Starting phenix.real_space_refine on Tue Mar 19 13:27:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pv4_13665/03_2024/7pv4_13665.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 15588 2.51 5 N 4020 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 83": "OD1" <-> "OD2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 281": "NH1" <-> "NH2" Residue "A GLU 284": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "B GLU 62": "OE1" <-> "OE2" Residue "B GLU 73": "OE1" <-> "OE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B ARG 281": "NH1" <-> "NH2" Residue "B GLU 284": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 300": "OE1" <-> "OE2" Residue "C GLU 62": "OE1" <-> "OE2" Residue "C GLU 73": "OE1" <-> "OE2" Residue "C PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 83": "OD1" <-> "OD2" Residue "C PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C ARG 141": "NH1" <-> "NH2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ARG 281": "NH1" <-> "NH2" Residue "C GLU 284": "OE1" <-> "OE2" Residue "C GLU 293": "OE1" <-> "OE2" Residue "C GLU 300": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 83": "OD1" <-> "OD2" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 106": "OD1" <-> "OD2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 132": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D ARG 275": "NH1" <-> "NH2" Residue "D ARG 281": "NH1" <-> "NH2" Residue "D GLU 284": "OE1" <-> "OE2" Residue "D GLU 293": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 106": "OD1" <-> "OD2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 132": "OD1" <-> "OD2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ARG 141": "NH1" <-> "NH2" Residue "E PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E ARG 281": "NH1" <-> "NH2" Residue "E GLU 284": "OE1" <-> "OE2" Residue "E GLU 293": "OE1" <-> "OE2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F ASP 109": "OD1" <-> "OD2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 132": "OD1" <-> "OD2" Residue "F ASP 134": "OD1" <-> "OD2" Residue "F ARG 141": "NH1" <-> "NH2" Residue "F PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F ARG 275": "NH1" <-> "NH2" Residue "F ARG 281": "NH1" <-> "NH2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 300": "OE1" <-> "OE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G GLU 73": "OE1" <-> "OE2" Residue "G PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 83": "OD1" <-> "OD2" Residue "G PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 106": "OD1" <-> "OD2" Residue "G ASP 109": "OD1" <-> "OD2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 132": "OD1" <-> "OD2" Residue "G ASP 134": "OD1" <-> "OD2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 222": "OD1" <-> "OD2" Residue "G GLU 269": "OE1" <-> "OE2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ARG 281": "NH1" <-> "NH2" Residue "G GLU 284": "OE1" <-> "OE2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "G GLU 300": "OE1" <-> "OE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 83": "OD1" <-> "OD2" Residue "H PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 106": "OD1" <-> "OD2" Residue "H ASP 109": "OD1" <-> "OD2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 132": "OD1" <-> "OD2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H ARG 141": "NH1" <-> "NH2" Residue "H PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 222": "OD1" <-> "OD2" Residue "H GLU 269": "OE1" <-> "OE2" Residue "H ARG 275": "NH1" <-> "NH2" Residue "H ARG 281": "NH1" <-> "NH2" Residue "H GLU 284": "OE1" <-> "OE2" Residue "H GLU 293": "OE1" <-> "OE2" Residue "H GLU 300": "OE1" <-> "OE2" Residue "I GLU 62": "OE1" <-> "OE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 83": "OD1" <-> "OD2" Residue "I PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 106": "OD1" <-> "OD2" Residue "I ASP 109": "OD1" <-> "OD2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 132": "OD1" <-> "OD2" Residue "I ASP 134": "OD1" <-> "OD2" Residue "I ARG 141": "NH1" <-> "NH2" Residue "I PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 222": "OD1" <-> "OD2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ARG 281": "NH1" <-> "NH2" Residue "I GLU 284": "OE1" <-> "OE2" Residue "I GLU 293": "OE1" <-> "OE2" Residue "I GLU 300": "OE1" <-> "OE2" Residue "J GLU 62": "OE1" <-> "OE2" Residue "J GLU 73": "OE1" <-> "OE2" Residue "J PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 83": "OD1" <-> "OD2" Residue "J PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 106": "OD1" <-> "OD2" Residue "J ASP 109": "OD1" <-> "OD2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 132": "OD1" <-> "OD2" Residue "J ASP 134": "OD1" <-> "OD2" Residue "J ARG 141": "NH1" <-> "NH2" Residue "J PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 222": "OD1" <-> "OD2" Residue "J GLU 269": "OE1" <-> "OE2" Residue "J ARG 275": "NH1" <-> "NH2" Residue "J ARG 281": "NH1" <-> "NH2" Residue "J GLU 284": "OE1" <-> "OE2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J GLU 300": "OE1" <-> "OE2" Residue "K GLU 62": "OE1" <-> "OE2" Residue "K GLU 73": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 106": "OD1" <-> "OD2" Residue "K ASP 109": "OD1" <-> "OD2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 132": "OD1" <-> "OD2" Residue "K ASP 134": "OD1" <-> "OD2" Residue "K ARG 141": "NH1" <-> "NH2" Residue "K PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 222": "OD1" <-> "OD2" Residue "K GLU 269": "OE1" <-> "OE2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K ARG 281": "NH1" <-> "NH2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K GLU 293": "OE1" <-> "OE2" Residue "K GLU 300": "OE1" <-> "OE2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L GLU 73": "OE1" <-> "OE2" Residue "L PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 83": "OD1" <-> "OD2" Residue "L PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 106": "OD1" <-> "OD2" Residue "L ASP 109": "OD1" <-> "OD2" Residue "L TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 132": "OD1" <-> "OD2" Residue "L ASP 134": "OD1" <-> "OD2" Residue "L ARG 141": "NH1" <-> "NH2" Residue "L PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 222": "OD1" <-> "OD2" Residue "L GLU 269": "OE1" <-> "OE2" Residue "L ARG 275": "NH1" <-> "NH2" Residue "L ARG 281": "NH1" <-> "NH2" Residue "L GLU 284": "OE1" <-> "OE2" Residue "L GLU 293": "OE1" <-> "OE2" Residue "L GLU 300": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24336 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "H" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "J" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "K" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "L" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 13.01, per 1000 atoms: 0.53 Number of scatterers: 24336 At special positions: 0 Unit cell: (172.27, 172.27, 96.3, 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 144 16.00 O 4584 8.00 N 4020 7.00 C 15588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.59 Conformation dependent library (CDL) restraints added in 4.6 seconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 36 sheets defined 47.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 220 through 239 Processing helix chain 'B' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 47 " --> pdb=" O TYR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 Processing helix chain 'C' and resid 220 through 239 Processing helix chain 'C' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 220 through 239 Processing helix chain 'D' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 281 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG E 39 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'E' and resid 220 through 239 Processing helix chain 'E' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG F 39 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR F 40 " --> pdb=" O MET F 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET F 47 " --> pdb=" O TYR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE F 143 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 203 Processing helix chain 'F' and resid 220 through 239 Processing helix chain 'F' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 281 " --> pdb=" O ASP F 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG G 39 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 40 " --> pdb=" O MET G 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE G 143 " --> pdb=" O PRO G 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 203 Processing helix chain 'G' and resid 220 through 239 Processing helix chain 'G' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 281 " --> pdb=" O ASP G 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 40 " --> pdb=" O MET H 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET H 47 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE H 143 " --> pdb=" O PRO H 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 203 Processing helix chain 'H' and resid 220 through 239 Processing helix chain 'H' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG H 275 " --> pdb=" O ALA H 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG H 281 " --> pdb=" O ASP H 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG I 39 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET I 47 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE I 66 " --> pdb=" O GLU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE I 143 " --> pdb=" O PRO I 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS I 186 " --> pdb=" O ASN I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 203 Processing helix chain 'I' and resid 220 through 239 Processing helix chain 'I' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG I 275 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG I 281 " --> pdb=" O ASP I 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG J 39 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR J 40 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE J 143 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR J 145 " --> pdb=" O ARG J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS J 186 " --> pdb=" O ASN J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 203 Processing helix chain 'J' and resid 220 through 239 Processing helix chain 'J' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG J 275 " --> pdb=" O ALA J 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 281 " --> pdb=" O ASP J 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG K 39 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET K 47 " --> pdb=" O TYR K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE K 66 " --> pdb=" O GLU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE K 143 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 145 " --> pdb=" O ARG K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS K 186 " --> pdb=" O ASN K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 203 Processing helix chain 'K' and resid 220 through 239 Processing helix chain 'K' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG K 275 " --> pdb=" O ALA K 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG K 281 " --> pdb=" O ASP K 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG L 39 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR L 40 " --> pdb=" O MET L 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE L 143 " --> pdb=" O PRO L 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR L 145 " --> pdb=" O ARG L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS L 186 " --> pdb=" O ASN L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 203 Processing helix chain 'L' and resid 220 through 239 Processing helix chain 'L' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG L 275 " --> pdb=" O ALA L 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 281 " --> pdb=" O ASP L 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 114 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 120 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY A 112 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN A 75 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU A 195 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 170 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 114 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR B 120 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 112 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 75 " --> pdb=" O CYS B 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU B 195 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 170 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AA8, first strand: chain 'C' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY C 114 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR C 120 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY C 112 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 75 " --> pdb=" O CYS C 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU C 195 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 170 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'D' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY D 114 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR D 120 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY D 112 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN D 75 " --> pdb=" O CYS D 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU D 195 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 170 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY E 114 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR E 120 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY E 112 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN E 75 " --> pdb=" O CYS E 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU E 195 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE E 170 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AB8, first strand: chain 'F' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY F 114 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR F 120 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY F 112 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN F 75 " --> pdb=" O CYS F 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU F 195 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE F 170 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AC2, first strand: chain 'G' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 114 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR G 120 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY G 112 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN G 75 " --> pdb=" O CYS G 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU G 195 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE G 170 " --> pdb=" O LEU G 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY H 114 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR H 120 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY H 112 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN H 75 " --> pdb=" O CYS H 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU H 195 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE H 170 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AC8, first strand: chain 'I' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR I 118 " --> pdb=" O GLY I 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY I 114 " --> pdb=" O TYR I 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR I 120 " --> pdb=" O GLY I 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY I 112 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN I 75 " --> pdb=" O CYS I 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU I 195 " --> pdb=" O ILE I 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE I 170 " --> pdb=" O LEU I 195 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 52 through 54 Processing sheet with id=AD2, first strand: chain 'J' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR J 118 " --> pdb=" O GLY J 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY J 114 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR J 120 " --> pdb=" O GLY J 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY J 112 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN J 75 " --> pdb=" O CYS J 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU J 195 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE J 170 " --> pdb=" O LEU J 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD5, first strand: chain 'K' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR K 118 " --> pdb=" O GLY K 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY K 114 " --> pdb=" O TYR K 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR K 120 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY K 112 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN K 75 " --> pdb=" O CYS K 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU K 195 " --> pdb=" O ILE K 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE K 170 " --> pdb=" O LEU K 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 52 through 54 Processing sheet with id=AD8, first strand: chain 'L' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR L 118 " --> pdb=" O GLY L 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY L 114 " --> pdb=" O TYR L 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR L 120 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY L 112 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN L 75 " --> pdb=" O CYS L 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU L 195 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE L 170 " --> pdb=" O LEU L 195 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.55 Time building geometry restraints manager: 10.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4896 1.32 - 1.45: 5700 1.45 - 1.57: 14004 1.57 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 24840 Sorted by residual: bond pdb=" CZ ARG J 275 " pdb=" NH2 ARG J 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG A 275 " pdb=" NH2 ARG A 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG G 275 " pdb=" NH2 ARG G 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG D 275 " pdb=" NH2 ARG D 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG D 64 " pdb=" NH2 ARG D 64 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 24835 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.92: 624 105.92 - 113.39: 11464 113.39 - 120.86: 13984 120.86 - 128.33: 7480 128.33 - 135.80: 96 Bond angle restraints: 33648 Sorted by residual: angle pdb=" CB LEU K 204 " pdb=" CG LEU K 204 " pdb=" CD1 LEU K 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU B 204 " pdb=" CG LEU B 204 " pdb=" CD1 LEU B 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU E 204 " pdb=" CG LEU E 204 " pdb=" CD1 LEU E 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU H 204 " pdb=" CG LEU H 204 " pdb=" CD1 LEU H 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU L 204 " pdb=" CG LEU L 204 " pdb=" CD1 LEU L 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 ... (remaining 33643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 13776 17.64 - 35.27: 1020 35.27 - 52.91: 144 52.91 - 70.54: 48 70.54 - 88.18: 12 Dihedral angle restraints: 15000 sinusoidal: 5976 harmonic: 9024 Sorted by residual: dihedral pdb=" C ASN L 289 " pdb=" N ASN L 289 " pdb=" CA ASN L 289 " pdb=" CB ASN L 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" C ASN I 289 " pdb=" N ASN I 289 " pdb=" CA ASN I 289 " pdb=" CB ASN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" C ASN C 289 " pdb=" N ASN C 289 " pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 14997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 3540 0.208 - 0.415: 96 0.415 - 0.623: 24 0.623 - 0.831: 0 0.831 - 1.038: 12 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CG LEU E 204 " pdb=" CB LEU E 204 " pdb=" CD1 LEU E 204 " pdb=" CD2 LEU E 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CG LEU H 204 " pdb=" CB LEU H 204 " pdb=" CD1 LEU H 204 " pdb=" CD2 LEU H 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CG LEU K 204 " pdb=" CB LEU K 204 " pdb=" CD1 LEU K 204 " pdb=" CD2 LEU K 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 ... (remaining 3669 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 145 " 0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR E 145 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR E 145 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR E 145 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR E 145 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 145 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 145 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR E 145 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 145 " -0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR K 145 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR K 145 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR K 145 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR K 145 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR K 145 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR K 145 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR K 145 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " 0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR B 145 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " 0.072 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 96 2.62 - 3.19: 19000 3.19 - 3.76: 36332 3.76 - 4.33: 51904 4.33 - 4.90: 83524 Nonbonded interactions: 190856 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE2 GLU B 198 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR D 173 " pdb=" OE2 GLU E 198 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR J 173 " pdb=" OE2 GLU K 198 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR G 173 " pdb=" OE2 GLU H 198 " model vdw 2.051 2.440 nonbonded pdb=" OG1 THR B 173 " pdb=" OE2 GLU C 198 " model vdw 2.051 2.440 ... (remaining 190851 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' } 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: 4.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 7.340 Check model and map are aligned: 0.430 Set scattering table: 0.370 Process input model: 62.560 Find NCS groups from input model: 1.510 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 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 : 0.013 0.044 24840 Z= 0.828 Angle : 1.959 25.099 33648 Z= 1.325 Chirality : 0.119 1.038 3672 Planarity : 0.016 0.158 4440 Dihedral : 13.223 88.176 9192 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.19 % Favored : 98.41 % Rotamer: Outliers : 1.40 % Allowed : 2.33 % Favored : 96.28 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.13), residues: 3024 helix: -0.30 (0.12), residues: 1344 sheet: 1.99 (0.23), residues: 348 loop : -1.14 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.021 TRP A 54 HIS 0.013 0.006 HIS J 65 PHE 0.059 0.013 PHE E 190 TYR 0.119 0.024 TYR H 148 ARG 0.008 0.002 ARG A 64 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 560 time to evaluate : 2.282 Fit side-chains REVERT: A 148 TYR cc_start: 0.6831 (t80) cc_final: 0.6578 (t80) REVERT: A 285 MET cc_start: 0.7168 (ttm) cc_final: 0.6939 (ttp) REVERT: B 148 TYR cc_start: 0.6711 (t80) cc_final: 0.6420 (t80) REVERT: C 148 TYR cc_start: 0.6783 (t80) cc_final: 0.6512 (t80) REVERT: D 148 TYR cc_start: 0.6839 (t80) cc_final: 0.6587 (t80) REVERT: D 285 MET cc_start: 0.7169 (ttm) cc_final: 0.6939 (ttp) REVERT: E 148 TYR cc_start: 0.6710 (t80) cc_final: 0.6423 (t80) REVERT: F 148 TYR cc_start: 0.6782 (t80) cc_final: 0.6511 (t80) REVERT: G 148 TYR cc_start: 0.6847 (t80) cc_final: 0.6594 (t80) REVERT: G 285 MET cc_start: 0.7165 (ttm) cc_final: 0.6937 (ttp) REVERT: H 148 TYR cc_start: 0.6709 (t80) cc_final: 0.6420 (t80) REVERT: I 148 TYR cc_start: 0.6779 (t80) cc_final: 0.6505 (t80) REVERT: J 148 TYR cc_start: 0.6843 (t80) cc_final: 0.6589 (t80) REVERT: J 285 MET cc_start: 0.7167 (ttm) cc_final: 0.6940 (ttp) REVERT: K 148 TYR cc_start: 0.6714 (t80) cc_final: 0.6422 (t80) REVERT: L 148 TYR cc_start: 0.6779 (t80) cc_final: 0.6505 (t80) outliers start: 36 outliers final: 0 residues processed: 596 average time/residue: 1.2324 time to fit residues: 845.6556 Evaluate side-chains 360 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 2.9990 chunk 227 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 77 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 235 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 121 ASN A 202 GLN A 289 ASN B 101 GLN B 121 ASN B 182 ASN B 202 GLN B 289 ASN C 65 HIS C 99 ASN C 121 ASN C 289 ASN D 101 GLN D 121 ASN D 289 ASN E 101 GLN E 121 ASN E 182 ASN E 289 ASN F 65 HIS F 99 ASN F 121 ASN F 289 ASN G 101 GLN G 121 ASN G 289 ASN H 85 ASN H 101 GLN H 121 ASN H 182 ASN H 289 ASN I 65 HIS I 99 ASN I 121 ASN I 289 ASN J 101 GLN J 121 ASN J 289 ASN K 85 ASN K 101 GLN K 121 ASN K 182 ASN K 202 GLN K 289 ASN L 65 HIS L 85 ASN L 99 ASN L 121 ASN L 289 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 24840 Z= 0.262 Angle : 0.692 6.871 33648 Z= 0.368 Chirality : 0.046 0.121 3672 Planarity : 0.004 0.036 4440 Dihedral : 5.150 25.338 3312 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.29 % Allowed : 12.40 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.14), residues: 3024 helix: 1.65 (0.13), residues: 1404 sheet: 1.73 (0.23), residues: 336 loop : -0.68 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 54 HIS 0.005 0.002 HIS G 142 PHE 0.013 0.002 PHE J 119 TYR 0.010 0.002 TYR L 184 ARG 0.005 0.001 ARG H 141 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 450 time to evaluate : 2.928 Fit side-chains REVERT: B 141 ARG cc_start: 0.8202 (mmm-85) cc_final: 0.7960 (mmm160) REVERT: B 162 ASP cc_start: 0.8486 (t70) cc_final: 0.7894 (t70) REVERT: C 110 PHE cc_start: 0.7899 (m-80) cc_final: 0.7695 (m-10) REVERT: C 150 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8028 (mtt) REVERT: E 141 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7958 (mmm160) REVERT: E 162 ASP cc_start: 0.8480 (t70) cc_final: 0.7881 (t70) REVERT: F 110 PHE cc_start: 0.7898 (m-80) cc_final: 0.7695 (m-10) REVERT: F 150 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8020 (mtt) REVERT: H 141 ARG cc_start: 0.8200 (mmm-85) cc_final: 0.7959 (mmm160) REVERT: H 162 ASP cc_start: 0.8484 (t70) cc_final: 0.7890 (t70) REVERT: I 110 PHE cc_start: 0.7901 (m-80) cc_final: 0.7696 (m-10) REVERT: I 150 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8014 (mtt) REVERT: K 141 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7958 (mmm160) REVERT: K 162 ASP cc_start: 0.8489 (t70) cc_final: 0.7902 (t70) REVERT: L 110 PHE cc_start: 0.7901 (m-80) cc_final: 0.7697 (m-10) REVERT: L 150 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.8022 (mtt) outliers start: 59 outliers final: 12 residues processed: 477 average time/residue: 1.4595 time to fit residues: 790.5268 Evaluate side-chains 338 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 322 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 289 ASN Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 289 ASN Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 289 ASN Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain J residue 289 ASN Chi-restraints excluded: chain K residue 95 CYS Chi-restraints excluded: chain K residue 289 ASN Chi-restraints excluded: chain L residue 150 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 272 optimal weight: 0.8980 chunk 294 optimal weight: 0.9990 chunk 243 optimal weight: 0.0870 chunk 270 optimal weight: 0.7980 chunk 93 optimal weight: 0.0470 chunk 218 optimal weight: 0.5980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 182 ASN A 289 ASN B 99 ASN B 289 ASN C 182 ASN D 101 GLN D 182 ASN D 289 ASN E 99 ASN E 289 ASN F 182 ASN G 101 GLN G 182 ASN G 289 ASN H 99 ASN H 289 ASN I 182 ASN J 101 GLN J 182 ASN J 289 ASN K 99 ASN K 289 ASN L 182 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.7420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24840 Z= 0.145 Angle : 0.510 5.069 33648 Z= 0.270 Chirality : 0.042 0.196 3672 Planarity : 0.003 0.034 4440 Dihedral : 4.182 16.204 3312 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 3.26 % Allowed : 15.74 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.15), residues: 3024 helix: 2.56 (0.14), residues: 1404 sheet: 1.57 (0.24), residues: 336 loop : -0.56 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 54 HIS 0.003 0.001 HIS H 65 PHE 0.011 0.001 PHE J 119 TYR 0.009 0.001 TYR L 146 ARG 0.002 0.000 ARG J 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 468 time to evaluate : 2.943 Fit side-chains REVERT: A 132 ASP cc_start: 0.7578 (t70) cc_final: 0.7316 (t70) REVERT: D 132 ASP cc_start: 0.7576 (t70) cc_final: 0.7318 (t70) REVERT: G 132 ASP cc_start: 0.7578 (t70) cc_final: 0.7320 (t70) REVERT: J 132 ASP cc_start: 0.7574 (t70) cc_final: 0.7316 (t70) outliers start: 84 outliers final: 20 residues processed: 504 average time/residue: 1.3168 time to fit residues: 760.9484 Evaluate side-chains 422 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 402 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 289 ASN Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 289 ASN Chi-restraints excluded: chain E residue 289 ASN Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain F residue 289 ASN Chi-restraints excluded: chain H residue 289 ASN Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 279 CYS Chi-restraints excluded: chain I residue 289 ASN Chi-restraints excluded: chain K residue 289 ASN Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 168 ILE Chi-restraints excluded: chain L residue 279 CYS Chi-restraints excluded: chain L residue 289 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.4980 chunk 205 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 259 optimal weight: 5.9990 chunk 78 optimal weight: 0.1980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 160 ASN B 99 ASN B 160 ASN B 289 ASN C 160 ASN D 65 HIS D 160 ASN E 99 ASN E 160 ASN E 289 ASN F 160 ASN G 65 HIS G 160 ASN H 99 ASN H 160 ASN H 289 ASN I 160 ASN J 65 HIS J 160 ASN K 99 ASN K 160 ASN K 289 ASN L 160 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.9656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24840 Z= 0.230 Angle : 0.591 10.155 33648 Z= 0.306 Chirality : 0.044 0.227 3672 Planarity : 0.004 0.031 4440 Dihedral : 4.471 18.894 3312 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.95 % Allowed : 18.37 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.15), residues: 3024 helix: 2.34 (0.14), residues: 1404 sheet: 0.96 (0.23), residues: 480 loop : -0.42 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 54 HIS 0.003 0.001 HIS C 142 PHE 0.014 0.002 PHE A 90 TYR 0.014 0.002 TYR H 44 ARG 0.003 0.000 ARG J 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 512 time to evaluate : 3.107 Fit side-chains REVERT: A 178 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 285 MET cc_start: 0.7944 (ttt) cc_final: 0.7730 (ttt) REVERT: C 61 MET cc_start: 0.8258 (ttt) cc_final: 0.7943 (ttt) REVERT: C 178 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8521 (mt) REVERT: D 178 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8330 (mp) REVERT: D 226 ASP cc_start: 0.7747 (m-30) cc_final: 0.7534 (m-30) REVERT: D 285 MET cc_start: 0.7945 (ttt) cc_final: 0.7728 (ttt) REVERT: F 61 MET cc_start: 0.8257 (ttt) cc_final: 0.7942 (ttt) REVERT: F 178 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8516 (mt) REVERT: G 178 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8330 (mp) REVERT: G 226 ASP cc_start: 0.7736 (m-30) cc_final: 0.7529 (m-30) REVERT: G 285 MET cc_start: 0.7943 (ttt) cc_final: 0.7720 (ttt) REVERT: I 61 MET cc_start: 0.8257 (ttt) cc_final: 0.7942 (ttt) REVERT: I 178 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8518 (mt) REVERT: J 178 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8325 (mp) REVERT: J 226 ASP cc_start: 0.7742 (m-30) cc_final: 0.7534 (m-30) REVERT: J 285 MET cc_start: 0.7943 (ttt) cc_final: 0.7729 (ttt) REVERT: L 61 MET cc_start: 0.8259 (ttt) cc_final: 0.7942 (ttt) REVERT: L 178 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8524 (mt) outliers start: 76 outliers final: 24 residues processed: 536 average time/residue: 1.3272 time to fit residues: 818.5231 Evaluate side-chains 424 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 392 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 279 CYS Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 279 CYS Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 279 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 215 optimal weight: 0.0070 chunk 119 optimal weight: 0.9980 chunk 247 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 148 optimal weight: 0.8980 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 289 ASN C 202 GLN D 202 GLN E 202 GLN F 202 GLN G 202 GLN H 202 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN J 202 GLN K 289 ASN L 202 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 1.0051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24840 Z= 0.206 Angle : 0.544 9.969 33648 Z= 0.285 Chirality : 0.043 0.158 3672 Planarity : 0.004 0.031 4440 Dihedral : 4.243 17.047 3312 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.87 % Allowed : 21.01 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.15), residues: 3024 helix: 2.37 (0.14), residues: 1404 sheet: 1.10 (0.25), residues: 336 loop : -0.67 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 54 HIS 0.003 0.001 HIS K 142 PHE 0.013 0.002 PHE L 266 TYR 0.012 0.001 TYR D 146 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 410 time to evaluate : 2.802 Fit side-chains REVERT: B 150 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8323 (mpp) REVERT: C 178 LEU cc_start: 0.8739 (mp) cc_final: 0.8491 (mt) REVERT: D 162 ASP cc_start: 0.8592 (t70) cc_final: 0.8263 (t0) REVERT: E 150 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8310 (mpp) REVERT: F 178 LEU cc_start: 0.8736 (mp) cc_final: 0.8489 (mt) REVERT: G 162 ASP cc_start: 0.8581 (t70) cc_final: 0.8245 (t0) REVERT: H 150 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8310 (mpp) REVERT: I 178 LEU cc_start: 0.8736 (mp) cc_final: 0.8485 (mt) REVERT: J 162 ASP cc_start: 0.8581 (t70) cc_final: 0.8251 (t0) REVERT: K 150 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8311 (mpp) REVERT: L 178 LEU cc_start: 0.8741 (mp) cc_final: 0.8488 (mt) outliers start: 74 outliers final: 15 residues processed: 438 average time/residue: 1.3497 time to fit residues: 676.7242 Evaluate side-chains 420 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 401 time to evaluate : 2.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 175 LYS Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 175 LYS Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 170 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 290 optimal weight: 0.6980 chunk 240 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 289 ASN ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 1.0278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24840 Z= 0.155 Angle : 0.519 9.359 33648 Z= 0.266 Chirality : 0.042 0.140 3672 Planarity : 0.003 0.031 4440 Dihedral : 4.072 17.302 3312 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.71 % Allowed : 22.21 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.15), residues: 3024 helix: 2.59 (0.14), residues: 1404 sheet: 1.09 (0.25), residues: 336 loop : -0.64 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 54 HIS 0.002 0.001 HIS H 142 PHE 0.012 0.001 PHE J 78 TYR 0.011 0.001 TYR J 146 ARG 0.002 0.000 ARG A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 402 time to evaluate : 2.807 Fit side-chains REVERT: B 150 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8339 (mpp) REVERT: C 178 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8474 (mt) REVERT: E 150 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8338 (mpp) REVERT: F 178 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8475 (mt) REVERT: H 150 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8330 (mpp) REVERT: I 178 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8475 (mt) REVERT: K 150 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8329 (mpp) REVERT: L 178 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8477 (mt) outliers start: 70 outliers final: 14 residues processed: 441 average time/residue: 1.2507 time to fit residues: 639.7109 Evaluate side-chains 394 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 372 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 178 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 211 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 289 optimal weight: 0.5980 chunk 180 optimal weight: 10.0000 chunk 176 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 289 ASN ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 1.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 24840 Z= 0.170 Angle : 0.519 8.573 33648 Z= 0.269 Chirality : 0.042 0.133 3672 Planarity : 0.003 0.031 4440 Dihedral : 4.046 16.652 3312 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.26 % Allowed : 21.78 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.15), residues: 3024 helix: 2.57 (0.14), residues: 1404 sheet: 1.01 (0.25), residues: 336 loop : -0.61 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 54 HIS 0.002 0.001 HIS B 142 PHE 0.028 0.001 PHE K 266 TYR 0.012 0.001 TYR A 146 ARG 0.002 0.000 ARG J 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 383 time to evaluate : 3.025 Fit side-chains REVERT: A 68 GLN cc_start: 0.8579 (pt0) cc_final: 0.8349 (pt0) REVERT: B 141 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7661 (mtm180) REVERT: B 150 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8339 (mpp) REVERT: C 178 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8496 (mt) REVERT: C 291 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6884 (pt0) REVERT: D 68 GLN cc_start: 0.8556 (pt0) cc_final: 0.8338 (pt0) REVERT: E 141 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7660 (mtm180) REVERT: E 150 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8341 (mpp) REVERT: F 178 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8496 (mt) REVERT: F 291 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6869 (pt0) REVERT: G 68 GLN cc_start: 0.8557 (pt0) cc_final: 0.8334 (pt0) REVERT: H 141 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7654 (mtm180) REVERT: H 150 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8333 (mpp) REVERT: I 178 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8494 (mt) REVERT: I 291 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6881 (pt0) REVERT: J 68 GLN cc_start: 0.8554 (pt0) cc_final: 0.8330 (pt0) REVERT: J 178 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8293 (mp) REVERT: J 211 ASP cc_start: 0.7727 (p0) cc_final: 0.7507 (p0) REVERT: K 141 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7655 (mtm180) REVERT: K 150 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8333 (mpp) REVERT: L 178 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8494 (mt) outliers start: 84 outliers final: 30 residues processed: 414 average time/residue: 1.3075 time to fit residues: 622.7488 Evaluate side-chains 400 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 354 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 141 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 291 GLU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 141 ARG Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 0.6980 chunk 115 optimal weight: 0.2980 chunk 172 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 56 optimal weight: 0.0470 chunk 183 optimal weight: 0.8980 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 chunk 263 optimal weight: 2.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 1.0570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24840 Z= 0.140 Angle : 0.489 8.258 33648 Z= 0.253 Chirality : 0.041 0.131 3672 Planarity : 0.003 0.030 4440 Dihedral : 3.903 16.369 3312 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.13 % Allowed : 23.06 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.15), residues: 3024 helix: 2.68 (0.14), residues: 1404 sheet: 1.09 (0.26), residues: 336 loop : -0.55 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP J 54 HIS 0.001 0.000 HIS K 142 PHE 0.017 0.001 PHE K 266 TYR 0.011 0.001 TYR J 146 ARG 0.002 0.000 ARG G 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 364 time to evaluate : 2.748 Fit side-chains REVERT: A 68 GLN cc_start: 0.8578 (pt0) cc_final: 0.8367 (pt0) REVERT: A 178 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8266 (mp) REVERT: B 141 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7559 (mtm180) REVERT: B 150 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8324 (mpp) REVERT: B 154 GLU cc_start: 0.7779 (tt0) cc_final: 0.7579 (pt0) REVERT: C 178 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8487 (mt) REVERT: D 68 GLN cc_start: 0.8581 (pt0) cc_final: 0.8365 (pt0) REVERT: E 141 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7552 (mtm180) REVERT: E 150 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8322 (mpp) REVERT: E 154 GLU cc_start: 0.7780 (tt0) cc_final: 0.7573 (pt0) REVERT: F 178 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (mt) REVERT: G 68 GLN cc_start: 0.8582 (pt0) cc_final: 0.8372 (pt0) REVERT: H 141 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7553 (mtm180) REVERT: H 150 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8313 (mpp) REVERT: I 178 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8486 (mt) REVERT: J 68 GLN cc_start: 0.8575 (pt0) cc_final: 0.8367 (pt0) REVERT: K 141 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: K 150 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8313 (mpp) REVERT: L 178 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8488 (mt) outliers start: 55 outliers final: 27 residues processed: 389 average time/residue: 1.3320 time to fit residues: 598.4001 Evaluate side-chains 385 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 345 time to evaluate : 2.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 141 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 141 ARG Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.5980 chunk 252 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 1.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24840 Z= 0.168 Angle : 0.506 8.209 33648 Z= 0.262 Chirality : 0.041 0.132 3672 Planarity : 0.003 0.030 4440 Dihedral : 3.970 16.112 3312 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.02 % Allowed : 23.57 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.15), residues: 3024 helix: 2.65 (0.14), residues: 1404 sheet: 1.05 (0.25), residues: 336 loop : -0.54 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 54 HIS 0.003 0.001 HIS E 142 PHE 0.016 0.001 PHE H 266 TYR 0.012 0.001 TYR D 146 ARG 0.003 0.000 ARG K 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 346 time to evaluate : 3.361 Fit side-chains REVERT: A 68 GLN cc_start: 0.8577 (pt0) cc_final: 0.8326 (pt0) REVERT: A 178 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8268 (mp) REVERT: B 141 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7643 (mtm180) REVERT: B 150 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8342 (mpp) REVERT: B 154 GLU cc_start: 0.7782 (tt0) cc_final: 0.7575 (pt0) REVERT: C 178 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8497 (mt) REVERT: D 68 GLN cc_start: 0.8559 (pt0) cc_final: 0.8310 (pt0) REVERT: E 141 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7641 (mtm180) REVERT: E 150 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (mpp) REVERT: E 154 GLU cc_start: 0.7785 (tt0) cc_final: 0.7568 (pt0) REVERT: F 178 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8498 (mt) REVERT: G 68 GLN cc_start: 0.8564 (pt0) cc_final: 0.8316 (pt0) REVERT: H 141 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7630 (mtm180) REVERT: H 150 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8270 (mpp) REVERT: H 198 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6880 (pt0) REVERT: I 178 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8492 (mt) REVERT: J 68 GLN cc_start: 0.8550 (pt0) cc_final: 0.8306 (pt0) REVERT: K 141 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7631 (mtm180) REVERT: K 150 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8268 (mpp) REVERT: L 178 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8498 (mt) outliers start: 52 outliers final: 36 residues processed: 369 average time/residue: 1.4118 time to fit residues: 595.7230 Evaluate side-chains 390 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 340 time to evaluate : 2.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 141 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 141 ARG Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 2.9990 chunk 284 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 135 optimal weight: 0.0170 chunk 198 optimal weight: 6.9990 chunk 298 optimal weight: 1.9990 chunk 275 optimal weight: 30.0000 chunk 237 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 1.0779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24840 Z= 0.164 Angle : 0.504 8.136 33648 Z= 0.262 Chirality : 0.041 0.132 3672 Planarity : 0.003 0.031 4440 Dihedral : 3.970 16.105 3312 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.09 % Allowed : 23.57 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.15), residues: 3024 helix: 2.65 (0.14), residues: 1404 sheet: 0.94 (0.25), residues: 336 loop : -0.56 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 54 HIS 0.002 0.001 HIS B 142 PHE 0.015 0.001 PHE I 266 TYR 0.012 0.001 TYR I 146 ARG 0.003 0.000 ARG K 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 345 time to evaluate : 2.759 Fit side-chains REVERT: A 68 GLN cc_start: 0.8556 (pt0) cc_final: 0.8322 (pt0) REVERT: B 141 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7624 (mtm180) REVERT: B 150 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8319 (mpp) REVERT: B 154 GLU cc_start: 0.7776 (tt0) cc_final: 0.7572 (pt0) REVERT: C 178 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8491 (mt) REVERT: D 68 GLN cc_start: 0.8559 (pt0) cc_final: 0.8320 (pt0) REVERT: D 178 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8232 (mp) REVERT: E 141 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7623 (mtm180) REVERT: E 150 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8330 (mpp) REVERT: E 154 GLU cc_start: 0.7778 (tt0) cc_final: 0.7566 (pt0) REVERT: F 178 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8490 (mt) REVERT: G 68 GLN cc_start: 0.8561 (pt0) cc_final: 0.8317 (pt0) REVERT: G 178 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8231 (mp) REVERT: H 141 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7791 (mtm180) REVERT: H 150 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8324 (mpp) REVERT: H 198 GLU cc_start: 0.7295 (OUTLIER) cc_final: 0.7069 (pt0) REVERT: I 178 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8487 (mt) REVERT: J 68 GLN cc_start: 0.8581 (pt0) cc_final: 0.8344 (pt0) REVERT: K 141 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7792 (mtm180) REVERT: K 150 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8320 (mpp) REVERT: L 178 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8491 (mt) outliers start: 54 outliers final: 34 residues processed: 371 average time/residue: 1.4608 time to fit residues: 621.2276 Evaluate side-chains 390 residues out of total 2736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 341 time to evaluate : 3.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 101 GLN Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 101 GLN Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 155 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 141 ARG Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 101 GLN Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 155 MET Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 141 ARG Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 198 GLU Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 101 GLN Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 155 MET Chi-restraints excluded: chain I residue 178 LEU Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 141 ARG Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 219 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 238 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 43 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.107193 restraints weight = 27684.887| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.98 r_work: 0.2902 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 1.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 24840 Z= 0.137 Angle : 0.481 8.063 33648 Z= 0.249 Chirality : 0.040 0.131 3672 Planarity : 0.003 0.030 4440 Dihedral : 3.879 15.886 3312 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.71 % Allowed : 23.95 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.15), residues: 3024 helix: 2.72 (0.14), residues: 1404 sheet: 0.97 (0.25), residues: 336 loop : -0.54 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 54 HIS 0.001 0.000 HIS F 142 PHE 0.024 0.001 PHE F 266 TYR 0.011 0.001 TYR C 146 ARG 0.002 0.000 ARG K 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10157.55 seconds wall clock time: 179 minutes 26.81 seconds (10766.81 seconds total)