8212 (mmm-85) cc_final: 0.6935 (mpp-170) REVERT: A 439 ASP cc_start: 0.7848 (m-30) cc_final: 0.7541 (m-30) REVERT: A 466 LYS cc_start: 0.8491 (mtmt) cc_final: 0.8013 (mmpt) REVERT: B 328 THR cc_start: 0.8872 (m) cc_final: 0.8605 (p) REVERT: C 24 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 27 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8230 (mtpm) REVERT: C 51 GLU cc_start: 0.7876 (tt0) cc_final: 0.7641 (mt-10) REVERT: E 27 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8442 (mtpp) REVERT: E 98 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8762 (p) REVERT: E 328 THR cc_start: 0.8942 (m) cc_final: 0.8607 (p) REVERT: E 439 ASP cc_start: 0.8352 (t0) cc_final: 0.8106 (m-30) REVERT: E 450 ASN cc_start: 0.7943 (t0) cc_final: 0.7698 (t0) REVERT: E 453 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: G 27 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7927 (mtmt) REVERT: G 117 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7900 (tm-30) REVERT: G 232 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7329 (mt-10) REVERT: G 323 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8416 (ptt) REVERT: G 456 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.7610 (mm-40) REVERT: H 56 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7637 (mm-30) REVERT: H 108 ASP cc_start: 0.7969 (m-30) cc_final: 0.7656 (m-30) REVERT: H 488 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.7957 (ttt-90) REVERT: I 453 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7785 (mp0) REVERT: I 464 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: I 481 ARG cc_start: 0.8839 (mtp85) cc_final: 0.7252 (mmp-170) REVERT: J 51 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7654 (mt-10) REVERT: J 52 LEU cc_start: 0.8242 (mp) cc_final: 0.7941 (mm) REVERT: J 56 GLU cc_start: 0.7840 (mp0) cc_final: 0.7580 (mp0) REVERT: J 453 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7617 (tm-30) REVERT: K 87 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7697 (mt-10) REVERT: K 328 THR cc_start: 0.8703 (m) cc_final: 0.8331 (p) REVERT: L 87 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7927 (mt-10) REVERT: L 427 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7538 (ttm-80) REVERT: M 173 SER cc_start: 0.8866 (t) cc_final: 0.8577 (p) REVERT: M 201 SER cc_start: 0.8119 (m) cc_final: 0.7810 (t) REVERT: M 500 ASN cc_start: 0.8645 (OUTLIER) cc_final: 0.8416 (m-40) REVERT: N 37 ASP cc_start: 0.8386 (t0) cc_final: 0.8169 (t0) REVERT: N 126 VAL cc_start: 0.8714 (t) cc_final: 0.8506 (p) REVERT: N 418 ARG cc_start: 0.8161 (mtt-85) cc_final: 0.7897 (mtt-85) REVERT: N 427 ARG cc_start: 0.8231 (ttm-80) cc_final: 0.7726 (ttp80) REVERT: N 452 ASN cc_start: 0.8455 (m110) cc_final: 0.8208 (m-40) REVERT: O 439 ASP cc_start: 0.8408 (m-30) cc_final: 0.8174 (m-30) REVERT: P 232 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7207 (mt-10) REVERT: P 353 SER cc_start: 0.8762 (t) cc_final: 0.8382 (m) REVERT: Q 24 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6850 (tt0) REVERT: Q 46 THR cc_start: 0.8723 (p) cc_final: 0.8409 (t) REVERT: Q 76 LYS cc_start: 0.5427 (OUTLIER) cc_final: 0.4947 (pmtt) REVERT: Q 188 GLU cc_start: 0.7791 (tt0) cc_final: 0.7291 (tm-30) REVERT: Q 377 ARG cc_start: 0.4409 (OUTLIER) cc_final: 0.3212 (mtp85) REVERT: Q 452 ASN cc_start: 0.8692 (m110) cc_final: 0.8354 (m-40) REVERT: Q 499 ASP cc_start: 0.7948 (m-30) cc_final: 0.7433 (m-30) REVERT: R 51 GLU cc_start: 0.7634 (pm20) cc_final: 0.7338 (pm20) REVERT: R 173 SER cc_start: 0.8832 (t) cc_final: 0.8336 (p) REVERT: R 323 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8004 (ptt) REVERT: R 413 LYS cc_start: 0.8896 (pttm) cc_final: 0.8486 (ptpt) REVERT: S 188 GLU cc_start: 0.8192 (mp0) cc_final: 0.7730 (mp0) REVERT: S 384 ASP cc_start: 0.7677 (m-30) cc_final: 0.7465 (m-30) REVERT: S 418 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7795 (mtt-85) REVERT: S 435 LYS cc_start: 0.8420 (tptp) cc_final: 0.8077 (tptm) REVERT: T 232 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7122 (mm-30) REVERT: T 435 LYS cc_start: 0.8229 (tttm) cc_final: 0.7720 (tptt) REVERT: T 439 ASP cc_start: 0.8328 (m-30) cc_final: 0.8019 (m-30) REVERT: U 377 ARG cc_start: 0.5198 (OUTLIER) cc_final: 0.3818 (mtt-85) REVERT: U 418 ARG cc_start: 0.7766 (mmm-85) cc_final: 0.7151 (mpp-170) REVERT: V 427 ARG cc_start: 0.8248 (ttp-110) cc_final: 0.7954 (ttm-80) REVERT: V 488 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7954 (ttt180) REVERT: W 13 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8452 (tt) REVERT: W 24 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.6260 (tt0) REVERT: W 51 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7264 (mt-10) REVERT: W 488 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7889 (ttt90) outliers start: 302 outliers final: 145 residues processed: 1052 average time/residue: 1.5682 time to fit residues: 2284.6467 Evaluate side-chains 851 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 684 time to evaluate : 7.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 98 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 197 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 184 SER Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 319 SER Chi-restraints excluded: chain P residue 320 CYS Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 248 GLN Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 491 VAL Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 414 ASN Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 14 CYS Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain V residue 115 MET Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 414 ASN Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 390 optimal weight: 5.9990 chunk 1044 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 681 optimal weight: 0.9990 chunk 286 optimal weight: 8.9990 chunk 1161 optimal weight: 9.9990 chunk 963 optimal weight: 8.9990 chunk 537 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 384 optimal weight: 5.9990 chunk 609 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 438 GLN H 304 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 355 GLN N 414 ASN ** O 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 203 ASN Q 416 ASN R 355 GLN S 425 ASN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 425 ASN U 20 ASN U 456 GLN X 252 HIS X 379 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 91896 Z= 0.364 Angle : 0.589 7.980 125520 Z= 0.308 Chirality : 0.044 0.162 14520 Planarity : 0.004 0.037 16632 Dihedral : 5.218 56.593 12888 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.73 % Allowed : 15.27 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -0.14 (0.08), residues: 11952 helix: 1.01 (0.09), residues: 3456 sheet: -0.28 (0.12), residues: 2088 loop : -0.59 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 242 HIS 0.005 0.001 HIS H 252 PHE 0.017 0.002 PHE D 194 TYR 0.027 0.002 TYR O 176 ARG 0.011 0.001 ARG J 377 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 695 time to evaluate : 8.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7890 (tt0) REVERT: D 188 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: D 452 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.8462 (m110) REVERT: D 499 ASP cc_start: 0.5924 (OUTLIER) cc_final: 0.5298 (m-30) REVERT: A 34 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8515 (ptt) REVERT: A 108 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: A 418 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.6664 (mpt180) REVERT: A 439 ASP cc_start: 0.7915 (m-30) cc_final: 0.7639 (m-30) REVERT: A 466 LYS cc_start: 0.8518 (mtmt) cc_final: 0.8039 (mmpt) REVERT: C 13 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9017 (mp) REVERT: C 24 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7621 (mm-30) REVERT: C 51 GLU cc_start: 0.7878 (tt0) cc_final: 0.7607 (mt-10) REVERT: E 34 MET cc_start: 0.9228 (ptt) cc_final: 0.8657 (ptt) REVERT: E 439 ASP cc_start: 0.8425 (t0) cc_final: 0.8107 (m-30) REVERT: E 450 ASN cc_start: 0.8042 (t0) cc_final: 0.7734 (t0) REVERT: E 453 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7517 (pt0) REVERT: G 27 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7902 (mtmt) REVERT: G 117 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7897 (tm-30) REVERT: G 188 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: G 232 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7338 (mt-10) REVERT: G 323 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8550 (ptt) REVERT: G 456 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7640 (mm-40) REVERT: H 56 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: H 108 ASP cc_start: 0.8109 (m-30) cc_final: 0.7826 (m-30) REVERT: H 488 ARG cc_start: 0.8555 (ttm-80) cc_final: 0.7970 (ttt-90) REVERT: I 24 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7359 (tp30) REVERT: I 481 ARG cc_start: 0.8867 (mtp85) cc_final: 0.7184 (mmp-170) REVERT: J 51 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7638 (mt-10) REVERT: J 52 LEU cc_start: 0.8284 (mp) cc_final: 0.7968 (mm) REVERT: J 56 GLU cc_start: 0.7842 (mp0) cc_final: 0.7559 (mp0) REVERT: K 87 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7775 (mt-10) REVERT: L 87 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: L 260 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8552 (p) REVERT: L 313 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: L 427 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7672 (ttm-80) REVERT: M 173 SER cc_start: 0.8872 (t) cc_final: 0.8609 (p) REVERT: M 201 SER cc_start: 0.8198 (m) cc_final: 0.7931 (t) REVERT: M 500 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8439 (m-40) REVERT: N 313 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7874 (mp10) REVERT: N 418 ARG cc_start: 0.8200 (mtt-85) cc_final: 0.7899 (mtt-85) REVERT: N 427 ARG cc_start: 0.8286 (ttm-80) cc_final: 0.7752 (ttp80) REVERT: N 452 ASN cc_start: 0.8500 (m110) cc_final: 0.8189 (m-40) REVERT: N 466 LYS cc_start: 0.4561 (OUTLIER) cc_final: 0.4174 (mmtt) REVERT: P 232 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7225 (mt-10) REVERT: P 353 SER cc_start: 0.8825 (t) cc_final: 0.8395 (m) REVERT: P 456 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: Q 34 MET cc_start: 0.8840 (ptm) cc_final: 0.8576 (ptm) REVERT: Q 46 THR cc_start: 0.8760 (p) cc_final: 0.8430 (t) REVERT: Q 76 LYS cc_start: 0.5459 (OUTLIER) cc_final: 0.5042 (pmtt) REVERT: Q 377 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.3210 (mtp85) REVERT: Q 452 ASN cc_start: 0.8771 (m110) cc_final: 0.8427 (m-40) REVERT: R 51 GLU cc_start: 0.7676 (pm20) cc_final: 0.7377 (pm20) REVERT: R 173 SER cc_start: 0.8842 (t) cc_final: 0.8363 (p) REVERT: R 323 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8101 (ptt) REVERT: R 413 LYS cc_start: 0.8936 (pttm) cc_final: 0.8543 (ptpt) REVERT: R 488 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7529 (ttp-170) REVERT: S 384 ASP cc_start: 0.7786 (m-30) cc_final: 0.7561 (m-30) REVERT: T 435 LYS cc_start: 0.8236 (tttm) cc_final: 0.7753 (tptt) REVERT: U 87 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7840 (mt-10) REVERT: U 249 CYS cc_start: 0.5990 (OUTLIER) cc_final: 0.5521 (m) REVERT: U 377 ARG cc_start: 0.5365 (OUTLIER) cc_final: 0.3806 (mtt-85) REVERT: U 418 ARG cc_start: 0.7805 (mmm-85) cc_final: 0.7044 (mpp-170) REVERT: U 456 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.7778 (mt0) REVERT: W 13 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8534 (tt) REVERT: W 24 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.6244 (tt0) REVERT: W 51 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7244 (mt-10) REVERT: W 488 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7948 (ttt90) REVERT: W 500 ASN cc_start: 0.8662 (t0) cc_final: 0.8314 (t0) outliers start: 363 outliers final: 208 residues processed: 971 average time/residue: 1.5302 time to fit residues: 2071.3173 Evaluate side-chains 897 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 657 time to evaluate : 7.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 445 PHE Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain G residue 491 VAL Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain I residue 24 GLU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 14 CYS Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 50 SER Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 313 GLN Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 313 GLN Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 445 PHE Chi-restraints excluded: chain N residue 466 LYS Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 14 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 458 LEU Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 427 ARG Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 491 VAL Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 211 THR Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 456 GLN Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 108 ASP Chi-restraints excluded: chain V residue 115 MET Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 228 THR Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 445 PHE Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain W residue 24 GLU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain W residue 499 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 191 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 319 SER Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1119 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 661 optimal weight: 7.9990 chunk 847 optimal weight: 0.9990 chunk 656 optimal weight: 7.9990 chunk 977 optimal weight: 3.9990 chunk 648 optimal weight: 0.0970 chunk 1156 optimal weight: 4.9990 chunk 723 optimal weight: 3.9990 chunk 705 optimal weight: 5.9990 chunk 533 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 ASN ** O 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 416 ASN R 355 GLN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 456 GLN X 379 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 91896 Z= 0.235 Angle : 0.537 7.156 125520 Z= 0.280 Chirality : 0.042 0.167 14520 Planarity : 0.004 0.040 16632 Dihedral : 4.992 55.313 12888 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.40 % Allowed : 16.00 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 11952 helix: 1.14 (0.09), residues: 3456 sheet: -0.19 (0.12), residues: 2088 loop : -0.53 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 237 HIS 0.003 0.001 HIS T 252 PHE 0.018 0.001 PHE D 194 TYR 0.019 0.001 TYR S 114 ARG 0.010 0.000 ARG J 377 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 736 time to evaluate : 8.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 117 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: D 188 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6616 (mp0) REVERT: D 198 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8143 (t) REVERT: D 499 ASP cc_start: 0.5929 (OUTLIER) cc_final: 0.5307 (m-30) REVERT: A 34 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8439 (ptt) REVERT: A 108 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: A 323 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8339 (ptt) REVERT: A 377 ARG cc_start: 0.4574 (tmt170) cc_final: 0.4372 (mmt180) REVERT: A 418 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.6653 (mpt180) REVERT: A 439 ASP cc_start: 0.7879 (m-30) cc_final: 0.7584 (m-30) REVERT: A 466 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8033 (mmpt) REVERT: B 328 THR cc_start: 0.8928 (m) cc_final: 0.8677 (p) REVERT: C 13 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9018 (mp) REVERT: C 24 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7573 (mm-30) REVERT: C 51 GLU cc_start: 0.7890 (tt0) cc_final: 0.7641 (mt-10) REVERT: E 328 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8662 (p) REVERT: E 439 ASP cc_start: 0.8386 (t0) cc_final: 0.8129 (m-30) REVERT: E 450 ASN cc_start: 0.8014 (t0) cc_final: 0.7751 (t0) REVERT: E 453 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: G 232 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7287 (mt-10) REVERT: G 323 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8473 (ptt) REVERT: G 456 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: H 56 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: H 108 ASP cc_start: 0.8096 (m-30) cc_final: 0.7808 (m-30) REVERT: H 488 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.7972 (ttt-90) REVERT: I 435 LYS cc_start: 0.8454 (tppt) cc_final: 0.7983 (tttt) REVERT: I 464 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: I 481 ARG cc_start: 0.8869 (mtp85) cc_final: 0.7205 (mmp-170) REVERT: J 51 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7679 (mt-10) REVERT: J 52 LEU cc_start: 0.8260 (mp) cc_final: 0.7941 (mm) REVERT: J 56 GLU cc_start: 0.7814 (mp0) cc_final: 0.7568 (mp0) REVERT: K 87 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7769 (mt-10) REVERT: K 328 THR cc_start: 0.8735 (m) cc_final: 0.8356 (p) REVERT: K 418 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.6653 (mtt90) REVERT: L 87 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: L 260 THR cc_start: 0.8823 (OUTLIER) cc_final: 0.8560 (p) REVERT: L 427 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7638 (ttm-80) REVERT: M 173 SER cc_start: 0.8902 (t) cc_final: 0.8636 (p) REVERT: M 500 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8404 (m-40) REVERT: N 76 LYS cc_start: 0.4889 (pmtt) cc_final: 0.4074 (ptpt) REVERT: N 418 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7884 (mtt-85) REVERT: N 427 ARG cc_start: 0.8279 (ttm-80) cc_final: 0.7775 (ttp80) REVERT: N 452 ASN cc_start: 0.8487 (m110) cc_final: 0.8169 (m-40) REVERT: P 232 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: P 353 SER cc_start: 0.8800 (t) cc_final: 0.8378 (m) REVERT: P 453 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7414 (mp0) REVERT: P 456 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7962 (mt0) REVERT: Q 24 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6976 (tt0) REVERT: Q 34 MET cc_start: 0.8823 (ptm) cc_final: 0.8512 (ptm) REVERT: Q 46 THR cc_start: 0.8730 (p) cc_final: 0.8409 (t) REVERT: Q 76 LYS cc_start: 0.5336 (OUTLIER) cc_final: 0.4911 (pmtt) REVERT: Q 373 ASP cc_start: 0.6928 (m-30) cc_final: 0.6327 (m-30) REVERT: Q 377 ARG cc_start: 0.4510 (OUTLIER) cc_final: 0.3307 (mtp85) REVERT: Q 452 ASN cc_start: 0.8763 (m110) cc_final: 0.8403 (m-40) REVERT: Q 493 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8373 (mtm) REVERT: R 51 GLU cc_start: 0.7688 (pm20) cc_final: 0.7387 (pm20) REVERT: R 173 SER cc_start: 0.8836 (t) cc_final: 0.8357 (p) REVERT: R 323 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.8058 (ptt) REVERT: R 413 LYS cc_start: 0.8912 (pttm) cc_final: 0.8532 (ptpt) REVERT: R 488 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7488 (ttp-170) REVERT: S 478 MET cc_start: 0.9038 (ttm) cc_final: 0.8576 (ttm) REVERT: U 27 LYS cc_start: 0.8411 (mtpp) cc_final: 0.7831 (mttm) REVERT: U 377 ARG cc_start: 0.5182 (OUTLIER) cc_final: 0.3724 (mtt-85) REVERT: U 418 ARG cc_start: 0.7845 (mmm-85) cc_final: 0.7030 (mpp-170) REVERT: V 8 ASP cc_start: 0.8730 (p0) cc_final: 0.8502 (p0) REVERT: V 119 GLU cc_start: 0.8050 (tt0) cc_final: 0.7831 (tm-30) REVERT: V 427 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7959 (ttm-80) REVERT: W 488 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7904 (ttt90) REVERT: W 500 ASN cc_start: 0.8687 (t0) cc_final: 0.8297 (t0) outliers start: 330 outliers final: 214 residues processed: 979 average time/residue: 1.5432 time to fit residues: 2109.0414 Evaluate side-chains 926 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 683 time to evaluate : 7.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 117 GLU Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 115 MET Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 445 PHE Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 246 LYS Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 14 CYS Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 249 CYS Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 320 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 14 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 445 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 55 ILE Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 320 CYS Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 76 LYS Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 248 GLN Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 373 ASP Chi-restraints excluded: chain R residue 443 THR Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 491 VAL Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain T residue 493 MET Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 445 PHE Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 108 ASP Chi-restraints excluded: chain V residue 115 MET Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 445 PHE Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 314 THR Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 190 VAL Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 414 ASN Chi-restraints excluded: chain X residue 466 LYS Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 715 optimal weight: 7.9990 chunk 461 optimal weight: 7.9990 chunk 690 optimal weight: 4.9990 chunk 348 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 224 optimal weight: 0.9980 chunk 735 optimal weight: 10.0000 chunk 787 optimal weight: 3.9990 chunk 571 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 909 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN C 492 ASN E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN ** G 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN N 414 ASN ** O 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 112 GLN Q 416 ASN ** R 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 425 ASN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 425 ASN U 456 GLN X 379 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 91896 Z= 0.234 Angle : 0.534 7.089 125520 Z= 0.279 Chirality : 0.042 0.153 14520 Planarity : 0.004 0.038 16632 Dihedral : 4.946 55.023 12888 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 3.34 % Allowed : 16.40 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.06 (0.08), residues: 11952 helix: 1.20 (0.09), residues: 3456 sheet: -0.15 (0.12), residues: 2088 loop : -0.49 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 237 HIS 0.003 0.001 HIS T 252 PHE 0.017 0.001 PHE D 194 TYR 0.019 0.001 TYR S 114 ARG 0.012 0.000 ARG K 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 723 time to evaluate : 7.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: D 198 THR cc_start: 0.8413 (OUTLIER) cc_final: 0.8167 (t) REVERT: D 452 ASN cc_start: 0.8675 (OUTLIER) cc_final: 0.8447 (m110) REVERT: D 499 ASP cc_start: 0.5954 (OUTLIER) cc_final: 0.5318 (m-30) REVERT: A 34 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8450 (ptt) REVERT: A 108 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: A 418 ARG cc_start: 0.8328 (mmm-85) cc_final: 0.6655 (mpt180) REVERT: A 439 ASP cc_start: 0.7868 (m-30) cc_final: 0.7642 (m-30) REVERT: A 466 LYS cc_start: 0.8501 (mtmt) cc_final: 0.7980 (mmpt) REVERT: B 328 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8607 (p) REVERT: C 13 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9027 (mp) REVERT: C 24 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7593 (mm-30) REVERT: C 51 GLU cc_start: 0.7876 (tt0) cc_final: 0.7648 (mt-10) REVERT: E 328 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8604 (p) REVERT: E 439 ASP cc_start: 0.8367 (t0) cc_final: 0.8070 (m-30) REVERT: E 450 ASN cc_start: 0.7982 (t0) cc_final: 0.7721 (t0) REVERT: E 453 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: G 232 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: G 323 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8481 (ptt) REVERT: G 456 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: H 56 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7619 (mm-30) REVERT: H 108 ASP cc_start: 0.8095 (m-30) cc_final: 0.7805 (m-30) REVERT: H 427 ARG cc_start: 0.8137 (ttp-110) cc_final: 0.7526 (ttm-80) REVERT: H 488 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.7945 (ttt-90) REVERT: I 375 LYS cc_start: 0.7890 (mmtp) cc_final: 0.6886 (mmtt) REVERT: I 435 LYS cc_start: 0.8459 (tppt) cc_final: 0.8005 (tttt) REVERT: I 453 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7827 (mt-10) REVERT: I 464 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: I 466 LYS cc_start: 0.5596 (OUTLIER) cc_final: 0.4648 (mmpt) REVERT: I 481 ARG cc_start: 0.8899 (mtp85) cc_final: 0.7225 (mmp-170) REVERT: J 56 GLU cc_start: 0.7838 (mp0) cc_final: 0.7600 (mp0) REVERT: K 87 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7767 (mt-10) REVERT: K 328 THR cc_start: 0.8718 (m) cc_final: 0.8315 (p) REVERT: K 418 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.6636 (mtt90) REVERT: L 87 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: L 260 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8571 (p) REVERT: L 313 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8201 (mt0) REVERT: L 427 ARG cc_start: 0.8141 (ttp-110) cc_final: 0.7630 (ttm-80) REVERT: M 173 SER cc_start: 0.8905 (t) cc_final: 0.8641 (p) REVERT: M 372 ARG cc_start: 0.8189 (ptp90) cc_final: 0.7853 (mtm-85) REVERT: M 500 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8403 (m-40) REVERT: N 76 LYS cc_start: 0.4861 (pmtt) cc_final: 0.4173 (ptpt) REVERT: N 188 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7079 (mm-30) REVERT: N 418 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7880 (mtt-85) REVERT: N 452 ASN cc_start: 0.8471 (m110) cc_final: 0.8162 (m-40) REVERT: P 117 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8206 (tm-30) REVERT: P 232 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: P 353 SER cc_start: 0.8777 (t) cc_final: 0.8363 (m) REVERT: P 453 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7464 (mp0) REVERT: P 456 GLN cc_start: 0.8868 (OUTLIER) cc_final: 0.7939 (mt0) REVERT: Q 24 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7003 (tt0) REVERT: Q 34 MET cc_start: 0.8853 (ptm) cc_final: 0.8579 (ptm) REVERT: Q 46 THR cc_start: 0.8738 (p) cc_final: 0.8411 (t) REVERT: Q 373 ASP cc_start: 0.6916 (m-30) cc_final: 0.6354 (m-30) REVERT: Q 377 ARG cc_start: 0.4461 (OUTLIER) cc_final: 0.3266 (mtp85) REVERT: Q 452 ASN cc_start: 0.8784 (m110) cc_final: 0.8411 (m-40) REVERT: Q 493 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8360 (mtm) REVERT: R 51 GLU cc_start: 0.7644 (pm20) cc_final: 0.7330 (pm20) REVERT: R 173 SER cc_start: 0.8836 (t) cc_final: 0.8367 (p) REVERT: R 323 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8058 (ptt) REVERT: R 413 LYS cc_start: 0.8909 (pttm) cc_final: 0.8506 (ptpt) REVERT: R 466 LYS cc_start: 0.7134 (mmpt) cc_final: 0.6371 (tmtt) REVERT: R 488 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7453 (ttp-170) REVERT: S 188 GLU cc_start: 0.8232 (mp0) cc_final: 0.7631 (mp0) REVERT: U 27 LYS cc_start: 0.8402 (mtpp) cc_final: 0.7891 (mttm) REVERT: U 87 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7870 (mt-10) REVERT: U 249 CYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5217 (m) REVERT: U 377 ARG cc_start: 0.5175 (OUTLIER) cc_final: 0.3663 (mtt-85) REVERT: U 418 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.6958 (mpp-170) REVERT: V 119 GLU cc_start: 0.8058 (tt0) cc_final: 0.7840 (tm-30) REVERT: W 488 ARG cc_start: 0.8316 (tpp80) cc_final: 0.7913 (ttt90) REVERT: X 323 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8250 (mtp) outliers start: 325 outliers final: 236 residues processed: 960 average time/residue: 1.5272 time to fit residues: 2041.1929 Evaluate side-chains 961 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 691 time to evaluate : 7.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 37 ASP Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 323 MET Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 445 PHE Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 246 LYS Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 261 LEU Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain I residue 466 LYS Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 323 MET Chi-restraints excluded: chain J residue 466 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 14 CYS Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 320 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 313 GLN Chi-restraints excluded: chain L residue 443 THR Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 249 CYS Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 320 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 462 GLU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 14 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 445 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain P residue 117 GLU Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 320 CYS Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 24 GLU Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 14 CYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 384 ASP Chi-restraints excluded: chain R residue 443 THR Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 470 GLN Chi-restraints excluded: chain S residue 499 ASP Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 413 LYS Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain T residue 493 MET Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 211 THR Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 445 PHE Chi-restraints excluded: chain V residue 20 ASN Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 108 ASP Chi-restraints excluded: chain V residue 115 MET Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 445 PHE Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain W residue 449 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 115 MET Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 323 MET Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 466 LYS Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1052 optimal weight: 0.8980 chunk 1108 optimal weight: 1.9990 chunk 1010 optimal weight: 5.9990 chunk 1077 optimal weight: 1.9990 chunk 1107 optimal weight: 8.9990 chunk 648 optimal weight: 10.0000 chunk 469 optimal weight: 10.0000 chunk 846 optimal weight: 8.9990 chunk 330 optimal weight: 10.0000 chunk 973 optimal weight: 6.9990 chunk 1019 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN H 60 GLN I 414 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 355 GLN N 60 GLN ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 ASN O 112 GLN ** O 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 416 ASN ** R 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 404 GLN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 112 GLN U 456 GLN W 379 ASN X 379 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 91896 Z= 0.335 Angle : 0.580 7.435 125520 Z= 0.303 Chirality : 0.043 0.159 14520 Planarity : 0.004 0.040 16632 Dihedral : 5.161 56.231 12888 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.36 % Allowed : 16.57 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 11952 helix: 1.10 (0.09), residues: 3456 sheet: -0.18 (0.12), residues: 2088 loop : -0.50 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 242 HIS 0.003 0.001 HIS H 252 PHE 0.020 0.001 PHE P 218 TYR 0.023 0.002 TYR Q 176 ARG 0.012 0.001 ARG K 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 327 poor density : 694 time to evaluate : 8.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 188 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.6630 (mp0) REVERT: D 198 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8330 (t) REVERT: D 452 ASN cc_start: 0.8718 (OUTLIER) cc_final: 0.8470 (m110) REVERT: D 499 ASP cc_start: 0.5647 (OUTLIER) cc_final: 0.4983 (m-30) REVERT: A 34 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8523 (ptt) REVERT: A 377 ARG cc_start: 0.4660 (tmt170) cc_final: 0.4458 (mmt180) REVERT: A 418 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.6590 (mpt180) REVERT: A 466 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8029 (mmpt) REVERT: C 13 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9002 (mp) REVERT: C 24 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7610 (mm-30) REVERT: C 51 GLU cc_start: 0.7879 (tt0) cc_final: 0.7619 (mt-10) REVERT: E 34 MET cc_start: 0.9210 (ptt) cc_final: 0.8666 (ptt) REVERT: E 328 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8642 (p) REVERT: E 439 ASP cc_start: 0.8422 (t0) cc_final: 0.8125 (m-30) REVERT: E 450 ASN cc_start: 0.8041 (t0) cc_final: 0.7751 (t0) REVERT: E 453 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: F 163 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8369 (mpt90) REVERT: G 188 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: G 232 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7324 (mt-10) REVERT: G 323 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8551 (ptt) REVERT: G 456 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: H 56 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7659 (mm-30) REVERT: H 108 ASP cc_start: 0.8102 (m-30) cc_final: 0.7808 (m-30) REVERT: H 427 ARG cc_start: 0.8171 (ttp-110) cc_final: 0.7562 (ttm-80) REVERT: H 488 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.7958 (ttt-90) REVERT: I 435 LYS cc_start: 0.8465 (tppt) cc_final: 0.8005 (tttt) REVERT: I 464 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.7437 (mp10) REVERT: I 466 LYS cc_start: 0.5612 (OUTLIER) cc_final: 0.4657 (mmpt) REVERT: I 481 ARG cc_start: 0.8892 (mtp85) cc_final: 0.7215 (mmp-170) REVERT: J 56 GLU cc_start: 0.7838 (mp0) cc_final: 0.7576 (mp0) REVERT: K 87 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7797 (mt-10) REVERT: K 328 THR cc_start: 0.8767 (m) cc_final: 0.8378 (p) REVERT: K 418 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.6656 (mtt90) REVERT: L 87 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: L 260 THR cc_start: 0.8826 (OUTLIER) cc_final: 0.8539 (p) REVERT: L 313 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: L 427 ARG cc_start: 0.8167 (ttp-110) cc_final: 0.7661 (ttm-80) REVERT: M 173 SER cc_start: 0.8936 (t) cc_final: 0.8677 (p) REVERT: M 372 ARG cc_start: 0.8226 (ptp90) cc_final: 0.7966 (ptp-110) REVERT: M 500 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8431 (m-40) REVERT: N 76 LYS cc_start: 0.4899 (pmtt) cc_final: 0.4254 (ptpt) REVERT: N 188 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7139 (mm-30) REVERT: N 418 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7895 (mtt-85) REVERT: N 452 ASN cc_start: 0.8526 (m110) cc_final: 0.8182 (m-40) REVERT: O 24 GLU cc_start: 0.7942 (tp30) cc_final: 0.7729 (tp30) REVERT: P 232 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7239 (mt-10) REVERT: P 353 SER cc_start: 0.8862 (t) cc_final: 0.8368 (m) REVERT: P 453 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: P 456 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: Q 46 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8410 (t) REVERT: Q 377 ARG cc_start: 0.4489 (OUTLIER) cc_final: 0.3148 (mtp85) REVERT: Q 452 ASN cc_start: 0.8846 (m110) cc_final: 0.8468 (m-40) REVERT: Q 478 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.8727 (ttp) REVERT: R 51 GLU cc_start: 0.7688 (pm20) cc_final: 0.7385 (pm20) REVERT: R 173 SER cc_start: 0.8848 (t) cc_final: 0.8372 (p) REVERT: R 323 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8100 (ptt) REVERT: R 413 LYS cc_start: 0.8887 (pttm) cc_final: 0.8485 (ptpt) REVERT: R 488 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7531 (ttp-170) REVERT: T 232 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7274 (mm-30) REVERT: U 87 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: U 249 CYS cc_start: 0.5856 (OUTLIER) cc_final: 0.5396 (m) REVERT: U 377 ARG cc_start: 0.5153 (OUTLIER) cc_final: 0.3610 (mtt-85) REVERT: U 418 ARG cc_start: 0.7770 (mmm-85) cc_final: 0.6810 (mpp-170) REVERT: W 488 ARG cc_start: 0.8386 (tpp80) cc_final: 0.7970 (ttt90) outliers start: 327 outliers final: 240 residues processed: 933 average time/residue: 1.5414 time to fit residues: 1998.5830 Evaluate side-chains 937 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 665 time to evaluate : 7.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 445 PHE Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain I residue 466 LYS Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 466 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 14 CYS Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 320 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 313 GLN Chi-restraints excluded: chain L residue 443 THR Chi-restraints excluded: chain L residue 453 GLU Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain L residue 491 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 249 CYS Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 320 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 462 GLU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 14 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 445 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 320 CYS Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 248 GLN Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 478 MET Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 14 CYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 443 THR Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 499 ASP Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 413 LYS Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain T residue 466 LYS Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 87 GLU Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 211 THR Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 445 PHE Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 108 ASP Chi-restraints excluded: chain V residue 115 MET Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 445 PHE Chi-restraints excluded: chain V residue 449 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 131 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 314 THR Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain W residue 449 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 1074 optimal weight: 5.9990 chunk 707 optimal weight: 6.9990 chunk 1139 optimal weight: 2.9990 chunk 695 optimal weight: 9.9990 chunk 540 optimal weight: 3.9990 chunk 792 optimal weight: 8.9990 chunk 1195 optimal weight: 5.9990 chunk 1100 optimal weight: 7.9990 chunk 951 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 735 optimal weight: 4.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN ** L 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN ** N 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 414 ASN O 112 GLN ** O 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 355 GLN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 456 GLN X 379 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 91896 Z= 0.341 Angle : 0.582 8.371 125520 Z= 0.304 Chirality : 0.043 0.181 14520 Planarity : 0.004 0.040 16632 Dihedral : 5.202 56.577 12888 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.10 % Allowed : 17.04 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.08), residues: 11952 helix: 1.07 (0.09), residues: 3456 sheet: -0.19 (0.12), residues: 2088 loop : -0.52 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 242 HIS 0.003 0.001 HIS H 252 PHE 0.021 0.002 PHE K 218 TYR 0.022 0.002 TYR Q 176 ARG 0.012 0.001 ARG K 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23904 Ramachandran restraints generated. 11952 Oldfield, 0 Emsley, 11952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 677 time to evaluate : 8.041 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 188 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6613 (mp0) REVERT: D 198 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8377 (t) REVERT: D 452 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8403 (m110) REVERT: D 499 ASP cc_start: 0.5684 (OUTLIER) cc_final: 0.5005 (m-30) REVERT: A 34 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8497 (ptt) REVERT: A 377 ARG cc_start: 0.4523 (tmt170) cc_final: 0.4317 (mmt180) REVERT: A 418 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.6531 (mpt180) REVERT: A 466 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8018 (mmpt) REVERT: C 13 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9000 (mp) REVERT: C 24 GLU cc_start: 0.7886 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 51 GLU cc_start: 0.7908 (tt0) cc_final: 0.7630 (mt-10) REVERT: E 34 MET cc_start: 0.9210 (ptt) cc_final: 0.8657 (ptt) REVERT: E 439 ASP cc_start: 0.8432 (t0) cc_final: 0.8107 (m-30) REVERT: E 450 ASN cc_start: 0.8060 (t0) cc_final: 0.7781 (t0) REVERT: E 453 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7494 (pt0) REVERT: E 466 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7660 (tmtt) REVERT: F 163 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8365 (mpt90) REVERT: G 117 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7961 (tm-30) REVERT: G 188 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7986 (mm-30) REVERT: G 232 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: G 323 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8542 (ptt) REVERT: G 456 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7637 (mm-40) REVERT: H 56 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: H 108 ASP cc_start: 0.8096 (m-30) cc_final: 0.7802 (m-30) REVERT: H 427 ARG cc_start: 0.8166 (ttp-110) cc_final: 0.7572 (ttm-80) REVERT: H 488 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.7960 (ttt-90) REVERT: I 435 LYS cc_start: 0.8472 (tppt) cc_final: 0.8013 (tttt) REVERT: I 464 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7446 (mp10) REVERT: I 466 LYS cc_start: 0.5614 (OUTLIER) cc_final: 0.4665 (mmpt) REVERT: I 481 ARG cc_start: 0.8889 (mtp85) cc_final: 0.7180 (mmp-170) REVERT: J 56 GLU cc_start: 0.7832 (mp0) cc_final: 0.7582 (mp0) REVERT: K 87 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7832 (mt-10) REVERT: K 328 THR cc_start: 0.8776 (m) cc_final: 0.8397 (p) REVERT: K 418 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.6650 (mtt90) REVERT: L 87 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: L 260 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8560 (p) REVERT: L 313 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: L 427 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7663 (ttm-80) REVERT: M 173 SER cc_start: 0.8947 (t) cc_final: 0.8691 (p) REVERT: M 372 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7925 (ptp-110) REVERT: M 500 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8386 (m-40) REVERT: N 76 LYS cc_start: 0.4908 (pmtt) cc_final: 0.4131 (ptpt) REVERT: N 188 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7130 (mm-30) REVERT: N 418 ARG cc_start: 0.8211 (mtt-85) cc_final: 0.7885 (mtt-85) REVERT: N 452 ASN cc_start: 0.8541 (m110) cc_final: 0.8186 (m-40) REVERT: O 24 GLU cc_start: 0.7963 (tp30) cc_final: 0.7691 (tp30) REVERT: P 232 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: P 353 SER cc_start: 0.8866 (t) cc_final: 0.8367 (m) REVERT: P 453 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7476 (mp0) REVERT: P 456 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7970 (mt0) REVERT: Q 34 MET cc_start: 0.8877 (ptm) cc_final: 0.8637 (ptm) REVERT: Q 46 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8455 (t) REVERT: Q 54 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8580 (mm) REVERT: Q 377 ARG cc_start: 0.4538 (OUTLIER) cc_final: 0.3100 (mtp85) REVERT: Q 452 ASN cc_start: 0.8829 (m110) cc_final: 0.8470 (m-40) REVERT: Q 478 MET cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (ttp) REVERT: R 51 GLU cc_start: 0.7682 (pm20) cc_final: 0.7370 (pm20) REVERT: R 173 SER cc_start: 0.8843 (t) cc_final: 0.8366 (p) REVERT: R 323 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (ptt) REVERT: R 413 LYS cc_start: 0.8884 (pttm) cc_final: 0.8486 (ptpt) REVERT: R 488 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7531 (ttp-170) REVERT: T 232 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7269 (mm-30) REVERT: U 27 LYS cc_start: 0.8397 (mtpp) cc_final: 0.7867 (mttm) REVERT: U 249 CYS cc_start: 0.5839 (OUTLIER) cc_final: 0.5406 (m) REVERT: U 377 ARG cc_start: 0.5246 (OUTLIER) cc_final: 0.3640 (mtt-85) REVERT: U 418 ARG cc_start: 0.7780 (mmm-85) cc_final: 0.6799 (mpp-170) REVERT: V 215 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7961 (mm-30) REVERT: W 488 ARG cc_start: 0.8387 (tpp80) cc_final: 0.7965 (ttt90) outliers start: 301 outliers final: 245 residues processed: 902 average time/residue: 1.5398 time to fit residues: 1925.4193 Evaluate side-chains 941 residues out of total 9720 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 665 time to evaluate : 7.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 CYS Chi-restraints excluded: chain D residue 188 GLU Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 300 CYS Chi-restraints excluded: chain D residue 414 ASN Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 452 ASN Chi-restraints excluded: chain D residue 499 ASP Chi-restraints excluded: chain A residue 14 CYS Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 249 CYS Chi-restraints excluded: chain A residue 300 CYS Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 300 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 100 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 300 CYS Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 419 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 445 PHE Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain E residue 14 CYS Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 49 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 300 CYS Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 373 ASP Chi-restraints excluded: chain E residue 379 ASN Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 491 VAL Chi-restraints excluded: chain F residue 14 CYS Chi-restraints excluded: chain F residue 28 ILE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 75 CYS Chi-restraints excluded: chain F residue 152 THR Chi-restraints excluded: chain F residue 163 ARG Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 211 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 384 ASP Chi-restraints excluded: chain G residue 14 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 ILE Chi-restraints excluded: chain G residue 115 MET Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 191 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 260 THR Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 313 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 445 PHE Chi-restraints excluded: chain G residue 449 ASP Chi-restraints excluded: chain G residue 456 GLN Chi-restraints excluded: chain H residue 28 ILE Chi-restraints excluded: chain H residue 56 GLU Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 115 MET Chi-restraints excluded: chain H residue 300 CYS Chi-restraints excluded: chain H residue 314 THR Chi-restraints excluded: chain H residue 347 SER Chi-restraints excluded: chain I residue 13 LEU Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 115 MET Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain I residue 205 THR Chi-restraints excluded: chain I residue 249 CYS Chi-restraints excluded: chain I residue 300 CYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 464 GLN Chi-restraints excluded: chain I residue 466 LYS Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain J residue 28 ILE Chi-restraints excluded: chain J residue 37 ASP Chi-restraints excluded: chain J residue 232 GLU Chi-restraints excluded: chain J residue 281 THR Chi-restraints excluded: chain J residue 300 CYS Chi-restraints excluded: chain J residue 466 LYS Chi-restraints excluded: chain J residue 491 VAL Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 14 CYS Chi-restraints excluded: chain K residue 37 ASP Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 100 THR Chi-restraints excluded: chain K residue 115 MET Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 183 THR Chi-restraints excluded: chain K residue 300 CYS Chi-restraints excluded: chain K residue 320 CYS Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 418 ARG Chi-restraints excluded: chain K residue 443 THR Chi-restraints excluded: chain K residue 491 VAL Chi-restraints excluded: chain L residue 13 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 37 ASP Chi-restraints excluded: chain L residue 41 THR Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 260 THR Chi-restraints excluded: chain L residue 300 CYS Chi-restraints excluded: chain L residue 313 GLN Chi-restraints excluded: chain L residue 443 THR Chi-restraints excluded: chain L residue 453 GLU Chi-restraints excluded: chain L residue 466 LYS Chi-restraints excluded: chain L residue 491 VAL Chi-restraints excluded: chain M residue 8 ASP Chi-restraints excluded: chain M residue 14 CYS Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain M residue 185 VAL Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 193 THR Chi-restraints excluded: chain M residue 249 CYS Chi-restraints excluded: chain M residue 300 CYS Chi-restraints excluded: chain M residue 320 CYS Chi-restraints excluded: chain M residue 327 CYS Chi-restraints excluded: chain M residue 347 SER Chi-restraints excluded: chain M residue 384 ASP Chi-restraints excluded: chain M residue 386 SER Chi-restraints excluded: chain M residue 419 THR Chi-restraints excluded: chain M residue 424 THR Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain M residue 462 GLU Chi-restraints excluded: chain M residue 466 LYS Chi-restraints excluded: chain M residue 500 ASN Chi-restraints excluded: chain N residue 8 ASP Chi-restraints excluded: chain N residue 14 CYS Chi-restraints excluded: chain N residue 46 THR Chi-restraints excluded: chain N residue 54 ILE Chi-restraints excluded: chain N residue 300 CYS Chi-restraints excluded: chain N residue 328 THR Chi-restraints excluded: chain N residue 419 THR Chi-restraints excluded: chain N residue 445 PHE Chi-restraints excluded: chain N residue 491 VAL Chi-restraints excluded: chain O residue 14 CYS Chi-restraints excluded: chain O residue 46 THR Chi-restraints excluded: chain O residue 248 GLN Chi-restraints excluded: chain O residue 300 CYS Chi-restraints excluded: chain O residue 327 CYS Chi-restraints excluded: chain O residue 386 SER Chi-restraints excluded: chain O residue 445 PHE Chi-restraints excluded: chain O residue 491 VAL Chi-restraints excluded: chain P residue 52 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain P residue 115 MET Chi-restraints excluded: chain P residue 184 SER Chi-restraints excluded: chain P residue 202 VAL Chi-restraints excluded: chain P residue 232 GLU Chi-restraints excluded: chain P residue 245 SER Chi-restraints excluded: chain P residue 300 CYS Chi-restraints excluded: chain P residue 314 THR Chi-restraints excluded: chain P residue 347 SER Chi-restraints excluded: chain P residue 443 THR Chi-restraints excluded: chain P residue 446 SER Chi-restraints excluded: chain P residue 453 GLU Chi-restraints excluded: chain P residue 456 GLN Chi-restraints excluded: chain P residue 491 VAL Chi-restraints excluded: chain Q residue 13 LEU Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Q residue 54 ILE Chi-restraints excluded: chain Q residue 190 VAL Chi-restraints excluded: chain Q residue 198 THR Chi-restraints excluded: chain Q residue 300 CYS Chi-restraints excluded: chain Q residue 327 CYS Chi-restraints excluded: chain Q residue 377 ARG Chi-restraints excluded: chain Q residue 384 ASP Chi-restraints excluded: chain Q residue 462 GLU Chi-restraints excluded: chain Q residue 478 MET Chi-restraints excluded: chain Q residue 491 VAL Chi-restraints excluded: chain Q residue 493 MET Chi-restraints excluded: chain R residue 8 ASP Chi-restraints excluded: chain R residue 14 CYS Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 300 CYS Chi-restraints excluded: chain R residue 323 MET Chi-restraints excluded: chain R residue 352 THR Chi-restraints excluded: chain R residue 443 THR Chi-restraints excluded: chain R residue 488 ARG Chi-restraints excluded: chain R residue 491 VAL Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain S residue 202 VAL Chi-restraints excluded: chain S residue 228 THR Chi-restraints excluded: chain S residue 300 CYS Chi-restraints excluded: chain S residue 323 MET Chi-restraints excluded: chain S residue 326 SER Chi-restraints excluded: chain S residue 443 THR Chi-restraints excluded: chain S residue 462 GLU Chi-restraints excluded: chain S residue 491 VAL Chi-restraints excluded: chain S residue 499 ASP Chi-restraints excluded: chain T residue 46 THR Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 202 VAL Chi-restraints excluded: chain T residue 300 CYS Chi-restraints excluded: chain T residue 314 THR Chi-restraints excluded: chain T residue 413 LYS Chi-restraints excluded: chain T residue 443 THR Chi-restraints excluded: chain T residue 458 LEU Chi-restraints excluded: chain U residue 28 ILE Chi-restraints excluded: chain U residue 41 THR Chi-restraints excluded: chain U residue 115 MET Chi-restraints excluded: chain U residue 190 VAL Chi-restraints excluded: chain U residue 211 THR Chi-restraints excluded: chain U residue 249 CYS Chi-restraints excluded: chain U residue 300 CYS Chi-restraints excluded: chain U residue 377 ARG Chi-restraints excluded: chain U residue 445 PHE Chi-restraints excluded: chain V residue 49 THR Chi-restraints excluded: chain V residue 108 ASP Chi-restraints excluded: chain V residue 190 VAL Chi-restraints excluded: chain V residue 300 CYS Chi-restraints excluded: chain V residue 387 SER Chi-restraints excluded: chain V residue 419 THR Chi-restraints excluded: chain V residue 445 PHE Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 100 THR Chi-restraints excluded: chain W residue 185 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 202 VAL Chi-restraints excluded: chain W residue 300 CYS Chi-restraints excluded: chain W residue 314 THR Chi-restraints excluded: chain W residue 419 THR Chi-restraints excluded: chain W residue 449 ASP Chi-restraints excluded: chain W residue 499 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 37 ASP Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 73 CYS Chi-restraints excluded: chain X residue 100 THR Chi-restraints excluded: chain X residue 202 VAL Chi-restraints excluded: chain X residue 300 CYS Chi-restraints excluded: chain X residue 314 THR Chi-restraints excluded: chain X residue 387 SER Chi-restraints excluded: chain X residue 443 THR Chi-restraints excluded: chain X residue 499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1200 random chunks: chunk 583 optimal weight: 4.9990 chunk 756 optimal weight: 0.9980 chunk 1014 optimal weight: 0.8980 chunk 291 optimal weight: 10.0000 chunk 877 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 264 optimal weight: 0.5980 chunk 953 optimal weight: 1.9990 chunk 399 optimal weight: 7.9990 chunk 979 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 414 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN G 404 GLN ** H 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 414 ASN I 450 ASN L 464 GLN M 357 ASN N 60 GLN N 414 ASN O 112 GLN Q 416 ASN R 112 GLN R 355 GLN ** T 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 20 ASN U 456 GLN X 379 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.101207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089307 restraints weight = 142862.144| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.01 r_work: 0.2993 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 91896 Z= 0.165 Angle : 0.507 8.297 125520 Z= 0.264 Chirality : 0.041 0.165 14520 Planarity : 0.003 0.037 16632 Dihedral : 4.745 54.121 12888 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.43 % Allowed : 17.67 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.17 (0.08), residues: 11952 helix: 1.33 (0.09), residues: 3456 sheet: -0.10 (0.12), residues: 2088 loop : -0.43 (0.08), residues: 6408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 237 HIS 0.002 0.000 HIS T 252 PHE 0.019 0.001 PHE P 218 TYR 0.021 0.001 TYR S 114 ARG 0.010 0.000 ARG K 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32360.20 seconds wall clock time: 563 minutes 24.09 seconds (33804.09 seconds total)