Starting phenix.real_space_refine on Thu Apr 11 01:54:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/04_2024/8fma_29290.pdb" } resolution = 3.1 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= -0.008 sd= 0.592 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: 5 Type Number sf(0) Gaussians S 99 5.16 5 C 26367 2.51 5 N 8767 2.21 5 O 9108 1.98 5 H 28633 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 78": "OD1" <-> "OD2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 154": "OD1" <-> "OD2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 289": "OD1" <-> "OD2" Residue "B GLU 305": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 154": "OD1" <-> "OD2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 168": "OE1" <-> "OE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 289": "OD1" <-> "OD2" Residue "C GLU 305": "OE1" <-> "OE2" Residue "C GLU 329": "OE1" <-> "OE2" Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D GLU 329": "OE1" <-> "OE2" Residue "D TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 289": "OD1" <-> "OD2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 154": "OD1" <-> "OD2" Residue "F TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 289": "OD1" <-> "OD2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F GLU 329": "OE1" <-> "OE2" Residue "F TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 78": "OD1" <-> "OD2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 154": "OD1" <-> "OD2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 168": "OE1" <-> "OE2" Residue "G PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 289": "OD1" <-> "OD2" Residue "G GLU 305": "OE1" <-> "OE2" Residue "G GLU 329": "OE1" <-> "OE2" Residue "G TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 78": "OD1" <-> "OD2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 154": "OD1" <-> "OD2" Residue "H TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 168": "OE1" <-> "OE2" Residue "H PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 289": "OD1" <-> "OD2" Residue "H GLU 305": "OE1" <-> "OE2" Residue "H GLU 329": "OE1" <-> "OE2" Residue "H TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 168": "OE1" <-> "OE2" Residue "I PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 289": "OD1" <-> "OD2" Residue "I GLU 305": "OE1" <-> "OE2" Residue "I GLU 329": "OE1" <-> "OE2" Residue "I TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 78": "OD1" <-> "OD2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 168": "OE1" <-> "OE2" Residue "J PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 289": "OD1" <-> "OD2" Residue "J GLU 305": "OE1" <-> "OE2" Residue "J GLU 329": "OE1" <-> "OE2" Residue "J TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 78": "OD1" <-> "OD2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 154": "OD1" <-> "OD2" Residue "K TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 168": "OE1" <-> "OE2" Residue "K PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 289": "OD1" <-> "OD2" Residue "K GLU 305": "OE1" <-> "OE2" Residue "K GLU 329": "OE1" <-> "OE2" Residue "K TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 154": "OD1" <-> "OD2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 289": "OD1" <-> "OD2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 329": "OE1" <-> "OE2" Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 681": "OD1" <-> "OD2" Residue "L PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 681": "OD1" <-> "OD2" Residue "M PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 681": "OD1" <-> "OD2" Residue "N PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 681": "OD1" <-> "OD2" Residue "O PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 681": "OD1" <-> "OD2" Residue "P PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 681": "OD1" <-> "OD2" Residue "Q PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 681": "OD1" <-> "OD2" Residue "R PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 681": "OD1" <-> "OD2" Residue "S PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 681": "OD1" <-> "OD2" Residue "T PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 681": "OD1" <-> "OD2" Residue "U PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 681": "OD1" <-> "OD2" Residue "V PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 72974 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "C" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "D" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "E" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "F" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "G" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "H" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "I" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "J" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "K" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "A" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 5223 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 19, 'TRANS': 304} Chain breaks: 1 Chain: "L" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "M" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "N" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "O" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "P" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "Q" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "R" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "S" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "T" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "U" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Chain: "V" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 1411 Classifications: {'peptide': 333} Incomplete info: {'backbone_only': 301} Link IDs: {'PTRANS': 18, 'TRANS': 314} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1299 Unresolved non-hydrogen angles: 1884 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 396 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 8, 'TYR:plan': 10, 'ASN:plan1': 13, 'TRP:plan': 2, 'ASP:plan': 24, 'PHE:plan': 12, 'GLU:plan': 20, 'ARG:plan': 24} Unresolved non-hydrogen planarities: 620 Time building chain proxies: 26.03, per 1000 atoms: 0.36 Number of scatterers: 72974 At special positions: 0 Unit cell: (223.244, 224.077, 123.284, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 O 9108 8.00 N 8767 7.00 C 26367 6.00 H 28633 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.32 Conformation dependent library (CDL) restraints added in 7.7 seconds 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7150 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 66 sheets defined 48.1% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.57 Creating SS restraints... Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.516A pdb=" N GLN B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 115 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU B 172 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 250 Proline residue: B 245 - end of helix removed outlier: 3.646A pdb=" N ILE B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 350 through 362 removed outlier: 3.561A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.859A pdb=" N MET B 371 " --> pdb=" O GLN B 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 Processing helix chain 'C' and resid 95 through 115 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU C 172 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 250 Proline residue: C 245 - end of helix removed outlier: 3.647A pdb=" N ILE C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 346 Processing helix chain 'C' and resid 350 through 362 removed outlier: 3.561A pdb=" N VAL C 354 " --> pdb=" O ALA C 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 64 Processing helix chain 'D' and resid 95 through 115 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU D 172 " --> pdb=" O GLU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 250 Proline residue: D 245 - end of helix removed outlier: 3.646A pdb=" N ILE D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 346 Processing helix chain 'D' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN D 355 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET D 371 " --> pdb=" O GLN D 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 64 Processing helix chain 'E' and resid 95 through 115 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU E 172 " --> pdb=" O GLU E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 236 through 250 Proline residue: E 245 - end of helix removed outlier: 3.646A pdb=" N ILE E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 346 Processing helix chain 'E' and resid 350 through 362 removed outlier: 3.561A pdb=" N VAL E 354 " --> pdb=" O ALA E 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 355 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET E 371 " --> pdb=" O GLN E 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 64 Processing helix chain 'F' and resid 95 through 115 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU F 172 " --> pdb=" O GLU F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 250 Proline residue: F 245 - end of helix removed outlier: 3.646A pdb=" N ILE F 249 " --> pdb=" O PRO F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 346 Processing helix chain 'F' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL F 354 " --> pdb=" O ALA F 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN F 355 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET F 371 " --> pdb=" O GLN F 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 64 Processing helix chain 'G' and resid 95 through 115 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU G 172 " --> pdb=" O GLU G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 236 through 250 Proline residue: G 245 - end of helix removed outlier: 3.647A pdb=" N ILE G 249 " --> pdb=" O PRO G 245 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 346 Processing helix chain 'G' and resid 350 through 362 removed outlier: 3.561A pdb=" N VAL G 354 " --> pdb=" O ALA G 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 355 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 378 removed outlier: 3.859A pdb=" N MET G 371 " --> pdb=" O GLN G 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 64 Processing helix chain 'H' and resid 95 through 115 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 168 through 174 removed outlier: 4.196A pdb=" N LEU H 172 " --> pdb=" O GLU H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 250 Proline residue: H 245 - end of helix removed outlier: 3.647A pdb=" N ILE H 249 " --> pdb=" O PRO H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 346 Processing helix chain 'H' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL H 354 " --> pdb=" O ALA H 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN H 355 " --> pdb=" O THR H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 378 removed outlier: 3.859A pdb=" N MET H 371 " --> pdb=" O GLN H 367 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 64 Processing helix chain 'I' and resid 95 through 115 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 168 through 174 removed outlier: 4.197A pdb=" N LEU I 172 " --> pdb=" O GLU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 236 through 250 Proline residue: I 245 - end of helix removed outlier: 3.647A pdb=" N ILE I 249 " --> pdb=" O PRO I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 346 Processing helix chain 'I' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL I 354 " --> pdb=" O ALA I 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 355 " --> pdb=" O THR I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET I 371 " --> pdb=" O GLN I 367 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 64 Processing helix chain 'J' and resid 95 through 115 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 168 through 174 removed outlier: 4.196A pdb=" N LEU J 172 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 250 Proline residue: J 245 - end of helix removed outlier: 3.646A pdb=" N ILE J 249 " --> pdb=" O PRO J 245 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 346 Processing helix chain 'J' and resid 350 through 362 removed outlier: 3.561A pdb=" N VAL J 354 " --> pdb=" O ALA J 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 355 " --> pdb=" O THR J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 365 through 378 removed outlier: 3.860A pdb=" N MET J 371 " --> pdb=" O GLN J 367 " (cutoff:3.500A) Processing helix chain 'K' and resid 56 through 64 Processing helix chain 'K' and resid 95 through 115 Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 168 through 174 removed outlier: 4.196A pdb=" N LEU K 172 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 250 Proline residue: K 245 - end of helix removed outlier: 3.646A pdb=" N ILE K 249 " --> pdb=" O PRO K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 346 Processing helix chain 'K' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL K 354 " --> pdb=" O ALA K 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN K 355 " --> pdb=" O THR K 351 " (cutoff:3.500A) Processing helix chain 'K' and resid 365 through 378 removed outlier: 3.859A pdb=" N MET K 371 " --> pdb=" O GLN K 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 64 Processing helix chain 'A' and resid 95 through 115 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 168 through 174 removed outlier: 4.196A pdb=" N LEU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Proline residue: A 245 - end of helix removed outlier: 3.647A pdb=" N ILE A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 350 through 362 removed outlier: 3.560A pdb=" N VAL A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.859A pdb=" N MET A 371 " --> pdb=" O GLN A 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA L 457 " --> pdb=" O SER L 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS L 458 " --> pdb=" O ASP L 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE L 459 " --> pdb=" O ARG L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 478 through 485 Processing helix chain 'L' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL L 538 " --> pdb=" O PHE L 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR L 541 " --> pdb=" O LYS L 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA L 544 " --> pdb=" O ARG L 540 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU L 556 " --> pdb=" O GLU L 553 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 579 Processing helix chain 'L' and resid 596 through 603 Processing helix chain 'L' and resid 603 through 612 Processing helix chain 'L' and resid 613 through 615 No H-bonds generated for 'chain 'L' and resid 613 through 615' Processing helix chain 'L' and resid 616 through 629 Processing helix chain 'L' and resid 655 through 674 Processing helix chain 'L' and resid 678 through 684 Processing helix chain 'L' and resid 699 through 701 No H-bonds generated for 'chain 'L' and resid 699 through 701' Processing helix chain 'L' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG L 706 " --> pdb=" O LYS L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR L 749 " --> pdb=" O ASP L 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG L 751 " --> pdb=" O LEU L 747 " (cutoff:3.500A) Processing helix chain 'L' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA L 780 " --> pdb=" O LEU L 776 " (cutoff:3.500A) Processing helix chain 'L' and resid 785 through 800 Proline residue: L 798 - end of helix Processing helix chain 'L' and resid 802 through 808 Processing helix chain 'L' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN L 813 " --> pdb=" O ARG L 810 " (cutoff:3.500A) Processing helix chain 'L' and resid 829 through 831 No H-bonds generated for 'chain 'L' and resid 829 through 831' Processing helix chain 'L' and resid 832 through 845 Processing helix chain 'L' and resid 847 through 861 Processing helix chain 'M' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA M 457 " --> pdb=" O SER M 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS M 458 " --> pdb=" O ASP M 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 485 Processing helix chain 'M' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL M 538 " --> pdb=" O PHE M 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR M 541 " --> pdb=" O LYS M 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA M 544 " --> pdb=" O ARG M 540 " (cutoff:3.500A) Processing helix chain 'M' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU M 556 " --> pdb=" O GLU M 553 " (cutoff:3.500A) Processing helix chain 'M' and resid 564 through 579 Processing helix chain 'M' and resid 596 through 603 Processing helix chain 'M' and resid 603 through 612 Processing helix chain 'M' and resid 613 through 615 No H-bonds generated for 'chain 'M' and resid 613 through 615' Processing helix chain 'M' and resid 616 through 629 Processing helix chain 'M' and resid 655 through 674 Processing helix chain 'M' and resid 678 through 684 Processing helix chain 'M' and resid 699 through 701 No H-bonds generated for 'chain 'M' and resid 699 through 701' Processing helix chain 'M' and resid 702 through 712 removed outlier: 4.093A pdb=" N ARG M 706 " --> pdb=" O LYS M 702 " (cutoff:3.500A) Processing helix chain 'M' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR M 749 " --> pdb=" O ASP M 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG M 751 " --> pdb=" O LEU M 747 " (cutoff:3.500A) Processing helix chain 'M' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA M 780 " --> pdb=" O LEU M 776 " (cutoff:3.500A) Processing helix chain 'M' and resid 785 through 800 Proline residue: M 798 - end of helix Processing helix chain 'M' and resid 802 through 808 Processing helix chain 'M' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN M 813 " --> pdb=" O ARG M 810 " (cutoff:3.500A) Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'M' and resid 832 through 845 Processing helix chain 'M' and resid 847 through 861 Processing helix chain 'N' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA N 457 " --> pdb=" O SER N 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS N 458 " --> pdb=" O ASP N 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE N 459 " --> pdb=" O ARG N 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 478 through 485 Processing helix chain 'N' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL N 538 " --> pdb=" O PHE N 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR N 541 " --> pdb=" O LYS N 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA N 544 " --> pdb=" O ARG N 540 " (cutoff:3.500A) Processing helix chain 'N' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU N 556 " --> pdb=" O GLU N 553 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 579 Processing helix chain 'N' and resid 596 through 603 Processing helix chain 'N' and resid 603 through 612 Processing helix chain 'N' and resid 613 through 615 No H-bonds generated for 'chain 'N' and resid 613 through 615' Processing helix chain 'N' and resid 616 through 629 Processing helix chain 'N' and resid 655 through 674 Processing helix chain 'N' and resid 678 through 684 Processing helix chain 'N' and resid 699 through 701 No H-bonds generated for 'chain 'N' and resid 699 through 701' Processing helix chain 'N' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG N 706 " --> pdb=" O LYS N 702 " (cutoff:3.500A) Processing helix chain 'N' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR N 749 " --> pdb=" O ASP N 745 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG N 751 " --> pdb=" O LEU N 747 " (cutoff:3.500A) Processing helix chain 'N' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA N 780 " --> pdb=" O LEU N 776 " (cutoff:3.500A) Processing helix chain 'N' and resid 785 through 800 Proline residue: N 798 - end of helix Processing helix chain 'N' and resid 802 through 808 Processing helix chain 'N' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN N 813 " --> pdb=" O ARG N 810 " (cutoff:3.500A) Processing helix chain 'N' and resid 829 through 831 No H-bonds generated for 'chain 'N' and resid 829 through 831' Processing helix chain 'N' and resid 832 through 845 Processing helix chain 'N' and resid 847 through 861 Processing helix chain 'O' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA O 457 " --> pdb=" O SER O 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS O 458 " --> pdb=" O ASP O 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE O 459 " --> pdb=" O ARG O 455 " (cutoff:3.500A) Processing helix chain 'O' and resid 478 through 485 Processing helix chain 'O' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL O 538 " --> pdb=" O PHE O 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR O 541 " --> pdb=" O LYS O 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA O 544 " --> pdb=" O ARG O 540 " (cutoff:3.500A) Processing helix chain 'O' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU O 556 " --> pdb=" O GLU O 553 " (cutoff:3.500A) Processing helix chain 'O' and resid 564 through 579 Processing helix chain 'O' and resid 596 through 603 Processing helix chain 'O' and resid 603 through 612 Processing helix chain 'O' and resid 613 through 615 No H-bonds generated for 'chain 'O' and resid 613 through 615' Processing helix chain 'O' and resid 616 through 629 Processing helix chain 'O' and resid 655 through 674 Processing helix chain 'O' and resid 678 through 684 Processing helix chain 'O' and resid 699 through 701 No H-bonds generated for 'chain 'O' and resid 699 through 701' Processing helix chain 'O' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG O 706 " --> pdb=" O LYS O 702 " (cutoff:3.500A) Processing helix chain 'O' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR O 749 " --> pdb=" O ASP O 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG O 751 " --> pdb=" O LEU O 747 " (cutoff:3.500A) Processing helix chain 'O' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA O 780 " --> pdb=" O LEU O 776 " (cutoff:3.500A) Processing helix chain 'O' and resid 785 through 800 Proline residue: O 798 - end of helix Processing helix chain 'O' and resid 802 through 808 Processing helix chain 'O' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN O 813 " --> pdb=" O ARG O 810 " (cutoff:3.500A) Processing helix chain 'O' and resid 829 through 831 No H-bonds generated for 'chain 'O' and resid 829 through 831' Processing helix chain 'O' and resid 832 through 845 Processing helix chain 'O' and resid 847 through 861 Processing helix chain 'P' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA P 457 " --> pdb=" O SER P 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS P 458 " --> pdb=" O ASP P 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE P 459 " --> pdb=" O ARG P 455 " (cutoff:3.500A) Processing helix chain 'P' and resid 478 through 485 Processing helix chain 'P' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL P 538 " --> pdb=" O PHE P 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR P 541 " --> pdb=" O LYS P 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA P 544 " --> pdb=" O ARG P 540 " (cutoff:3.500A) Processing helix chain 'P' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU P 556 " --> pdb=" O GLU P 553 " (cutoff:3.500A) Processing helix chain 'P' and resid 564 through 579 Processing helix chain 'P' and resid 596 through 603 Processing helix chain 'P' and resid 603 through 612 Processing helix chain 'P' and resid 613 through 615 No H-bonds generated for 'chain 'P' and resid 613 through 615' Processing helix chain 'P' and resid 616 through 629 Processing helix chain 'P' and resid 655 through 674 Processing helix chain 'P' and resid 678 through 684 Processing helix chain 'P' and resid 699 through 701 No H-bonds generated for 'chain 'P' and resid 699 through 701' Processing helix chain 'P' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG P 706 " --> pdb=" O LYS P 702 " (cutoff:3.500A) Processing helix chain 'P' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR P 749 " --> pdb=" O ASP P 745 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG P 751 " --> pdb=" O LEU P 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA P 780 " --> pdb=" O LEU P 776 " (cutoff:3.500A) Processing helix chain 'P' and resid 785 through 800 Proline residue: P 798 - end of helix Processing helix chain 'P' and resid 802 through 808 Processing helix chain 'P' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN P 813 " --> pdb=" O ARG P 810 " (cutoff:3.500A) Processing helix chain 'P' and resid 829 through 831 No H-bonds generated for 'chain 'P' and resid 829 through 831' Processing helix chain 'P' and resid 832 through 845 Processing helix chain 'P' and resid 847 through 861 Processing helix chain 'Q' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA Q 457 " --> pdb=" O SER Q 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS Q 458 " --> pdb=" O ASP Q 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE Q 459 " --> pdb=" O ARG Q 455 " (cutoff:3.500A) Processing helix chain 'Q' and resid 478 through 485 Processing helix chain 'Q' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL Q 538 " --> pdb=" O PHE Q 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR Q 541 " --> pdb=" O LYS Q 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA Q 544 " --> pdb=" O ARG Q 540 " (cutoff:3.500A) Processing helix chain 'Q' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU Q 556 " --> pdb=" O GLU Q 553 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 579 Processing helix chain 'Q' and resid 596 through 603 Processing helix chain 'Q' and resid 603 through 612 Processing helix chain 'Q' and resid 613 through 615 No H-bonds generated for 'chain 'Q' and resid 613 through 615' Processing helix chain 'Q' and resid 616 through 629 Processing helix chain 'Q' and resid 655 through 674 Processing helix chain 'Q' and resid 678 through 684 Processing helix chain 'Q' and resid 699 through 701 No H-bonds generated for 'chain 'Q' and resid 699 through 701' Processing helix chain 'Q' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG Q 706 " --> pdb=" O LYS Q 702 " (cutoff:3.500A) Processing helix chain 'Q' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR Q 749 " --> pdb=" O ASP Q 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG Q 751 " --> pdb=" O LEU Q 747 " (cutoff:3.500A) Processing helix chain 'Q' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA Q 780 " --> pdb=" O LEU Q 776 " (cutoff:3.500A) Processing helix chain 'Q' and resid 785 through 800 Proline residue: Q 798 - end of helix Processing helix chain 'Q' and resid 802 through 808 Processing helix chain 'Q' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN Q 813 " --> pdb=" O ARG Q 810 " (cutoff:3.500A) Processing helix chain 'Q' and resid 829 through 831 No H-bonds generated for 'chain 'Q' and resid 829 through 831' Processing helix chain 'Q' and resid 832 through 845 Processing helix chain 'Q' and resid 847 through 861 Processing helix chain 'R' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA R 457 " --> pdb=" O SER R 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS R 458 " --> pdb=" O ASP R 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE R 459 " --> pdb=" O ARG R 455 " (cutoff:3.500A) Processing helix chain 'R' and resid 478 through 485 Processing helix chain 'R' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL R 538 " --> pdb=" O PHE R 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR R 541 " --> pdb=" O LYS R 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA R 544 " --> pdb=" O ARG R 540 " (cutoff:3.500A) Processing helix chain 'R' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU R 556 " --> pdb=" O GLU R 553 " (cutoff:3.500A) Processing helix chain 'R' and resid 564 through 579 Processing helix chain 'R' and resid 596 through 603 Processing helix chain 'R' and resid 603 through 612 Processing helix chain 'R' and resid 613 through 615 No H-bonds generated for 'chain 'R' and resid 613 through 615' Processing helix chain 'R' and resid 616 through 629 Processing helix chain 'R' and resid 655 through 674 Processing helix chain 'R' and resid 678 through 684 Processing helix chain 'R' and resid 699 through 701 No H-bonds generated for 'chain 'R' and resid 699 through 701' Processing helix chain 'R' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG R 706 " --> pdb=" O LYS R 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 745 through 751 removed outlier: 3.550A pdb=" N THR R 749 " --> pdb=" O ASP R 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG R 751 " --> pdb=" O LEU R 747 " (cutoff:3.500A) Processing helix chain 'R' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA R 780 " --> pdb=" O LEU R 776 " (cutoff:3.500A) Processing helix chain 'R' and resid 785 through 800 Proline residue: R 798 - end of helix Processing helix chain 'R' and resid 802 through 808 Processing helix chain 'R' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN R 813 " --> pdb=" O ARG R 810 " (cutoff:3.500A) Processing helix chain 'R' and resid 829 through 831 No H-bonds generated for 'chain 'R' and resid 829 through 831' Processing helix chain 'R' and resid 832 through 845 Processing helix chain 'R' and resid 847 through 861 Processing helix chain 'S' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA S 457 " --> pdb=" O SER S 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS S 458 " --> pdb=" O ASP S 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE S 459 " --> pdb=" O ARG S 455 " (cutoff:3.500A) Processing helix chain 'S' and resid 478 through 485 Processing helix chain 'S' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL S 538 " --> pdb=" O PHE S 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR S 541 " --> pdb=" O LYS S 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA S 544 " --> pdb=" O ARG S 540 " (cutoff:3.500A) Processing helix chain 'S' and resid 552 through 556 removed outlier: 3.839A pdb=" N GLU S 556 " --> pdb=" O GLU S 553 " (cutoff:3.500A) Processing helix chain 'S' and resid 564 through 579 Processing helix chain 'S' and resid 596 through 603 Processing helix chain 'S' and resid 603 through 612 Processing helix chain 'S' and resid 613 through 615 No H-bonds generated for 'chain 'S' and resid 613 through 615' Processing helix chain 'S' and resid 616 through 629 Processing helix chain 'S' and resid 655 through 674 Processing helix chain 'S' and resid 678 through 684 Processing helix chain 'S' and resid 699 through 701 No H-bonds generated for 'chain 'S' and resid 699 through 701' Processing helix chain 'S' and resid 702 through 712 removed outlier: 4.093A pdb=" N ARG S 706 " --> pdb=" O LYS S 702 " (cutoff:3.500A) Processing helix chain 'S' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR S 749 " --> pdb=" O ASP S 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG S 751 " --> pdb=" O LEU S 747 " (cutoff:3.500A) Processing helix chain 'S' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA S 780 " --> pdb=" O LEU S 776 " (cutoff:3.500A) Processing helix chain 'S' and resid 785 through 800 Proline residue: S 798 - end of helix Processing helix chain 'S' and resid 802 through 808 Processing helix chain 'S' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN S 813 " --> pdb=" O ARG S 810 " (cutoff:3.500A) Processing helix chain 'S' and resid 829 through 831 No H-bonds generated for 'chain 'S' and resid 829 through 831' Processing helix chain 'S' and resid 832 through 845 Processing helix chain 'S' and resid 847 through 861 Processing helix chain 'T' and resid 453 through 469 removed outlier: 3.536A pdb=" N ALA T 457 " --> pdb=" O SER T 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS T 458 " --> pdb=" O ASP T 454 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE T 459 " --> pdb=" O ARG T 455 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 485 Processing helix chain 'T' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL T 538 " --> pdb=" O PHE T 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR T 541 " --> pdb=" O LYS T 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA T 544 " --> pdb=" O ARG T 540 " (cutoff:3.500A) Processing helix chain 'T' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU T 556 " --> pdb=" O GLU T 553 " (cutoff:3.500A) Processing helix chain 'T' and resid 564 through 579 Processing helix chain 'T' and resid 596 through 603 Processing helix chain 'T' and resid 603 through 612 Processing helix chain 'T' and resid 613 through 615 No H-bonds generated for 'chain 'T' and resid 613 through 615' Processing helix chain 'T' and resid 616 through 629 Processing helix chain 'T' and resid 655 through 674 Processing helix chain 'T' and resid 678 through 684 Processing helix chain 'T' and resid 699 through 701 No H-bonds generated for 'chain 'T' and resid 699 through 701' Processing helix chain 'T' and resid 702 through 712 removed outlier: 4.093A pdb=" N ARG T 706 " --> pdb=" O LYS T 702 " (cutoff:3.500A) Processing helix chain 'T' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR T 749 " --> pdb=" O ASP T 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG T 751 " --> pdb=" O LEU T 747 " (cutoff:3.500A) Processing helix chain 'T' and resid 763 through 780 removed outlier: 3.630A pdb=" N ALA T 780 " --> pdb=" O LEU T 776 " (cutoff:3.500A) Processing helix chain 'T' and resid 785 through 800 Proline residue: T 798 - end of helix Processing helix chain 'T' and resid 802 through 808 Processing helix chain 'T' and resid 809 through 814 removed outlier: 3.635A pdb=" N ASN T 813 " --> pdb=" O ARG T 810 " (cutoff:3.500A) Processing helix chain 'T' and resid 829 through 831 No H-bonds generated for 'chain 'T' and resid 829 through 831' Processing helix chain 'T' and resid 832 through 845 Processing helix chain 'T' and resid 847 through 861 Processing helix chain 'U' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA U 457 " --> pdb=" O SER U 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS U 458 " --> pdb=" O ASP U 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE U 459 " --> pdb=" O ARG U 455 " (cutoff:3.500A) Processing helix chain 'U' and resid 478 through 485 Processing helix chain 'U' and resid 534 through 549 removed outlier: 4.116A pdb=" N VAL U 538 " --> pdb=" O PHE U 534 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TYR U 541 " --> pdb=" O LYS U 537 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA U 544 " --> pdb=" O ARG U 540 " (cutoff:3.500A) Processing helix chain 'U' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU U 556 " --> pdb=" O GLU U 553 " (cutoff:3.500A) Processing helix chain 'U' and resid 564 through 579 Processing helix chain 'U' and resid 596 through 603 Processing helix chain 'U' and resid 603 through 612 Processing helix chain 'U' and resid 613 through 615 No H-bonds generated for 'chain 'U' and resid 613 through 615' Processing helix chain 'U' and resid 616 through 629 Processing helix chain 'U' and resid 655 through 674 Processing helix chain 'U' and resid 678 through 684 Processing helix chain 'U' and resid 699 through 701 No H-bonds generated for 'chain 'U' and resid 699 through 701' Processing helix chain 'U' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG U 706 " --> pdb=" O LYS U 702 " (cutoff:3.500A) Processing helix chain 'U' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR U 749 " --> pdb=" O ASP U 745 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG U 751 " --> pdb=" O LEU U 747 " (cutoff:3.500A) Processing helix chain 'U' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA U 780 " --> pdb=" O LEU U 776 " (cutoff:3.500A) Processing helix chain 'U' and resid 785 through 800 Proline residue: U 798 - end of helix Processing helix chain 'U' and resid 802 through 808 Processing helix chain 'U' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN U 813 " --> pdb=" O ARG U 810 " (cutoff:3.500A) Processing helix chain 'U' and resid 829 through 831 No H-bonds generated for 'chain 'U' and resid 829 through 831' Processing helix chain 'U' and resid 832 through 845 Processing helix chain 'U' and resid 847 through 861 Processing helix chain 'V' and resid 453 through 469 removed outlier: 3.537A pdb=" N ALA V 457 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS V 458 " --> pdb=" O ASP V 454 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE V 459 " --> pdb=" O ARG V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 478 through 485 Processing helix chain 'V' and resid 534 through 549 removed outlier: 4.115A pdb=" N VAL V 538 " --> pdb=" O PHE V 534 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR V 541 " --> pdb=" O LYS V 537 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA V 544 " --> pdb=" O ARG V 540 " (cutoff:3.500A) Processing helix chain 'V' and resid 552 through 556 removed outlier: 3.838A pdb=" N GLU V 556 " --> pdb=" O GLU V 553 " (cutoff:3.500A) Processing helix chain 'V' and resid 564 through 579 Processing helix chain 'V' and resid 596 through 603 Processing helix chain 'V' and resid 603 through 612 Processing helix chain 'V' and resid 613 through 615 No H-bonds generated for 'chain 'V' and resid 613 through 615' Processing helix chain 'V' and resid 616 through 629 Processing helix chain 'V' and resid 655 through 674 Processing helix chain 'V' and resid 678 through 684 Processing helix chain 'V' and resid 699 through 701 No H-bonds generated for 'chain 'V' and resid 699 through 701' Processing helix chain 'V' and resid 702 through 712 removed outlier: 4.094A pdb=" N ARG V 706 " --> pdb=" O LYS V 702 " (cutoff:3.500A) Processing helix chain 'V' and resid 745 through 751 removed outlier: 3.549A pdb=" N THR V 749 " --> pdb=" O ASP V 745 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ARG V 751 " --> pdb=" O LEU V 747 " (cutoff:3.500A) Processing helix chain 'V' and resid 763 through 780 removed outlier: 3.629A pdb=" N ALA V 780 " --> pdb=" O LEU V 776 " (cutoff:3.500A) Processing helix chain 'V' and resid 785 through 800 Proline residue: V 798 - end of helix Processing helix chain 'V' and resid 802 through 808 Processing helix chain 'V' and resid 809 through 814 removed outlier: 3.634A pdb=" N ASN V 813 " --> pdb=" O ARG V 810 " (cutoff:3.500A) Processing helix chain 'V' and resid 829 through 831 No H-bonds generated for 'chain 'V' and resid 829 through 831' Processing helix chain 'V' and resid 832 through 845 Processing helix chain 'V' and resid 847 through 861 Processing sheet with id=AA1, first strand: chain 'B' and resid 118 through 121 removed outlier: 3.534A pdb=" N VAL B 158 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 160 " --> pdb=" O VAL B 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE B 157 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS B 182 " --> pdb=" O ILE B 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY B 159 " --> pdb=" O HIS B 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE B 184 " --> pdb=" O GLY B 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR B 256 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL B 281 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL B 254 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP B 283 " --> pdb=" O GLU B 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU B 252 " --> pdb=" O TRP B 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AA3, first strand: chain 'B' and resid 200 through 201 Processing sheet with id=AA4, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE B 335 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 388 through 389 removed outlier: 7.278A pdb=" N VAL B 389 " --> pdb=" O VAL H 316 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU H 321 " --> pdb=" O THR H 317 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE H 335 " --> pdb=" O ILE H 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.532A pdb=" N VAL C 158 " --> pdb=" O PHE C 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL C 160 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE C 157 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS C 182 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 159 " --> pdb=" O HIS C 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE C 184 " --> pdb=" O GLY C 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 256 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL C 281 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 254 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP C 283 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU C 252 " --> pdb=" O TRP C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 191 through 193 Processing sheet with id=AA8, first strand: chain 'C' and resid 200 through 201 Processing sheet with id=AA9, first strand: chain 'C' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE C 335 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU C 321 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 388 through 389 removed outlier: 7.272A pdb=" N VAL C 389 " --> pdb=" O VAL I 316 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU I 321 " --> pdb=" O THR I 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 335 " --> pdb=" O ILE I 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 118 through 121 removed outlier: 3.533A pdb=" N VAL D 158 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL D 160 " --> pdb=" O VAL D 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE D 157 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS D 182 " --> pdb=" O ILE D 157 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY D 159 " --> pdb=" O HIS D 182 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE D 184 " --> pdb=" O GLY D 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR D 256 " --> pdb=" O GLN D 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL D 281 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL D 254 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP D 283 " --> pdb=" O GLU D 252 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU D 252 " --> pdb=" O TRP D 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AB4, first strand: chain 'D' and resid 200 through 201 Processing sheet with id=AB5, first strand: chain 'D' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE D 335 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU D 321 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 388 through 389 removed outlier: 7.320A pdb=" N VAL D 389 " --> pdb=" O VAL J 316 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU J 321 " --> pdb=" O THR J 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE J 335 " --> pdb=" O ILE J 326 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 118 through 121 removed outlier: 3.533A pdb=" N VAL E 158 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL E 160 " --> pdb=" O VAL E 121 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE E 157 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS E 182 " --> pdb=" O ILE E 157 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY E 159 " --> pdb=" O HIS E 182 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE E 184 " --> pdb=" O GLY E 159 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR E 256 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL E 281 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 254 " --> pdb=" O VAL E 281 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP E 283 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU E 252 " --> pdb=" O TRP E 283 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 191 through 193 Processing sheet with id=AB9, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AC1, first strand: chain 'E' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE E 335 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU E 321 " --> pdb=" O THR E 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 388 through 389 removed outlier: 7.279A pdb=" N VAL E 389 " --> pdb=" O VAL K 316 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU K 321 " --> pdb=" O THR K 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE K 335 " --> pdb=" O ILE K 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 118 through 121 removed outlier: 3.532A pdb=" N VAL F 158 " --> pdb=" O PHE F 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL F 160 " --> pdb=" O VAL F 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE F 157 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS F 182 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY F 159 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE F 184 " --> pdb=" O GLY F 159 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR F 256 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL F 281 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL F 254 " --> pdb=" O VAL F 281 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP F 283 " --> pdb=" O GLU F 252 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU F 252 " --> pdb=" O TRP F 283 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 191 through 193 Processing sheet with id=AC5, first strand: chain 'F' and resid 200 through 201 Processing sheet with id=AC6, first strand: chain 'F' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE F 335 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU F 321 " --> pdb=" O THR F 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 388 through 389 removed outlier: 7.303A pdb=" N VAL F 389 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU A 321 " --> pdb=" O THR A 317 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE A 335 " --> pdb=" O ILE A 326 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 118 through 121 removed outlier: 3.533A pdb=" N VAL G 158 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL G 160 " --> pdb=" O VAL G 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE G 157 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N HIS G 182 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY G 159 " --> pdb=" O HIS G 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE G 184 " --> pdb=" O GLY G 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR G 256 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL G 281 " --> pdb=" O VAL G 254 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL G 254 " --> pdb=" O VAL G 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP G 283 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU G 252 " --> pdb=" O TRP G 283 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 191 through 193 Processing sheet with id=AD1, first strand: chain 'G' and resid 200 through 201 Processing sheet with id=AD2, first strand: chain 'G' and resid 335 through 338 removed outlier: 3.596A pdb=" N ILE G 335 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 118 through 121 removed outlier: 3.534A pdb=" N VAL H 158 " --> pdb=" O PHE H 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL H 160 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE H 157 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS H 182 " --> pdb=" O ILE H 157 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY H 159 " --> pdb=" O HIS H 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE H 184 " --> pdb=" O GLY H 159 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR H 256 " --> pdb=" O GLN H 279 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL H 281 " --> pdb=" O VAL H 254 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL H 254 " --> pdb=" O VAL H 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP H 283 " --> pdb=" O GLU H 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU H 252 " --> pdb=" O TRP H 283 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 191 through 193 Processing sheet with id=AD5, first strand: chain 'H' and resid 200 through 201 Processing sheet with id=AD6, first strand: chain 'I' and resid 118 through 121 removed outlier: 3.533A pdb=" N VAL I 158 " --> pdb=" O PHE I 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL I 160 " --> pdb=" O VAL I 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE I 157 " --> pdb=" O VAL I 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS I 182 " --> pdb=" O ILE I 157 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY I 159 " --> pdb=" O HIS I 182 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N PHE I 184 " --> pdb=" O GLY I 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR I 256 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL I 281 " --> pdb=" O VAL I 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL I 254 " --> pdb=" O VAL I 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP I 283 " --> pdb=" O GLU I 252 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU I 252 " --> pdb=" O TRP I 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 191 through 193 Processing sheet with id=AD8, first strand: chain 'I' and resid 200 through 201 Processing sheet with id=AD9, first strand: chain 'J' and resid 118 through 121 removed outlier: 3.532A pdb=" N VAL J 158 " --> pdb=" O PHE J 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL J 160 " --> pdb=" O VAL J 121 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE J 157 " --> pdb=" O VAL J 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS J 182 " --> pdb=" O ILE J 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY J 159 " --> pdb=" O HIS J 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE J 184 " --> pdb=" O GLY J 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR J 256 " --> pdb=" O GLN J 279 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL J 281 " --> pdb=" O VAL J 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL J 254 " --> pdb=" O VAL J 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP J 283 " --> pdb=" O GLU J 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU J 252 " --> pdb=" O TRP J 283 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 191 through 193 Processing sheet with id=AE2, first strand: chain 'J' and resid 200 through 201 Processing sheet with id=AE3, first strand: chain 'K' and resid 118 through 121 removed outlier: 3.534A pdb=" N VAL K 158 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL K 160 " --> pdb=" O VAL K 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE K 157 " --> pdb=" O VAL K 180 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS K 182 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY K 159 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE K 184 " --> pdb=" O GLY K 159 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR K 256 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL K 281 " --> pdb=" O VAL K 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL K 254 " --> pdb=" O VAL K 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP K 283 " --> pdb=" O GLU K 252 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU K 252 " --> pdb=" O TRP K 283 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 191 through 193 Processing sheet with id=AE5, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AE6, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.532A pdb=" N VAL A 158 " --> pdb=" O PHE A 119 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL A 160 " --> pdb=" O VAL A 121 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE A 157 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N HIS A 182 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY A 159 " --> pdb=" O HIS A 182 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE A 184 " --> pdb=" O GLY A 159 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TYR A 256 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 281 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL A 254 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP A 283 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A 252 " --> pdb=" O TRP A 283 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AE8, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AE9, first strand: chain 'L' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY L 694 " --> pdb=" O THR L 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR L 586 " --> pdb=" O GLY L 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU L 585 " --> pdb=" O GLU L 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU L 718 " --> pdb=" O GLU L 585 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU L 726 " --> pdb=" O PHE L 733 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY M 694 " --> pdb=" O THR M 586 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR M 586 " --> pdb=" O GLY M 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU M 585 " --> pdb=" O GLU M 718 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU M 718 " --> pdb=" O GLU M 585 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU M 726 " --> pdb=" O PHE M 733 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 689 through 690 removed outlier: 4.071A pdb=" N GLY N 694 " --> pdb=" O THR N 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR N 586 " --> pdb=" O GLY N 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU N 585 " --> pdb=" O GLU N 718 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU N 718 " --> pdb=" O GLU N 585 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU N 726 " --> pdb=" O PHE N 733 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY O 694 " --> pdb=" O THR O 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR O 586 " --> pdb=" O GLY O 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU O 585 " --> pdb=" O GLU O 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU O 718 " --> pdb=" O GLU O 585 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU O 726 " --> pdb=" O PHE O 733 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY P 694 " --> pdb=" O THR P 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR P 586 " --> pdb=" O GLY P 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU P 585 " --> pdb=" O GLU P 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU P 718 " --> pdb=" O GLU P 585 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU P 726 " --> pdb=" O PHE P 733 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY Q 694 " --> pdb=" O THR Q 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR Q 586 " --> pdb=" O GLY Q 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU Q 585 " --> pdb=" O GLU Q 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU Q 718 " --> pdb=" O GLU Q 585 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU Q 726 " --> pdb=" O PHE Q 733 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY R 694 " --> pdb=" O THR R 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR R 586 " --> pdb=" O GLY R 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU R 585 " --> pdb=" O GLU R 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU R 718 " --> pdb=" O GLU R 585 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU R 726 " --> pdb=" O PHE R 733 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY S 694 " --> pdb=" O THR S 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR S 586 " --> pdb=" O GLY S 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU S 585 " --> pdb=" O GLU S 718 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU S 718 " --> pdb=" O GLU S 585 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU S 726 " --> pdb=" O PHE S 733 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY T 694 " --> pdb=" O THR T 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR T 586 " --> pdb=" O GLY T 694 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU T 585 " --> pdb=" O GLU T 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU T 718 " --> pdb=" O GLU T 585 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'T' and resid 726 through 728 removed outlier: 3.749A pdb=" N LEU T 726 " --> pdb=" O PHE T 733 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'U' and resid 689 through 690 removed outlier: 4.069A pdb=" N GLY U 694 " --> pdb=" O THR U 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR U 586 " --> pdb=" O GLY U 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU U 585 " --> pdb=" O GLU U 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU U 718 " --> pdb=" O GLU U 585 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'U' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU U 726 " --> pdb=" O PHE U 733 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 689 through 690 removed outlier: 4.070A pdb=" N GLY V 694 " --> pdb=" O THR V 586 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR V 586 " --> pdb=" O GLY V 694 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU V 585 " --> pdb=" O GLU V 718 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU V 718 " --> pdb=" O GLU V 585 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'V' and resid 726 through 728 removed outlier: 3.750A pdb=" N LEU V 726 " --> pdb=" O PHE V 733 " (cutoff:3.500A) 2509 hydrogen bonds defined for protein. 7164 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: 34.58 Time building geometry restraints manager: 41.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28600 1.03 - 1.23: 33 1.23 - 1.42: 20042 1.42 - 1.61: 24860 1.61 - 1.81: 165 Bond restraints: 73700 Sorted by residual: bond pdb=" N THR I 55 " pdb=" CA THR I 55 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.28e+00 bond pdb=" N THR E 55 " pdb=" CA THR E 55 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N THR B 55 " pdb=" CA THR B 55 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N THR H 55 " pdb=" CA THR H 55 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.22e+00 bond pdb=" N THR A 55 " pdb=" CA THR A 55 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 ... (remaining 73695 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.41: 2012 107.41 - 114.07: 73806 114.07 - 120.74: 26946 120.74 - 127.41: 21461 127.41 - 134.08: 493 Bond angle restraints: 124718 Sorted by residual: angle pdb=" N VAL I 162 " pdb=" CA VAL I 162 " pdb=" C VAL I 162 " ideal model delta sigma weight residual 111.91 109.51 2.40 8.90e-01 1.26e+00 7.26e+00 angle pdb=" N VAL C 162 " pdb=" CA VAL C 162 " pdb=" C VAL C 162 " ideal model delta sigma weight residual 111.91 109.53 2.38 8.90e-01 1.26e+00 7.16e+00 angle pdb=" N VAL E 162 " pdb=" CA VAL E 162 " pdb=" C VAL E 162 " ideal model delta sigma weight residual 111.91 109.53 2.38 8.90e-01 1.26e+00 7.14e+00 angle pdb=" N VAL G 162 " pdb=" CA VAL G 162 " pdb=" C VAL G 162 " ideal model delta sigma weight residual 111.91 109.54 2.37 8.90e-01 1.26e+00 7.11e+00 angle pdb=" N VAL K 162 " pdb=" CA VAL K 162 " pdb=" C VAL K 162 " ideal model delta sigma weight residual 111.91 109.54 2.37 8.90e-01 1.26e+00 7.10e+00 ... (remaining 124713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.18: 28253 14.18 - 28.37: 2651 28.37 - 42.55: 633 42.55 - 56.73: 220 56.73 - 70.91: 99 Dihedral angle restraints: 31856 sinusoidal: 15345 harmonic: 16511 Sorted by residual: dihedral pdb=" CA TRP I 220 " pdb=" C TRP I 220 " pdb=" N ASP I 221 " pdb=" CA ASP I 221 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA TRP F 220 " pdb=" C TRP F 220 " pdb=" N ASP F 221 " pdb=" CA ASP F 221 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA TRP E 220 " pdb=" C TRP E 220 " pdb=" N ASP E 221 " pdb=" CA ASP E 221 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 31853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 2571 0.027 - 0.054: 1247 0.054 - 0.081: 379 0.081 - 0.109: 301 0.109 - 0.136: 155 Chirality restraints: 4653 Sorted by residual: chirality pdb=" CA ILE M 743 " pdb=" N ILE M 743 " pdb=" C ILE M 743 " pdb=" CB ILE M 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ILE P 743 " pdb=" N ILE P 743 " pdb=" C ILE P 743 " pdb=" CB ILE P 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILE V 743 " pdb=" N ILE V 743 " pdb=" C ILE V 743 " pdb=" CB ILE V 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 4650 not shown) Planarity restraints: 12177 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 287 " -0.009 2.00e-02 2.50e+03 6.51e-03 1.70e+00 pdb=" CG TRP H 287 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP H 287 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP H 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 287 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP H 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 287 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 287 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TRP H 287 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP H 287 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP H 287 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP H 287 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP H 287 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP H 287 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 287 " -0.009 2.00e-02 2.50e+03 6.50e-03 1.69e+00 pdb=" CG TRP A 287 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 287 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 287 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 287 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 287 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 287 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP A 287 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 287 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP A 287 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 287 " -0.009 2.00e-02 2.50e+03 6.45e-03 1.66e+00 pdb=" CG TRP C 287 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP C 287 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP C 287 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 287 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 287 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 287 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 287 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 287 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 287 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP C 287 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP C 287 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP C 287 " 0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 287 " -0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 287 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP C 287 " -0.000 2.00e-02 2.50e+03 ... (remaining 12174 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 242 1.86 - 2.54: 49807 2.54 - 3.23: 185803 3.23 - 3.91: 234018 3.91 - 4.60: 362760 Nonbonded interactions: 832630 Sorted by model distance: nonbonded pdb="HD23 LEU F 77 " pdb="HD13 LEU F 80 " model vdw 1.170 2.440 nonbonded pdb="HD23 LEU D 77 " pdb="HD13 LEU D 80 " model vdw 1.170 2.440 nonbonded pdb="HD23 LEU J 77 " pdb="HD13 LEU J 80 " model vdw 1.170 2.440 nonbonded pdb="HD23 LEU C 77 " pdb="HD13 LEU C 80 " model vdw 1.171 2.440 nonbonded pdb="HD23 LEU G 77 " pdb="HD13 LEU G 80 " model vdw 1.171 2.440 ... (remaining 832625 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' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } 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: 19.030 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: 1.120 Extract box with map and model: 41.400 Check model and map are aligned: 1.010 Set scattering table: 0.520 Process input model: 181.490 Find NCS groups from input model: 4.210 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 252.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 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 : 0.002 0.034 45067 Z= 0.144 Angle : 0.485 4.530 59631 Z= 0.291 Chirality : 0.044 0.136 4653 Planarity : 0.003 0.039 8844 Dihedral : 11.367 70.107 15037 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % 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: 1.06 (0.10), residues: 7095 helix: 2.12 (0.10), residues: 3036 sheet: -0.12 (0.17), residues: 1023 loop : -0.43 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 287 HIS 0.002 0.001 HIS A 175 PHE 0.010 0.001 PHE A 192 TYR 0.006 0.001 TYR B 390 ARG 0.006 0.000 ARG I 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1113 time to evaluate : 5.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASP cc_start: 0.8394 (m-30) cc_final: 0.8025 (m-30) REVERT: B 119 PHE cc_start: 0.8304 (t80) cc_final: 0.8094 (t80) REVERT: B 201 LYS cc_start: 0.8623 (ttpt) cc_final: 0.8334 (tttp) REVERT: B 208 LYS cc_start: 0.7360 (mttm) cc_final: 0.7159 (mttm) REVERT: B 240 TRP cc_start: 0.5939 (t-100) cc_final: 0.5611 (t60) REVERT: B 319 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8166 (mtmt) REVERT: B 352 GLN cc_start: 0.8014 (mp10) cc_final: 0.7189 (tp-100) REVERT: C 101 ASP cc_start: 0.8501 (m-30) cc_final: 0.8151 (m-30) REVERT: C 119 PHE cc_start: 0.8273 (t80) cc_final: 0.7982 (t80) REVERT: C 146 PHE cc_start: 0.7185 (p90) cc_final: 0.6752 (p90) REVERT: C 201 LYS cc_start: 0.8818 (ttpt) cc_final: 0.8521 (tttm) REVERT: C 240 TRP cc_start: 0.5927 (t-100) cc_final: 0.5571 (t60) REVERT: C 319 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8155 (mtmt) REVERT: C 338 GLU cc_start: 0.8465 (mp0) cc_final: 0.8134 (mp0) REVERT: C 352 GLN cc_start: 0.7738 (mp10) cc_final: 0.7005 (tp-100) REVERT: C 394 MET cc_start: 0.7672 (mmt) cc_final: 0.7434 (mmt) REVERT: D 101 ASP cc_start: 0.8475 (m-30) cc_final: 0.8221 (m-30) REVERT: D 177 ARG cc_start: 0.8333 (mtp180) cc_final: 0.8027 (mtp180) REVERT: D 195 ASP cc_start: 0.7678 (m-30) cc_final: 0.7430 (m-30) REVERT: D 201 LYS cc_start: 0.8734 (ttpt) cc_final: 0.8308 (tttp) REVERT: D 234 ARG cc_start: 0.7342 (mtp85) cc_final: 0.7074 (mtm110) REVERT: D 299 ARG cc_start: 0.7823 (mtm180) cc_final: 0.7597 (mtm-85) REVERT: D 319 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8068 (mtpt) REVERT: D 321 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7875 (mt-10) REVERT: D 338 GLU cc_start: 0.8458 (mp0) cc_final: 0.8084 (mp0) REVERT: D 352 GLN cc_start: 0.7876 (mp10) cc_final: 0.7126 (tp-100) REVERT: D 394 MET cc_start: 0.7441 (mmt) cc_final: 0.6999 (mmt) REVERT: E 75 TYR cc_start: 0.8269 (t80) cc_final: 0.8032 (t80) REVERT: E 101 ASP cc_start: 0.8458 (m-30) cc_final: 0.8203 (m-30) REVERT: E 195 ASP cc_start: 0.7622 (m-30) cc_final: 0.7335 (m-30) REVERT: E 201 LYS cc_start: 0.8547 (ttpt) cc_final: 0.8136 (tttp) REVERT: E 232 ARG cc_start: 0.7836 (mtm180) cc_final: 0.7543 (mtm-85) REVERT: E 240 TRP cc_start: 0.6044 (t-100) cc_final: 0.5390 (t60) REVERT: E 313 LEU cc_start: 0.8705 (tp) cc_final: 0.8455 (tp) REVERT: E 319 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8205 (mtpt) REVERT: E 352 GLN cc_start: 0.7973 (mp10) cc_final: 0.7071 (tp-100) REVERT: E 394 MET cc_start: 0.7580 (mmt) cc_final: 0.6958 (mmt) REVERT: F 195 ASP cc_start: 0.7566 (m-30) cc_final: 0.7304 (m-30) REVERT: F 201 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8226 (tttm) REVERT: F 240 TRP cc_start: 0.6186 (t-100) cc_final: 0.5559 (t60) REVERT: F 319 LYS cc_start: 0.8506 (mtmt) cc_final: 0.7985 (mtpt) REVERT: F 352 GLN cc_start: 0.8061 (mp10) cc_final: 0.7250 (tp-100) REVERT: G 101 ASP cc_start: 0.8293 (m-30) cc_final: 0.7907 (m-30) REVERT: G 109 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7304 (mm-30) REVERT: G 146 PHE cc_start: 0.6546 (p90) cc_final: 0.6196 (p90) REVERT: G 201 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8224 (tttm) REVERT: G 228 PHE cc_start: 0.7496 (m-80) cc_final: 0.7117 (m-80) REVERT: G 229 ILE cc_start: 0.7948 (mm) cc_final: 0.7634 (mm) REVERT: G 240 TRP cc_start: 0.6160 (t-100) cc_final: 0.5621 (t60) REVERT: G 285 PHE cc_start: 0.7752 (m-80) cc_final: 0.7349 (m-80) REVERT: G 319 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8197 (mtpt) REVERT: G 352 GLN cc_start: 0.7854 (mp10) cc_final: 0.7039 (tp-100) REVERT: G 383 SER cc_start: 0.8826 (t) cc_final: 0.8441 (p) REVERT: G 390 TYR cc_start: 0.8741 (m-80) cc_final: 0.8498 (m-80) REVERT: G 394 MET cc_start: 0.7592 (mmt) cc_final: 0.7199 (mmt) REVERT: H 201 LYS cc_start: 0.8730 (ttpt) cc_final: 0.8371 (tttp) REVERT: H 228 PHE cc_start: 0.7390 (m-80) cc_final: 0.6972 (m-10) REVERT: H 232 ARG cc_start: 0.7567 (mtm180) cc_final: 0.7271 (mtm-85) REVERT: H 240 TRP cc_start: 0.5972 (t-100) cc_final: 0.5485 (t60) REVERT: H 319 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8121 (mtpt) REVERT: H 352 GLN cc_start: 0.7928 (mp10) cc_final: 0.7318 (tp-100) REVERT: I 101 ASP cc_start: 0.8470 (m-30) cc_final: 0.8264 (m-30) REVERT: I 170 ASP cc_start: 0.8532 (m-30) cc_final: 0.8325 (m-30) REVERT: I 201 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8048 (tptp) REVERT: I 206 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7494 (mt-10) REVERT: I 232 ARG cc_start: 0.7638 (mtm180) cc_final: 0.7208 (mtm-85) REVERT: I 240 TRP cc_start: 0.6369 (t-100) cc_final: 0.5853 (t60) REVERT: I 280 TYR cc_start: 0.7926 (p90) cc_final: 0.7256 (p90) REVERT: I 319 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7962 (mtpt) REVERT: I 352 GLN cc_start: 0.8004 (mp10) cc_final: 0.7114 (tp-100) REVERT: I 394 MET cc_start: 0.7571 (mmt) cc_final: 0.7348 (mmt) REVERT: J 101 ASP cc_start: 0.8403 (m-30) cc_final: 0.8107 (m-30) REVERT: J 109 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7627 (mt-10) REVERT: J 146 PHE cc_start: 0.6914 (p90) cc_final: 0.6116 (p90) REVERT: J 165 TYR cc_start: 0.7345 (m-10) cc_final: 0.6961 (m-80) REVERT: J 170 ASP cc_start: 0.8557 (m-30) cc_final: 0.8352 (m-30) REVERT: J 201 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8275 (tttm) REVERT: J 208 LYS cc_start: 0.7357 (mttm) cc_final: 0.7106 (mttm) REVERT: J 232 ARG cc_start: 0.7495 (mtm180) cc_final: 0.7235 (mtm-85) REVERT: J 285 PHE cc_start: 0.7567 (m-80) cc_final: 0.7302 (m-80) REVERT: J 319 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8093 (mtpt) REVERT: J 352 GLN cc_start: 0.7911 (mp10) cc_final: 0.7239 (tp-100) REVERT: J 390 TYR cc_start: 0.8826 (m-80) cc_final: 0.8515 (m-80) REVERT: J 394 MET cc_start: 0.7511 (mmt) cc_final: 0.7205 (mmt) REVERT: K 101 ASP cc_start: 0.8546 (m-30) cc_final: 0.8324 (m-30) REVERT: K 183 THR cc_start: 0.7553 (t) cc_final: 0.7314 (t) REVERT: K 201 LYS cc_start: 0.8696 (ttpt) cc_final: 0.8299 (tttm) REVERT: K 229 ILE cc_start: 0.8048 (mm) cc_final: 0.7782 (mm) REVERT: K 232 ARG cc_start: 0.7432 (mtm180) cc_final: 0.7221 (mtm110) REVERT: K 240 TRP cc_start: 0.6227 (t-100) cc_final: 0.5728 (t60) REVERT: K 319 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8180 (mtpt) REVERT: K 352 GLN cc_start: 0.7755 (mp10) cc_final: 0.7036 (tp-100) REVERT: K 368 TYR cc_start: 0.8034 (t80) cc_final: 0.7207 (t80) REVERT: K 394 MET cc_start: 0.7554 (mmt) cc_final: 0.7204 (mmt) REVERT: A 101 ASP cc_start: 0.8469 (m-30) cc_final: 0.8149 (m-30) REVERT: A 201 LYS cc_start: 0.8602 (ttpt) cc_final: 0.8181 (tttm) REVERT: A 232 ARG cc_start: 0.7683 (mtm180) cc_final: 0.7357 (mtm-85) REVERT: A 240 TRP cc_start: 0.6048 (t-100) cc_final: 0.5613 (t60) REVERT: A 319 LYS cc_start: 0.8572 (mtmt) cc_final: 0.8169 (mtpt) REVERT: A 352 GLN cc_start: 0.7887 (mp10) cc_final: 0.7210 (tp-100) REVERT: L 458 LYS cc_start: 0.8333 (mptt) cc_final: 0.7964 (mmtt) REVERT: L 473 ASP cc_start: 0.6906 (t70) cc_final: 0.6392 (m-30) REVERT: M 458 LYS cc_start: 0.8407 (mptt) cc_final: 0.8204 (mmtt) REVERT: N 458 LYS cc_start: 0.8461 (mptt) cc_final: 0.8073 (mmtt) REVERT: O 458 LYS cc_start: 0.8388 (mptt) cc_final: 0.8055 (mmtt) REVERT: P 458 LYS cc_start: 0.8403 (mptt) cc_final: 0.8083 (mmtm) REVERT: Q 458 LYS cc_start: 0.8327 (mptt) cc_final: 0.7896 (mmmt) REVERT: Q 473 ASP cc_start: 0.6089 (t70) cc_final: 0.5579 (m-30) REVERT: R 458 LYS cc_start: 0.8174 (mptt) cc_final: 0.7836 (mmtt) REVERT: S 458 LYS cc_start: 0.8569 (mptt) cc_final: 0.8257 (mmtt) REVERT: T 458 LYS cc_start: 0.8567 (mptt) cc_final: 0.8173 (mmtt) REVERT: U 458 LYS cc_start: 0.8254 (mptt) cc_final: 0.7965 (mmtt) REVERT: V 458 LYS cc_start: 0.8311 (mptt) cc_final: 0.8025 (mmtt) outliers start: 0 outliers final: 0 residues processed: 1113 average time/residue: 0.9775 time to fit residues: 1685.5944 Evaluate side-chains 822 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 822 time to evaluate : 4.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 603 optimal weight: 0.0000 chunk 541 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 185 optimal weight: 0.9980 chunk 365 optimal weight: 3.9990 chunk 289 optimal weight: 0.6980 chunk 560 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 340 optimal weight: 2.9990 chunk 417 optimal weight: 10.0000 chunk 649 optimal weight: 30.0000 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 320 ASN E 148 ASN F 320 ASN G 320 ASN H 122 ASN I 320 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 45067 Z= 0.205 Angle : 0.474 6.366 59631 Z= 0.255 Chirality : 0.045 0.153 4653 Planarity : 0.003 0.035 8844 Dihedral : 3.832 18.459 7546 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.53 % Allowed : 10.14 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.11), residues: 7095 helix: 2.76 (0.10), residues: 3069 sheet: -0.16 (0.17), residues: 1045 loop : -0.15 (0.12), residues: 2981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 287 HIS 0.005 0.001 HIS K 175 PHE 0.014 0.001 PHE F 198 TYR 0.009 0.001 TYR J 315 ARG 0.003 0.000 ARG F 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 841 time to evaluate : 4.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 PHE cc_start: 0.8372 (t80) cc_final: 0.8133 (t80) REVERT: B 201 LYS cc_start: 0.8692 (ttpt) cc_final: 0.8344 (tttm) REVERT: B 208 LYS cc_start: 0.7491 (mttm) cc_final: 0.7289 (mttm) REVERT: B 228 PHE cc_start: 0.7609 (m-80) cc_final: 0.6909 (m-10) REVERT: B 234 ARG cc_start: 0.8329 (mmt180) cc_final: 0.7801 (mtm110) REVERT: B 240 TRP cc_start: 0.6179 (t-100) cc_final: 0.5707 (t60) REVERT: B 319 LYS cc_start: 0.8584 (mtmt) cc_final: 0.8129 (mtmt) REVERT: B 352 GLN cc_start: 0.8071 (mp10) cc_final: 0.7229 (tp-100) REVERT: C 101 ASP cc_start: 0.8433 (m-30) cc_final: 0.8137 (m-30) REVERT: C 119 PHE cc_start: 0.8349 (t80) cc_final: 0.8060 (t80) REVERT: C 146 PHE cc_start: 0.7237 (p90) cc_final: 0.6768 (p90) REVERT: C 165 TYR cc_start: 0.7091 (m-80) cc_final: 0.6839 (m-80) REVERT: C 201 LYS cc_start: 0.8854 (ttpt) cc_final: 0.8507 (tttm) REVERT: C 240 TRP cc_start: 0.6136 (t-100) cc_final: 0.5646 (t60) REVERT: C 287 TRP cc_start: 0.7173 (p90) cc_final: 0.6965 (p90) REVERT: C 319 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8104 (mtmt) REVERT: C 338 GLU cc_start: 0.8528 (mp0) cc_final: 0.8218 (mp0) REVERT: C 352 GLN cc_start: 0.7815 (mp10) cc_final: 0.7047 (tp-100) REVERT: D 101 ASP cc_start: 0.8426 (m-30) cc_final: 0.8185 (m-30) REVERT: D 177 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7821 (mtp180) REVERT: D 201 LYS cc_start: 0.8705 (ttpt) cc_final: 0.8348 (tttm) REVERT: D 234 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7133 (mtm110) REVERT: D 299 ARG cc_start: 0.7988 (mtm180) cc_final: 0.7674 (mtm-85) REVERT: D 319 LYS cc_start: 0.8581 (mtmt) cc_final: 0.8023 (mtpt) REVERT: D 321 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8144 (mt-10) REVERT: D 352 GLN cc_start: 0.7937 (mp10) cc_final: 0.7157 (tp-100) REVERT: E 101 ASP cc_start: 0.8470 (m-30) cc_final: 0.8096 (m-30) REVERT: E 201 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8283 (tttp) REVERT: E 232 ARG cc_start: 0.7887 (mtm180) cc_final: 0.7641 (mtm-85) REVERT: E 240 TRP cc_start: 0.6379 (t-100) cc_final: 0.5550 (t60) REVERT: E 287 TRP cc_start: 0.7436 (p90) cc_final: 0.7153 (p90) REVERT: E 313 LEU cc_start: 0.8842 (tp) cc_final: 0.8642 (tp) REVERT: E 319 LYS cc_start: 0.8528 (mtmt) cc_final: 0.8189 (mtmt) REVERT: E 352 GLN cc_start: 0.8045 (mp10) cc_final: 0.7102 (tp-100) REVERT: F 195 ASP cc_start: 0.7493 (m-30) cc_final: 0.7215 (m-30) REVERT: F 201 LYS cc_start: 0.8680 (ttpt) cc_final: 0.8246 (tttm) REVERT: F 234 ARG cc_start: 0.8056 (mtp85) cc_final: 0.7617 (mmt-90) REVERT: F 285 PHE cc_start: 0.7602 (m-80) cc_final: 0.7378 (m-80) REVERT: F 319 LYS cc_start: 0.8478 (mtmt) cc_final: 0.7993 (mtpt) REVERT: F 352 GLN cc_start: 0.8095 (mp10) cc_final: 0.7252 (tp-100) REVERT: G 60 ARG cc_start: 0.9189 (mtp85) cc_final: 0.8532 (mmm160) REVERT: G 101 ASP cc_start: 0.8244 (m-30) cc_final: 0.7863 (m-30) REVERT: G 146 PHE cc_start: 0.6536 (p90) cc_final: 0.6126 (p90) REVERT: G 165 TYR cc_start: 0.7030 (m-80) cc_final: 0.6740 (m-80) REVERT: G 201 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8332 (tttm) REVERT: G 229 ILE cc_start: 0.8066 (mm) cc_final: 0.7744 (mm) REVERT: G 240 TRP cc_start: 0.6397 (t-100) cc_final: 0.5709 (t60) REVERT: G 285 PHE cc_start: 0.7745 (m-80) cc_final: 0.7329 (m-80) REVERT: G 319 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8228 (mtpt) REVERT: G 352 GLN cc_start: 0.7910 (mp10) cc_final: 0.7066 (tp-100) REVERT: H 201 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8385 (tttp) REVERT: H 228 PHE cc_start: 0.7395 (m-80) cc_final: 0.6985 (m-10) REVERT: H 240 TRP cc_start: 0.6200 (t-100) cc_final: 0.5565 (t60) REVERT: H 319 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8109 (mtpt) REVERT: H 352 GLN cc_start: 0.7992 (mp10) cc_final: 0.7295 (tp-100) REVERT: I 201 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8193 (tttp) REVERT: I 228 PHE cc_start: 0.7606 (m-80) cc_final: 0.7320 (m-80) REVERT: I 232 ARG cc_start: 0.7758 (mtm180) cc_final: 0.7458 (mtm-85) REVERT: I 319 LYS cc_start: 0.8481 (mtmt) cc_final: 0.7967 (mtpt) REVERT: I 352 GLN cc_start: 0.8034 (mp10) cc_final: 0.7123 (tp-100) REVERT: J 101 ASP cc_start: 0.8390 (m-30) cc_final: 0.7951 (m-30) REVERT: J 165 TYR cc_start: 0.7447 (m-10) cc_final: 0.7099 (m-80) REVERT: J 201 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8224 (tttm) REVERT: J 208 LYS cc_start: 0.7319 (mttm) cc_final: 0.7079 (mttm) REVERT: J 228 PHE cc_start: 0.8042 (m-80) cc_final: 0.7677 (m-80) REVERT: J 229 ILE cc_start: 0.8131 (mm) cc_final: 0.7873 (mm) REVERT: J 232 ARG cc_start: 0.7731 (mtm180) cc_final: 0.7286 (mtm-85) REVERT: J 287 TRP cc_start: 0.7726 (p90) cc_final: 0.7394 (p90) REVERT: J 319 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8128 (mtpt) REVERT: J 352 GLN cc_start: 0.7979 (mp10) cc_final: 0.7261 (tp-100) REVERT: J 390 TYR cc_start: 0.8867 (m-80) cc_final: 0.8578 (m-80) REVERT: J 394 MET cc_start: 0.7398 (mmt) cc_final: 0.7194 (mmt) REVERT: K 201 LYS cc_start: 0.8685 (ttpt) cc_final: 0.8362 (tttm) REVERT: K 319 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8088 (mtpt) REVERT: K 352 GLN cc_start: 0.7838 (mp10) cc_final: 0.7053 (tp-100) REVERT: A 101 ASP cc_start: 0.8454 (m-30) cc_final: 0.8109 (m-30) REVERT: A 109 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7383 (mt-10) REVERT: A 165 TYR cc_start: 0.7144 (m-80) cc_final: 0.6899 (m-80) REVERT: A 201 LYS cc_start: 0.8606 (ttpt) cc_final: 0.8275 (tttp) REVERT: A 228 PHE cc_start: 0.7756 (m-80) cc_final: 0.7472 (m-80) REVERT: A 234 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7901 (mtp85) REVERT: A 319 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8130 (mtpt) REVERT: A 352 GLN cc_start: 0.7952 (mp10) cc_final: 0.7244 (tp-100) REVERT: A 394 MET cc_start: 0.7195 (mmt) cc_final: 0.6631 (mmt) REVERT: L 458 LYS cc_start: 0.8266 (mptt) cc_final: 0.7857 (mmtt) REVERT: L 473 ASP cc_start: 0.6949 (t70) cc_final: 0.6380 (m-30) REVERT: M 458 LYS cc_start: 0.8334 (mptt) cc_final: 0.8121 (mmtt) REVERT: N 458 LYS cc_start: 0.8436 (mptt) cc_final: 0.8084 (mmtt) REVERT: P 458 LYS cc_start: 0.8359 (mptt) cc_final: 0.8051 (mmtt) REVERT: Q 458 LYS cc_start: 0.8366 (mptt) cc_final: 0.8002 (mmtt) REVERT: Q 473 ASP cc_start: 0.5992 (t70) cc_final: 0.5464 (m-30) REVERT: R 458 LYS cc_start: 0.8088 (mptt) cc_final: 0.7739 (mmtt) REVERT: T 458 LYS cc_start: 0.8599 (mptt) cc_final: 0.8200 (mmtt) REVERT: U 458 LYS cc_start: 0.8170 (mptt) cc_final: 0.7870 (mmtt) REVERT: V 458 LYS cc_start: 0.8200 (mptt) cc_final: 0.7944 (mmtt) outliers start: 51 outliers final: 34 residues processed: 855 average time/residue: 0.9119 time to fit residues: 1238.3648 Evaluate side-chains 803 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 768 time to evaluate : 5.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain H residue 370 SER Chi-restraints excluded: chain I residue 210 SER Chi-restraints excluded: chain I residue 370 SER Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 370 SER Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain L residue 676 ASP Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain N residue 676 ASP Chi-restraints excluded: chain O residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain Q residue 676 ASP Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain S residue 676 ASP Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain U residue 676 ASP Chi-restraints excluded: chain U residue 703 SER Chi-restraints excluded: chain V residue 676 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 360 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 540 optimal weight: 0.8980 chunk 442 optimal weight: 50.0000 chunk 179 optimal weight: 2.9990 chunk 650 optimal weight: 1.9990 chunk 702 optimal weight: 0.5980 chunk 579 optimal weight: 0.0050 chunk 645 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 521 optimal weight: 9.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 45067 Z= 0.136 Angle : 0.424 5.937 59631 Z= 0.224 Chirality : 0.044 0.138 4653 Planarity : 0.003 0.025 8844 Dihedral : 3.618 17.378 7546 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 10.92 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.11), residues: 7095 helix: 3.24 (0.10), residues: 2992 sheet: -0.30 (0.17), residues: 1023 loop : -0.04 (0.12), residues: 3080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 220 HIS 0.003 0.001 HIS K 175 PHE 0.008 0.001 PHE C 192 TYR 0.011 0.001 TYR H 275 ARG 0.002 0.000 ARG K 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 802 time to evaluate : 5.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 119 PHE cc_start: 0.8305 (t80) cc_final: 0.8095 (t80) REVERT: B 165 TYR cc_start: 0.7131 (m-80) cc_final: 0.6702 (t80) REVERT: B 201 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8403 (tttp) REVERT: B 208 LYS cc_start: 0.7399 (mttm) cc_final: 0.7199 (mttm) REVERT: B 228 PHE cc_start: 0.7646 (m-80) cc_final: 0.7315 (m-80) REVERT: B 319 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8129 (mtmt) REVERT: B 352 GLN cc_start: 0.8075 (mp10) cc_final: 0.7246 (tp-100) REVERT: C 101 ASP cc_start: 0.8389 (m-30) cc_final: 0.8025 (m-30) REVERT: C 119 PHE cc_start: 0.8308 (t80) cc_final: 0.8014 (t80) REVERT: C 201 LYS cc_start: 0.8899 (ttpt) cc_final: 0.8563 (tttm) REVERT: C 234 ARG cc_start: 0.8286 (mmt180) cc_final: 0.7926 (tpt170) REVERT: C 287 TRP cc_start: 0.7198 (p90) cc_final: 0.6997 (p90) REVERT: C 319 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8171 (mtpt) REVERT: C 352 GLN cc_start: 0.7785 (mp10) cc_final: 0.7024 (tp-100) REVERT: D 101 ASP cc_start: 0.8419 (m-30) cc_final: 0.8207 (m-30) REVERT: D 177 ARG cc_start: 0.8250 (mtp180) cc_final: 0.7744 (mtp180) REVERT: D 201 LYS cc_start: 0.8737 (ttpt) cc_final: 0.8374 (tttm) REVERT: D 234 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7345 (ptm-80) REVERT: D 299 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7647 (mtm-85) REVERT: D 305 GLU cc_start: 0.8365 (pm20) cc_final: 0.8136 (pm20) REVERT: D 319 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8034 (mtpt) REVERT: D 321 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 352 GLN cc_start: 0.7917 (mp10) cc_final: 0.7147 (tp-100) REVERT: E 101 ASP cc_start: 0.8397 (m-30) cc_final: 0.8060 (m-30) REVERT: E 201 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8303 (tttp) REVERT: E 232 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7736 (mtm-85) REVERT: E 240 TRP cc_start: 0.6303 (t-100) cc_final: 0.5439 (t60) REVERT: E 287 TRP cc_start: 0.7400 (p90) cc_final: 0.7127 (p90) REVERT: E 319 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8189 (mtmt) REVERT: E 352 GLN cc_start: 0.8030 (mp10) cc_final: 0.7093 (tp-100) REVERT: F 201 LYS cc_start: 0.8717 (ttpt) cc_final: 0.8276 (tttm) REVERT: F 234 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7606 (mmt-90) REVERT: F 319 LYS cc_start: 0.8485 (mtmt) cc_final: 0.7972 (mtpt) REVERT: F 352 GLN cc_start: 0.8065 (mp10) cc_final: 0.7286 (tp-100) REVERT: G 60 ARG cc_start: 0.9118 (mtp85) cc_final: 0.8508 (mmm160) REVERT: G 101 ASP cc_start: 0.8233 (m-30) cc_final: 0.7834 (m-30) REVERT: G 146 PHE cc_start: 0.6491 (p90) cc_final: 0.6090 (p90) REVERT: G 165 TYR cc_start: 0.7052 (m-80) cc_final: 0.6763 (m-80) REVERT: G 201 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8272 (tttm) REVERT: G 224 GLU cc_start: 0.8047 (tp30) cc_final: 0.7831 (tp30) REVERT: G 229 ILE cc_start: 0.8171 (mm) cc_final: 0.7824 (mm) REVERT: G 285 PHE cc_start: 0.7648 (m-80) cc_final: 0.7302 (m-80) REVERT: G 305 GLU cc_start: 0.8466 (pm20) cc_final: 0.8250 (pm20) REVERT: G 319 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8219 (mtmt) REVERT: G 352 GLN cc_start: 0.7866 (mp10) cc_final: 0.7024 (tp-100) REVERT: H 201 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8411 (tttp) REVERT: H 228 PHE cc_start: 0.7412 (m-80) cc_final: 0.6979 (m-10) REVERT: H 305 GLU cc_start: 0.8405 (pm20) cc_final: 0.8153 (pm20) REVERT: H 319 LYS cc_start: 0.8649 (mtmt) cc_final: 0.8182 (mtpt) REVERT: H 352 GLN cc_start: 0.7982 (mp10) cc_final: 0.7287 (tp-100) REVERT: I 201 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8232 (tttp) REVERT: I 232 ARG cc_start: 0.7714 (mtm180) cc_final: 0.7505 (mtm-85) REVERT: I 280 TYR cc_start: 0.7926 (p90) cc_final: 0.7208 (p90) REVERT: I 319 LYS cc_start: 0.8502 (mtmt) cc_final: 0.7978 (mtpt) REVERT: I 352 GLN cc_start: 0.8018 (mp10) cc_final: 0.7110 (tp-100) REVERT: J 101 ASP cc_start: 0.8380 (m-30) cc_final: 0.7944 (m-30) REVERT: J 201 LYS cc_start: 0.8595 (ttpt) cc_final: 0.8267 (tttm) REVERT: J 208 LYS cc_start: 0.7188 (mttm) cc_final: 0.6945 (mttm) REVERT: J 228 PHE cc_start: 0.8034 (m-80) cc_final: 0.7632 (m-80) REVERT: J 229 ILE cc_start: 0.7987 (mm) cc_final: 0.7692 (mm) REVERT: J 232 ARG cc_start: 0.7726 (mtm180) cc_final: 0.7437 (mtm-85) REVERT: J 287 TRP cc_start: 0.7702 (p90) cc_final: 0.7335 (p90) REVERT: J 319 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8101 (mtpt) REVERT: J 352 GLN cc_start: 0.7975 (mp10) cc_final: 0.7260 (tp-100) REVERT: K 201 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8404 (tttm) REVERT: K 319 LYS cc_start: 0.8558 (mtmt) cc_final: 0.8133 (mtpt) REVERT: K 352 GLN cc_start: 0.7860 (mp10) cc_final: 0.7078 (tp-100) REVERT: A 101 ASP cc_start: 0.8436 (m-30) cc_final: 0.8092 (m-30) REVERT: A 109 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7417 (mt-10) REVERT: A 201 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8289 (tttm) REVERT: A 234 ARG cc_start: 0.8265 (mmt180) cc_final: 0.7936 (mtp85) REVERT: A 319 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8121 (mtpt) REVERT: A 352 GLN cc_start: 0.7940 (mp10) cc_final: 0.7232 (tp-100) REVERT: A 394 MET cc_start: 0.7210 (mmt) cc_final: 0.6647 (mmt) REVERT: L 458 LYS cc_start: 0.8293 (mptt) cc_final: 0.7887 (mmtt) REVERT: M 458 LYS cc_start: 0.8353 (mptt) cc_final: 0.8142 (mmtt) REVERT: N 458 LYS cc_start: 0.8471 (mptt) cc_final: 0.8097 (mmtt) REVERT: O 458 LYS cc_start: 0.8403 (mptt) cc_final: 0.8014 (mmtt) REVERT: P 458 LYS cc_start: 0.8387 (mptt) cc_final: 0.8065 (mmtt) REVERT: Q 458 LYS cc_start: 0.8345 (mptt) cc_final: 0.7993 (mmtt) REVERT: Q 473 ASP cc_start: 0.6180 (t70) cc_final: 0.5421 (m-30) REVERT: R 458 LYS cc_start: 0.8114 (mptt) cc_final: 0.7777 (mmtt) REVERT: T 458 LYS cc_start: 0.8629 (mptt) cc_final: 0.8238 (mmtt) REVERT: U 458 LYS cc_start: 0.8193 (mptt) cc_final: 0.7920 (mmtt) REVERT: U 672 PHE cc_start: 0.8073 (m-80) cc_final: 0.7788 (m-10) REVERT: V 458 LYS cc_start: 0.8216 (mptt) cc_final: 0.7962 (mmtt) outliers start: 31 outliers final: 19 residues processed: 811 average time/residue: 0.9314 time to fit residues: 1212.2282 Evaluate side-chains 782 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 762 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 252 GLU Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 370 SER Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain Q residue 676 ASP Chi-restraints excluded: chain V residue 711 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 642 optimal weight: 30.0000 chunk 489 optimal weight: 20.0000 chunk 337 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 310 optimal weight: 1.9990 chunk 436 optimal weight: 40.0000 chunk 652 optimal weight: 20.0000 chunk 691 optimal weight: 6.9990 chunk 341 optimal weight: 3.9990 chunk 618 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 320 ASN ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 45067 Z= 0.529 Angle : 0.588 7.465 59631 Z= 0.321 Chirality : 0.051 0.205 4653 Planarity : 0.004 0.045 8844 Dihedral : 4.234 25.417 7546 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.64 % Allowed : 12.69 % Favored : 84.67 % 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: 1.62 (0.11), residues: 7095 helix: 2.94 (0.10), residues: 2992 sheet: -0.55 (0.16), residues: 1078 loop : -0.20 (0.12), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 265 HIS 0.006 0.002 HIS K 175 PHE 0.021 0.002 PHE B 228 TYR 0.016 0.002 TYR K 315 ARG 0.005 0.001 ARG H 328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 844 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 756 time to evaluate : 5.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8407 (tttp) REVERT: B 319 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8097 (mtmt) REVERT: B 352 GLN cc_start: 0.8298 (mp10) cc_final: 0.7435 (tp-100) REVERT: C 201 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8611 (tttp) REVERT: C 234 ARG cc_start: 0.8307 (mmt180) cc_final: 0.7962 (tpt170) REVERT: C 319 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8307 (mtpt) REVERT: C 352 GLN cc_start: 0.8038 (mp10) cc_final: 0.7263 (tp-100) REVERT: D 201 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8379 (tttm) REVERT: D 234 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7269 (mtp-110) REVERT: D 305 GLU cc_start: 0.8420 (pm20) cc_final: 0.8209 (pm20) REVERT: D 319 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8137 (mtmt) REVERT: D 321 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8382 (mt-10) REVERT: D 352 GLN cc_start: 0.8124 (mp10) cc_final: 0.7240 (tp-100) REVERT: E 193 ASP cc_start: 0.8242 (t0) cc_final: 0.7899 (t70) REVERT: E 201 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8306 (tttp) REVERT: E 232 ARG cc_start: 0.8203 (mtm180) cc_final: 0.8001 (mtm-85) REVERT: E 240 TRP cc_start: 0.6525 (t-100) cc_final: 0.5625 (t60) REVERT: E 319 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8224 (mtmt) REVERT: E 352 GLN cc_start: 0.8194 (mp10) cc_final: 0.7255 (tp-100) REVERT: F 201 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8301 (tttm) REVERT: F 319 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8160 (mtpt) REVERT: F 352 GLN cc_start: 0.8221 (mp10) cc_final: 0.7363 (tp-100) REVERT: G 101 ASP cc_start: 0.8191 (m-30) cc_final: 0.7968 (m-30) REVERT: G 146 PHE cc_start: 0.6475 (p90) cc_final: 0.6091 (p90) REVERT: G 201 LYS cc_start: 0.8774 (ttpt) cc_final: 0.8362 (tttm) REVERT: G 285 PHE cc_start: 0.7754 (m-80) cc_final: 0.7391 (m-80) REVERT: G 305 GLU cc_start: 0.8399 (pm20) cc_final: 0.8172 (pm20) REVERT: G 319 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8233 (mtmt) REVERT: G 352 GLN cc_start: 0.8094 (mp10) cc_final: 0.7267 (tp-100) REVERT: G 383 SER cc_start: 0.8852 (t) cc_final: 0.8518 (p) REVERT: H 201 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8415 (tttp) REVERT: H 319 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8110 (mtmt) REVERT: H 352 GLN cc_start: 0.8208 (mp10) cc_final: 0.7336 (tp-100) REVERT: I 201 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8292 (tttp) REVERT: I 228 PHE cc_start: 0.7953 (m-80) cc_final: 0.7660 (m-80) REVERT: I 232 ARG cc_start: 0.7994 (mtm180) cc_final: 0.7708 (mtm-85) REVERT: I 319 LYS cc_start: 0.8563 (mtmt) cc_final: 0.8169 (mtpt) REVERT: I 352 GLN cc_start: 0.8209 (mp10) cc_final: 0.7226 (tp-100) REVERT: J 201 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8328 (tttp) REVERT: J 208 LYS cc_start: 0.7658 (mttm) cc_final: 0.7391 (mttm) REVERT: J 229 ILE cc_start: 0.8455 (mm) cc_final: 0.8102 (mm) REVERT: J 319 LYS cc_start: 0.8726 (mtmt) cc_final: 0.8349 (mtpt) REVERT: J 331 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8326 (tt0) REVERT: J 352 GLN cc_start: 0.8146 (mp10) cc_final: 0.7412 (tp-100) REVERT: K 201 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8336 (tttm) REVERT: K 229 ILE cc_start: 0.8245 (mm) cc_final: 0.7886 (mm) REVERT: K 319 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8198 (mtmt) REVERT: K 352 GLN cc_start: 0.8159 (mp10) cc_final: 0.7290 (tp-100) REVERT: A 101 ASP cc_start: 0.8389 (m-30) cc_final: 0.7987 (m-30) REVERT: A 201 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8307 (tttm) REVERT: A 319 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8129 (mtpt) REVERT: A 352 GLN cc_start: 0.8168 (mp10) cc_final: 0.7365 (tp-100) REVERT: L 458 LYS cc_start: 0.8310 (mptt) cc_final: 0.7932 (mmtt) REVERT: M 458 LYS cc_start: 0.8383 (mptt) cc_final: 0.8156 (mmtt) REVERT: N 458 LYS cc_start: 0.8510 (mptt) cc_final: 0.8155 (mmtt) REVERT: P 458 LYS cc_start: 0.8435 (mptt) cc_final: 0.8140 (mmtt) REVERT: Q 458 LYS cc_start: 0.8270 (mptt) cc_final: 0.7995 (mmtt) REVERT: R 458 LYS cc_start: 0.8122 (mptt) cc_final: 0.7809 (mmtt) REVERT: T 458 LYS cc_start: 0.8668 (mptt) cc_final: 0.8293 (mmtt) REVERT: U 458 LYS cc_start: 0.8281 (mptt) cc_final: 0.7987 (mmtt) REVERT: V 458 LYS cc_start: 0.8291 (mptt) cc_final: 0.8020 (mmtt) outliers start: 88 outliers final: 65 residues processed: 794 average time/residue: 0.9509 time to fit residues: 1208.5581 Evaluate side-chains 771 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 705 time to evaluate : 5.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain I residue 336 THR Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain L residue 676 ASP Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain N residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain Q residue 711 PHE Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain S residue 676 ASP Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain U residue 676 ASP Chi-restraints excluded: chain V residue 676 ASP Chi-restraints excluded: chain V residue 711 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 575 optimal weight: 30.0000 chunk 392 optimal weight: 40.0000 chunk 10 optimal weight: 0.6980 chunk 514 optimal weight: 2.9990 chunk 285 optimal weight: 0.5980 chunk 589 optimal weight: 9.9990 chunk 477 optimal weight: 40.0000 chunk 0 optimal weight: 9.9990 chunk 352 optimal weight: 20.0000 chunk 620 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 148 ASN G 144 GLN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 144 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 45067 Z= 0.432 Angle : 0.548 6.264 59631 Z= 0.297 Chirality : 0.048 0.194 4653 Planarity : 0.004 0.042 8844 Dihedral : 4.288 24.746 7546 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.42 % Allowed : 15.69 % Favored : 80.89 % 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: 1.51 (0.11), residues: 7095 helix: 2.93 (0.10), residues: 2937 sheet: -0.58 (0.18), residues: 957 loop : -0.32 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 265 HIS 0.009 0.001 HIS K 175 PHE 0.018 0.002 PHE B 192 TYR 0.015 0.002 TYR I 165 ARG 0.004 0.001 ARG I 328 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 733 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8815 (ttpt) cc_final: 0.8433 (tttp) REVERT: B 319 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8138 (mtmt) REVERT: C 181 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8376 (tt) REVERT: C 201 LYS cc_start: 0.8929 (ttpt) cc_final: 0.8626 (tttp) REVERT: C 234 ARG cc_start: 0.8334 (mmt180) cc_final: 0.8088 (mmt180) REVERT: C 319 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8321 (mtpt) REVERT: C 352 GLN cc_start: 0.8081 (mp10) cc_final: 0.7348 (tp-100) REVERT: D 201 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8378 (tttm) REVERT: D 234 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7231 (mtp-110) REVERT: D 319 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8218 (mtpt) REVERT: D 352 GLN cc_start: 0.8113 (mp10) cc_final: 0.7344 (tp-100) REVERT: E 193 ASP cc_start: 0.8347 (t0) cc_final: 0.8056 (t70) REVERT: E 201 LYS cc_start: 0.8688 (ttpt) cc_final: 0.8317 (tttm) REVERT: E 232 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7867 (mtm-85) REVERT: E 240 TRP cc_start: 0.6563 (t-100) cc_final: 0.5432 (t60) REVERT: E 319 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8285 (mtpt) REVERT: E 352 GLN cc_start: 0.8230 (mp10) cc_final: 0.7968 (mp10) REVERT: F 201 LYS cc_start: 0.8763 (ttpt) cc_final: 0.8344 (tttm) REVERT: F 319 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8116 (mtpt) REVERT: F 352 GLN cc_start: 0.8236 (mp10) cc_final: 0.7367 (tp-100) REVERT: G 60 ARG cc_start: 0.9254 (mtp85) cc_final: 0.8616 (mmm160) REVERT: G 101 ASP cc_start: 0.8148 (m-30) cc_final: 0.7910 (m-30) REVERT: G 146 PHE cc_start: 0.6417 (p90) cc_final: 0.6065 (p90) REVERT: G 201 LYS cc_start: 0.8812 (ttpt) cc_final: 0.8404 (tttm) REVERT: G 285 PHE cc_start: 0.7790 (m-80) cc_final: 0.7496 (m-80) REVERT: G 305 GLU cc_start: 0.8356 (pm20) cc_final: 0.8089 (pm20) REVERT: G 319 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8228 (mtpt) REVERT: H 201 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8400 (tttp) REVERT: H 319 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8062 (mtmt) REVERT: I 201 LYS cc_start: 0.8715 (ttpt) cc_final: 0.8338 (tttp) REVERT: I 228 PHE cc_start: 0.8062 (m-80) cc_final: 0.7796 (m-80) REVERT: I 319 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8164 (mtpt) REVERT: I 331 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.8412 (mm-30) REVERT: J 201 LYS cc_start: 0.8718 (ttpt) cc_final: 0.8348 (tttp) REVERT: J 229 ILE cc_start: 0.8477 (mm) cc_final: 0.8147 (mm) REVERT: J 319 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8356 (mtpt) REVERT: J 390 TYR cc_start: 0.8865 (m-80) cc_final: 0.8425 (m-80) REVERT: K 201 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8388 (tttm) REVERT: K 229 ILE cc_start: 0.8299 (mm) cc_final: 0.7954 (mm) REVERT: K 319 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8235 (mtpt) REVERT: K 352 GLN cc_start: 0.8141 (mp10) cc_final: 0.7926 (mp-120) REVERT: A 101 ASP cc_start: 0.8325 (m-30) cc_final: 0.7910 (m-30) REVERT: A 201 LYS cc_start: 0.8710 (ttpt) cc_final: 0.8341 (tttp) REVERT: A 319 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8183 (mtmt) REVERT: L 458 LYS cc_start: 0.8332 (mptt) cc_final: 0.7958 (mmtt) REVERT: M 458 LYS cc_start: 0.8397 (mptt) cc_final: 0.8131 (mmtt) REVERT: N 458 LYS cc_start: 0.8510 (mptt) cc_final: 0.8137 (mmtt) REVERT: P 458 LYS cc_start: 0.8504 (mptt) cc_final: 0.8169 (mmtt) REVERT: Q 458 LYS cc_start: 0.8278 (mptt) cc_final: 0.7950 (mmmt) REVERT: R 458 LYS cc_start: 0.8158 (mptt) cc_final: 0.7820 (mmtt) REVERT: S 458 LYS cc_start: 0.8627 (mptt) cc_final: 0.8308 (mmtt) REVERT: T 458 LYS cc_start: 0.8680 (mptt) cc_final: 0.8268 (mmtt) REVERT: T 672 PHE cc_start: 0.8116 (m-80) cc_final: 0.7911 (m-10) REVERT: U 458 LYS cc_start: 0.8269 (mptt) cc_final: 0.7986 (mmtt) REVERT: V 458 LYS cc_start: 0.8288 (mptt) cc_final: 0.8025 (mmtt) outliers start: 114 outliers final: 97 residues processed: 783 average time/residue: 0.8934 time to fit residues: 1105.8209 Evaluate side-chains 802 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 703 time to evaluate : 5.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 346 SER Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 336 THR Chi-restraints excluded: chain F residue 346 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain L residue 676 ASP Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain S residue 703 SER Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain T residue 703 SER Chi-restraints excluded: chain U residue 676 ASP Chi-restraints excluded: chain U residue 703 SER Chi-restraints excluded: chain V residue 711 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 232 optimal weight: 2.9990 chunk 622 optimal weight: 20.0000 chunk 136 optimal weight: 1.9990 chunk 405 optimal weight: 40.0000 chunk 170 optimal weight: 0.4980 chunk 691 optimal weight: 8.9990 chunk 574 optimal weight: 50.0000 chunk 320 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 363 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN I 144 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 45067 Z= 0.215 Angle : 0.462 7.374 59631 Z= 0.246 Chirality : 0.045 0.166 4653 Planarity : 0.003 0.036 8844 Dihedral : 4.008 22.607 7546 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.19 % Allowed : 17.97 % Favored : 79.84 % 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: 1.81 (0.11), residues: 7095 helix: 3.28 (0.10), residues: 2926 sheet: -0.57 (0.18), residues: 924 loop : -0.20 (0.11), residues: 3245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 220 HIS 0.014 0.001 HIS K 175 PHE 0.014 0.001 PHE F 192 TYR 0.016 0.002 TYR J 315 ARG 0.003 0.000 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 743 time to evaluate : 5.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8817 (ttpt) cc_final: 0.8389 (tttm) REVERT: B 319 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8149 (mtmt) REVERT: C 119 PHE cc_start: 0.8374 (t80) cc_final: 0.8017 (t80) REVERT: C 181 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8327 (tt) REVERT: C 201 LYS cc_start: 0.8901 (ttpt) cc_final: 0.8604 (tttp) REVERT: C 221 ASP cc_start: 0.7980 (t0) cc_final: 0.7762 (t0) REVERT: C 234 ARG cc_start: 0.8328 (mmt180) cc_final: 0.8122 (mmt180) REVERT: C 319 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8339 (mtpt) REVERT: C 352 GLN cc_start: 0.7992 (mp10) cc_final: 0.7228 (tp-100) REVERT: D 201 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8370 (tttm) REVERT: D 234 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7223 (mtp-110) REVERT: D 319 LYS cc_start: 0.8705 (mtmt) cc_final: 0.8224 (mtpt) REVERT: D 352 GLN cc_start: 0.8047 (mp10) cc_final: 0.7314 (tp-100) REVERT: E 181 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8352 (tt) REVERT: E 201 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8285 (tttp) REVERT: E 240 TRP cc_start: 0.6582 (t-100) cc_final: 0.5455 (t60) REVERT: E 319 LYS cc_start: 0.8626 (mtmt) cc_final: 0.8282 (mtpt) REVERT: E 352 GLN cc_start: 0.8187 (mp10) cc_final: 0.7310 (tp-100) REVERT: F 201 LYS cc_start: 0.8755 (ttpt) cc_final: 0.8350 (tttm) REVERT: F 234 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7677 (mmt180) REVERT: F 319 LYS cc_start: 0.8524 (mtmt) cc_final: 0.8124 (mtpt) REVERT: F 352 GLN cc_start: 0.8156 (mp10) cc_final: 0.7306 (tp-100) REVERT: G 60 ARG cc_start: 0.9235 (mtp85) cc_final: 0.8538 (mmm160) REVERT: G 101 ASP cc_start: 0.8105 (m-30) cc_final: 0.7850 (m-30) REVERT: G 146 PHE cc_start: 0.6346 (p90) cc_final: 0.5986 (p90) REVERT: G 201 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8377 (tttm) REVERT: G 229 ILE cc_start: 0.8455 (mm) cc_final: 0.8085 (mm) REVERT: G 285 PHE cc_start: 0.7763 (m-80) cc_final: 0.7548 (m-80) REVERT: G 305 GLU cc_start: 0.8335 (pm20) cc_final: 0.8065 (pm20) REVERT: G 319 LYS cc_start: 0.8730 (mtmt) cc_final: 0.8236 (mtmt) REVERT: H 201 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8420 (tttp) REVERT: H 319 LYS cc_start: 0.8689 (mtmt) cc_final: 0.8192 (mtpt) REVERT: I 165 TYR cc_start: 0.7908 (m-10) cc_final: 0.7648 (m-80) REVERT: I 201 LYS cc_start: 0.8700 (ttpt) cc_final: 0.8335 (tttp) REVERT: I 228 PHE cc_start: 0.8099 (m-80) cc_final: 0.7883 (m-80) REVERT: I 319 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8195 (mtpt) REVERT: I 331 GLU cc_start: 0.8645 (OUTLIER) cc_final: 0.8280 (mm-30) REVERT: J 201 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8347 (tttp) REVERT: J 229 ILE cc_start: 0.8435 (mm) cc_final: 0.8122 (mm) REVERT: J 232 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7803 (mtm-85) REVERT: J 319 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8385 (mtpt) REVERT: J 331 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8378 (mt-10) REVERT: J 390 TYR cc_start: 0.8819 (m-80) cc_final: 0.8381 (m-80) REVERT: K 201 LYS cc_start: 0.8777 (ttpt) cc_final: 0.8385 (tttm) REVERT: K 319 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8219 (mtpt) REVERT: K 331 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8110 (mt-10) REVERT: K 352 GLN cc_start: 0.8088 (mp10) cc_final: 0.7864 (mp-120) REVERT: A 181 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8450 (tt) REVERT: A 201 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8317 (tttp) REVERT: A 319 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8182 (mtmt) REVERT: L 458 LYS cc_start: 0.8353 (mptt) cc_final: 0.7944 (mmtt) REVERT: M 458 LYS cc_start: 0.8386 (mptt) cc_final: 0.8126 (mmtt) REVERT: N 458 LYS cc_start: 0.8505 (mptt) cc_final: 0.8148 (mmtt) REVERT: P 458 LYS cc_start: 0.8457 (mptt) cc_final: 0.8141 (mmtt) REVERT: Q 458 LYS cc_start: 0.8284 (mptt) cc_final: 0.8004 (mmtt) REVERT: R 458 LYS cc_start: 0.8174 (mptt) cc_final: 0.7832 (mmtt) REVERT: S 458 LYS cc_start: 0.8595 (mptt) cc_final: 0.8272 (mmtt) REVERT: T 458 LYS cc_start: 0.8668 (mptt) cc_final: 0.8294 (mmtt) REVERT: U 458 LYS cc_start: 0.8327 (mptt) cc_final: 0.8019 (mmtt) REVERT: V 458 LYS cc_start: 0.8297 (mptt) cc_final: 0.8016 (mmtt) outliers start: 73 outliers final: 56 residues processed: 779 average time/residue: 0.9281 time to fit residues: 1152.6854 Evaluate side-chains 777 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 715 time to evaluate : 4.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 117 SER Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain G residue 117 SER Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain K residue 370 SER Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain L residue 676 ASP Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain Q residue 711 PHE Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain T residue 703 SER Chi-restraints excluded: chain U residue 676 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 666 optimal weight: 50.0000 chunk 77 optimal weight: 1.9990 chunk 394 optimal weight: 0.6980 chunk 505 optimal weight: 30.0000 chunk 391 optimal weight: 20.0000 chunk 582 optimal weight: 20.0000 chunk 386 optimal weight: 8.9990 chunk 689 optimal weight: 50.0000 chunk 431 optimal weight: 20.0000 chunk 420 optimal weight: 4.9990 chunk 318 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 GLN ** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** I 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 45067 Z= 0.576 Angle : 0.600 8.433 59631 Z= 0.327 Chirality : 0.051 0.218 4653 Planarity : 0.004 0.051 8844 Dihedral : 4.436 25.341 7546 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.54 % Allowed : 17.19 % Favored : 79.27 % 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: 1.43 (0.11), residues: 7095 helix: 2.89 (0.10), residues: 2937 sheet: -0.58 (0.18), residues: 924 loop : -0.41 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 265 HIS 0.008 0.002 HIS K 175 PHE 0.018 0.002 PHE D 228 TYR 0.026 0.003 TYR A 368 ARG 0.006 0.001 ARG H 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 711 time to evaluate : 5.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8814 (ttpt) cc_final: 0.8392 (tttm) REVERT: B 319 LYS cc_start: 0.8650 (mtmt) cc_final: 0.8147 (mtmt) REVERT: C 108 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7920 (t0) REVERT: C 201 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8591 (tttp) REVERT: C 234 ARG cc_start: 0.8342 (mmt180) cc_final: 0.8094 (mmt180) REVERT: C 319 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8342 (mtpt) REVERT: C 352 GLN cc_start: 0.8170 (mp10) cc_final: 0.7940 (pt0) REVERT: D 201 LYS cc_start: 0.8784 (ttpt) cc_final: 0.8342 (tttm) REVERT: D 234 ARG cc_start: 0.7853 (mtp85) cc_final: 0.7207 (mtp-110) REVERT: D 319 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8204 (mtmt) REVERT: D 352 GLN cc_start: 0.8106 (mp10) cc_final: 0.7789 (mp-120) REVERT: E 181 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8363 (tt) REVERT: E 193 ASP cc_start: 0.8385 (t0) cc_final: 0.8041 (t70) REVERT: E 201 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8296 (tttp) REVERT: E 240 TRP cc_start: 0.6578 (t-100) cc_final: 0.5749 (t60) REVERT: E 319 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8229 (mtmt) REVERT: E 352 GLN cc_start: 0.8258 (mp10) cc_final: 0.8024 (mp10) REVERT: F 201 LYS cc_start: 0.8759 (ttpt) cc_final: 0.8338 (tttm) REVERT: F 319 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8147 (mtpt) REVERT: F 352 GLN cc_start: 0.8261 (mp10) cc_final: 0.7382 (tp-100) REVERT: G 101 ASP cc_start: 0.8133 (m-30) cc_final: 0.7915 (m-30) REVERT: G 146 PHE cc_start: 0.6416 (p90) cc_final: 0.6062 (p90) REVERT: G 201 LYS cc_start: 0.8779 (ttpt) cc_final: 0.8343 (tttm) REVERT: G 285 PHE cc_start: 0.7831 (m-80) cc_final: 0.7592 (m-80) REVERT: G 319 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8265 (mtpt) REVERT: H 201 LYS cc_start: 0.8761 (ttpt) cc_final: 0.8387 (tttp) REVERT: H 253 LYS cc_start: 0.7964 (tttt) cc_final: 0.7685 (ttpt) REVERT: H 319 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8172 (mtpt) REVERT: H 331 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: I 193 ASP cc_start: 0.8472 (t0) cc_final: 0.8269 (t70) REVERT: I 201 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8363 (tttm) REVERT: I 319 LYS cc_start: 0.8595 (mtmt) cc_final: 0.8201 (mtpt) REVERT: I 331 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8499 (mm-30) REVERT: J 193 ASP cc_start: 0.8315 (t0) cc_final: 0.7802 (t70) REVERT: J 201 LYS cc_start: 0.8726 (ttpt) cc_final: 0.8357 (tttp) REVERT: J 319 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8360 (mtpt) REVERT: J 331 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: K 201 LYS cc_start: 0.8768 (ttpt) cc_final: 0.8368 (tttm) REVERT: K 319 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8232 (mtpt) REVERT: K 331 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: K 352 GLN cc_start: 0.8209 (mp10) cc_final: 0.7997 (mp10) REVERT: A 181 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 201 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8339 (tttp) REVERT: A 319 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8178 (mtmt) REVERT: L 458 LYS cc_start: 0.8357 (mptt) cc_final: 0.7990 (mmtt) REVERT: M 458 LYS cc_start: 0.8410 (mptt) cc_final: 0.8165 (mmtt) REVERT: N 458 LYS cc_start: 0.8527 (mptt) cc_final: 0.8144 (mmtt) REVERT: P 458 LYS cc_start: 0.8523 (mptt) cc_final: 0.8157 (mmtt) REVERT: Q 458 LYS cc_start: 0.8287 (mptt) cc_final: 0.7961 (mmmt) REVERT: R 458 LYS cc_start: 0.8149 (mptt) cc_final: 0.7818 (mmtt) REVERT: S 458 LYS cc_start: 0.8640 (mptt) cc_final: 0.8321 (mmtt) REVERT: T 458 LYS cc_start: 0.8681 (mptt) cc_final: 0.8295 (mmtt) REVERT: U 458 LYS cc_start: 0.8273 (mptt) cc_final: 0.7986 (mmtt) REVERT: V 458 LYS cc_start: 0.8281 (mptt) cc_final: 0.8018 (mmtt) outliers start: 118 outliers final: 101 residues processed: 771 average time/residue: 0.9175 time to fit residues: 1113.3082 Evaluate side-chains 797 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 689 time to evaluate : 5.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 240 TRP Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 153 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 82 THR Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 82 THR Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 329 GLU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain H residue 336 THR Chi-restraints excluded: chain H residue 346 SER Chi-restraints excluded: chain I residue 82 THR Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 82 THR Chi-restraints excluded: chain J residue 153 ASP Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain J residue 336 THR Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 82 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 227 GLU Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain L residue 556 GLU Chi-restraints excluded: chain L residue 676 ASP Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain N residue 676 ASP Chi-restraints excluded: chain O residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain Q residue 676 ASP Chi-restraints excluded: chain Q residue 711 PHE Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain T residue 703 SER Chi-restraints excluded: chain U residue 676 ASP Chi-restraints excluded: chain U residue 703 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 426 optimal weight: 5.9990 chunk 275 optimal weight: 0.5980 chunk 411 optimal weight: 6.9990 chunk 207 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 133 optimal weight: 0.3980 chunk 438 optimal weight: 50.0000 chunk 469 optimal weight: 0.0570 chunk 340 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 541 optimal weight: 40.0000 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 45067 Z= 0.159 Angle : 0.461 8.294 59631 Z= 0.245 Chirality : 0.045 0.160 4653 Planarity : 0.003 0.034 8844 Dihedral : 4.048 22.270 7546 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.13 % Allowed : 19.02 % Favored : 78.85 % 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 (0.11), residues: 7095 helix: 3.26 (0.10), residues: 2937 sheet: -0.72 (0.18), residues: 924 loop : -0.21 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 240 HIS 0.007 0.001 HIS K 175 PHE 0.012 0.001 PHE K 198 TYR 0.014 0.002 TYR J 315 ARG 0.005 0.000 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 754 time to evaluate : 5.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8798 (ttpt) cc_final: 0.8377 (tttm) REVERT: B 319 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8109 (mtmt) REVERT: C 108 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7789 (t0) REVERT: C 119 PHE cc_start: 0.8323 (t80) cc_final: 0.7953 (t80) REVERT: C 201 LYS cc_start: 0.8894 (ttpt) cc_final: 0.8565 (tttm) REVERT: C 221 ASP cc_start: 0.7908 (t0) cc_final: 0.7685 (t0) REVERT: C 319 LYS cc_start: 0.8709 (mtmt) cc_final: 0.8320 (mtpt) REVERT: C 352 GLN cc_start: 0.8003 (mp10) cc_final: 0.7270 (tp-100) REVERT: D 201 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8375 (tttm) REVERT: D 234 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7208 (mtp-110) REVERT: D 319 LYS cc_start: 0.8724 (mtmt) cc_final: 0.8202 (mtmt) REVERT: D 352 GLN cc_start: 0.8034 (mp10) cc_final: 0.7323 (tp-100) REVERT: E 181 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8359 (tt) REVERT: E 201 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8284 (tttp) REVERT: E 240 TRP cc_start: 0.6551 (t-100) cc_final: 0.5668 (t60) REVERT: E 319 LYS cc_start: 0.8588 (mtmt) cc_final: 0.8190 (mtmt) REVERT: E 352 GLN cc_start: 0.8163 (mp10) cc_final: 0.7313 (tp-100) REVERT: F 193 ASP cc_start: 0.8413 (t70) cc_final: 0.8039 (t70) REVERT: F 201 LYS cc_start: 0.8740 (ttpt) cc_final: 0.8335 (tttm) REVERT: F 229 ILE cc_start: 0.8676 (mm) cc_final: 0.8295 (mm) REVERT: F 319 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8113 (mtpt) REVERT: F 352 GLN cc_start: 0.8171 (mp10) cc_final: 0.7334 (tp-100) REVERT: G 60 ARG cc_start: 0.9226 (mtp85) cc_final: 0.8581 (mmm160) REVERT: G 101 ASP cc_start: 0.8084 (m-30) cc_final: 0.7848 (m-30) REVERT: G 201 LYS cc_start: 0.8764 (ttpt) cc_final: 0.8350 (tttm) REVERT: G 285 PHE cc_start: 0.7788 (m-80) cc_final: 0.7578 (m-80) REVERT: G 319 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8181 (mtmt) REVERT: G 383 SER cc_start: 0.8839 (t) cc_final: 0.8518 (p) REVERT: H 193 ASP cc_start: 0.8477 (t70) cc_final: 0.8051 (t70) REVERT: H 201 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8400 (tttp) REVERT: H 253 LYS cc_start: 0.7962 (tttt) cc_final: 0.7694 (ttpt) REVERT: H 319 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8159 (mtpt) REVERT: H 331 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8203 (mt-10) REVERT: I 165 TYR cc_start: 0.7885 (m-10) cc_final: 0.7625 (m-80) REVERT: I 201 LYS cc_start: 0.8701 (ttpt) cc_final: 0.8324 (tttp) REVERT: I 319 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8186 (mtpt) REVERT: I 331 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8351 (mm-30) REVERT: J 100 ARG cc_start: 0.7570 (mtp-110) cc_final: 0.7279 (ttp80) REVERT: J 201 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8382 (tttp) REVERT: J 232 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7751 (mtm-85) REVERT: J 319 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8331 (mtpt) REVERT: J 331 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: K 201 LYS cc_start: 0.8805 (ttpt) cc_final: 0.8403 (tttm) REVERT: K 319 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8237 (mtpt) REVERT: K 331 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: K 352 GLN cc_start: 0.8119 (mp10) cc_final: 0.7915 (mp-120) REVERT: A 181 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8435 (tt) REVERT: A 201 LYS cc_start: 0.8707 (ttpt) cc_final: 0.8347 (tttm) REVERT: A 319 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8173 (mtmt) REVERT: L 458 LYS cc_start: 0.8356 (mptt) cc_final: 0.7973 (mmtt) REVERT: M 458 LYS cc_start: 0.8383 (mptt) cc_final: 0.8123 (mmtt) REVERT: N 458 LYS cc_start: 0.8507 (mptt) cc_final: 0.8106 (mmtt) REVERT: P 458 LYS cc_start: 0.8457 (mptt) cc_final: 0.8135 (mmtt) REVERT: Q 458 LYS cc_start: 0.8291 (mptt) cc_final: 0.8010 (mmtt) REVERT: R 458 LYS cc_start: 0.8186 (mptt) cc_final: 0.7860 (mmtt) REVERT: S 458 LYS cc_start: 0.8599 (mptt) cc_final: 0.8245 (mmtt) REVERT: T 458 LYS cc_start: 0.8624 (mptt) cc_final: 0.8266 (mmtt) REVERT: U 458 LYS cc_start: 0.8261 (mptt) cc_final: 0.7972 (mmtt) REVERT: V 458 LYS cc_start: 0.8295 (mptt) cc_final: 0.8012 (mmtt) outliers start: 71 outliers final: 54 residues processed: 790 average time/residue: 0.9098 time to fit residues: 1130.1274 Evaluate side-chains 790 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 729 time to evaluate : 4.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 314 GLU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain Q residue 711 PHE Chi-restraints excluded: chain T residue 703 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 626 optimal weight: 0.7980 chunk 660 optimal weight: 2.9990 chunk 602 optimal weight: 5.9990 chunk 642 optimal weight: 40.0000 chunk 386 optimal weight: 9.9990 chunk 279 optimal weight: 0.1980 chunk 504 optimal weight: 30.0000 chunk 197 optimal weight: 1.9990 chunk 580 optimal weight: 0.2980 chunk 607 optimal weight: 40.0000 chunk 639 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN E 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 45067 Z= 0.223 Angle : 0.461 8.119 59631 Z= 0.244 Chirality : 0.045 0.164 4653 Planarity : 0.003 0.035 8844 Dihedral : 3.944 20.457 7546 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.19 % Allowed : 19.20 % Favored : 78.61 % 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: 1.86 (0.11), residues: 7095 helix: 3.36 (0.10), residues: 2937 sheet: -0.73 (0.18), residues: 924 loop : -0.17 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 240 HIS 0.005 0.001 HIS K 175 PHE 0.010 0.001 PHE I 198 TYR 0.024 0.002 TYR H 368 ARG 0.004 0.000 ARG G 60 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 730 time to evaluate : 4.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8789 (ttpt) cc_final: 0.8428 (tttp) REVERT: B 319 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8089 (mtmt) REVERT: C 108 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7782 (t0) REVERT: C 119 PHE cc_start: 0.8384 (t80) cc_final: 0.8019 (t80) REVERT: C 153 ASP cc_start: 0.8385 (p0) cc_final: 0.8045 (p0) REVERT: C 201 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8581 (tttp) REVERT: C 221 ASP cc_start: 0.7943 (t0) cc_final: 0.7735 (t0) REVERT: C 319 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8331 (mtpt) REVERT: C 352 GLN cc_start: 0.8016 (mp10) cc_final: 0.7242 (tp-100) REVERT: D 201 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8346 (tttm) REVERT: D 234 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7209 (mtp-110) REVERT: D 319 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8235 (mtmt) REVERT: D 352 GLN cc_start: 0.8051 (mp10) cc_final: 0.7319 (tp-100) REVERT: E 181 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8331 (tt) REVERT: E 201 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8273 (tttp) REVERT: E 240 TRP cc_start: 0.6489 (t-100) cc_final: 0.5620 (t60) REVERT: E 319 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8206 (mtmt) REVERT: E 352 GLN cc_start: 0.8165 (mp10) cc_final: 0.7318 (tp-100) REVERT: F 193 ASP cc_start: 0.8419 (t70) cc_final: 0.8047 (t70) REVERT: F 201 LYS cc_start: 0.8732 (ttpt) cc_final: 0.8316 (tttm) REVERT: F 319 LYS cc_start: 0.8522 (mtmt) cc_final: 0.8115 (mtpt) REVERT: F 352 GLN cc_start: 0.8165 (mp10) cc_final: 0.7323 (tp-100) REVERT: G 60 ARG cc_start: 0.9230 (mtp85) cc_final: 0.8568 (mmm160) REVERT: G 101 ASP cc_start: 0.8101 (m-30) cc_final: 0.7829 (m-30) REVERT: G 201 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8326 (tttm) REVERT: G 285 PHE cc_start: 0.7804 (m-80) cc_final: 0.7592 (m-80) REVERT: G 319 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8192 (mtpt) REVERT: H 201 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8375 (tttp) REVERT: H 253 LYS cc_start: 0.7952 (tttt) cc_final: 0.7682 (ttpt) REVERT: H 319 LYS cc_start: 0.8681 (mtmt) cc_final: 0.8162 (mtpt) REVERT: H 331 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: I 165 TYR cc_start: 0.7877 (m-10) cc_final: 0.7516 (m-80) REVERT: I 201 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8317 (tttp) REVERT: I 319 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8189 (mtpt) REVERT: I 331 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8394 (mm-30) REVERT: J 201 LYS cc_start: 0.8720 (ttpt) cc_final: 0.8350 (tttp) REVERT: J 232 ARG cc_start: 0.8006 (mtm180) cc_final: 0.7762 (mtm-85) REVERT: J 319 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8347 (mtpt) REVERT: J 331 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: K 201 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8371 (tttm) REVERT: K 319 LYS cc_start: 0.8615 (mtmt) cc_final: 0.8220 (mtpt) REVERT: K 331 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: K 352 GLN cc_start: 0.8142 (mp10) cc_final: 0.7935 (mp-120) REVERT: A 181 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8422 (tt) REVERT: A 201 LYS cc_start: 0.8690 (ttpt) cc_final: 0.8335 (tttm) REVERT: A 319 LYS cc_start: 0.8625 (mtmt) cc_final: 0.8174 (mtmt) REVERT: L 458 LYS cc_start: 0.8353 (mptt) cc_final: 0.7976 (mmtt) REVERT: M 458 LYS cc_start: 0.8382 (mptt) cc_final: 0.8122 (mmtt) REVERT: N 458 LYS cc_start: 0.8492 (mptt) cc_final: 0.8117 (mmtt) REVERT: P 458 LYS cc_start: 0.8458 (mptt) cc_final: 0.8143 (mmtt) REVERT: Q 458 LYS cc_start: 0.8288 (mptt) cc_final: 0.8031 (mmtt) REVERT: R 458 LYS cc_start: 0.8184 (mptt) cc_final: 0.7864 (mmtt) REVERT: R 472 LYS cc_start: 0.7943 (mmtt) cc_final: 0.7555 (mmtm) REVERT: S 458 LYS cc_start: 0.8604 (mptt) cc_final: 0.8280 (mmtt) REVERT: T 458 LYS cc_start: 0.8638 (mptt) cc_final: 0.8294 (mmtt) REVERT: U 458 LYS cc_start: 0.8315 (mptt) cc_final: 0.8015 (mmtt) REVERT: V 458 LYS cc_start: 0.8292 (mptt) cc_final: 0.8017 (mmtt) outliers start: 73 outliers final: 64 residues processed: 770 average time/residue: 0.9040 time to fit residues: 1094.3864 Evaluate side-chains 791 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 720 time to evaluate : 5.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 336 THR Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 148 ASN Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain Q residue 711 PHE Chi-restraints excluded: chain S residue 676 ASP Chi-restraints excluded: chain T residue 703 SER Chi-restraints excluded: chain U residue 676 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 421 optimal weight: 10.0000 chunk 679 optimal weight: 3.9990 chunk 414 optimal weight: 8.9990 chunk 322 optimal weight: 0.8980 chunk 472 optimal weight: 30.0000 chunk 712 optimal weight: 3.9990 chunk 655 optimal weight: 10.0000 chunk 567 optimal weight: 40.0000 chunk 58 optimal weight: 1.9990 chunk 438 optimal weight: 0.0770 chunk 347 optimal weight: 1.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** E 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 45067 Z= 0.294 Angle : 0.489 8.225 59631 Z= 0.260 Chirality : 0.046 0.195 4653 Planarity : 0.003 0.038 8844 Dihedral : 3.983 20.700 7546 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.40 % Allowed : 19.14 % Favored : 78.46 % 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: 1.81 (0.11), residues: 7095 helix: 3.34 (0.10), residues: 2937 sheet: -0.68 (0.17), residues: 957 loop : -0.23 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 240 HIS 0.005 0.001 HIS B 175 PHE 0.013 0.001 PHE K 119 TYR 0.028 0.002 TYR H 368 ARG 0.005 0.000 ARG E 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14190 Ramachandran restraints generated. 7095 Oldfield, 0 Emsley, 7095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 719 time to evaluate : 5.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 LYS cc_start: 0.8791 (ttpt) cc_final: 0.8431 (tttp) REVERT: B 319 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8090 (mtmt) REVERT: C 108 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7789 (t0) REVERT: C 119 PHE cc_start: 0.8423 (t80) cc_final: 0.8054 (t80) REVERT: C 153 ASP cc_start: 0.8406 (p0) cc_final: 0.8067 (p0) REVERT: C 201 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8591 (tttp) REVERT: C 319 LYS cc_start: 0.8675 (mtmt) cc_final: 0.8295 (mtpt) REVERT: C 352 GLN cc_start: 0.8066 (mp10) cc_final: 0.7307 (tp-100) REVERT: D 201 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8353 (tttm) REVERT: D 234 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7222 (mtp-110) REVERT: D 319 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8224 (mtmt) REVERT: D 352 GLN cc_start: 0.8077 (mp10) cc_final: 0.7333 (tp-100) REVERT: E 181 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8324 (tt) REVERT: E 201 LYS cc_start: 0.8635 (ttpt) cc_final: 0.8283 (tttp) REVERT: E 240 TRP cc_start: 0.6478 (t-100) cc_final: 0.5684 (t60) REVERT: E 319 LYS cc_start: 0.8616 (mtmt) cc_final: 0.8217 (mtmt) REVERT: E 352 GLN cc_start: 0.8191 (mp10) cc_final: 0.7935 (mp10) REVERT: F 193 ASP cc_start: 0.8464 (t70) cc_final: 0.8083 (t70) REVERT: F 201 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8321 (tttm) REVERT: F 319 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8131 (mtpt) REVERT: F 352 GLN cc_start: 0.8187 (mp10) cc_final: 0.7333 (tp-100) REVERT: G 60 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8571 (mmm160) REVERT: G 101 ASP cc_start: 0.8098 (m-30) cc_final: 0.7850 (m-30) REVERT: G 201 LYS cc_start: 0.8754 (ttpt) cc_final: 0.8328 (tttm) REVERT: G 285 PHE cc_start: 0.7817 (m-80) cc_final: 0.7605 (m-80) REVERT: G 319 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8219 (mtpt) REVERT: H 201 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8339 (tttp) REVERT: H 253 LYS cc_start: 0.7994 (tttt) cc_final: 0.7695 (ttpt) REVERT: H 319 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8139 (mtpt) REVERT: H 331 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: I 165 TYR cc_start: 0.7879 (m-10) cc_final: 0.7602 (m-80) REVERT: I 201 LYS cc_start: 0.8702 (ttpt) cc_final: 0.8330 (tttp) REVERT: I 319 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8167 (mtpt) REVERT: I 331 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8429 (mm-30) REVERT: J 201 LYS cc_start: 0.8724 (ttpt) cc_final: 0.8356 (tttp) REVERT: J 319 LYS cc_start: 0.8718 (mtmt) cc_final: 0.8316 (mtpt) REVERT: J 331 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8305 (tt0) REVERT: K 201 LYS cc_start: 0.8780 (ttpt) cc_final: 0.8389 (tttm) REVERT: K 319 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8229 (mtpt) REVERT: K 331 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: K 352 GLN cc_start: 0.8117 (mp10) cc_final: 0.7913 (mp-120) REVERT: A 181 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8419 (tt) REVERT: A 201 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8331 (tttm) REVERT: A 319 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8177 (mtmt) REVERT: L 458 LYS cc_start: 0.8349 (mptt) cc_final: 0.7984 (mmtt) REVERT: M 458 LYS cc_start: 0.8402 (mptt) cc_final: 0.8121 (mmtt) REVERT: N 458 LYS cc_start: 0.8523 (mptt) cc_final: 0.8135 (mmtt) REVERT: P 458 LYS cc_start: 0.8454 (mptt) cc_final: 0.8144 (mmtt) REVERT: Q 458 LYS cc_start: 0.8293 (mptt) cc_final: 0.8064 (mmtt) REVERT: R 458 LYS cc_start: 0.8188 (mptt) cc_final: 0.7873 (mmtt) REVERT: R 472 LYS cc_start: 0.7973 (mmtt) cc_final: 0.7601 (mptt) REVERT: S 458 LYS cc_start: 0.8667 (mptt) cc_final: 0.8323 (mmtt) REVERT: T 458 LYS cc_start: 0.8628 (mptt) cc_final: 0.8298 (mmtt) REVERT: U 458 LYS cc_start: 0.8243 (mptt) cc_final: 0.7972 (mmtt) REVERT: V 458 LYS cc_start: 0.8282 (mptt) cc_final: 0.8010 (mmtt) outliers start: 80 outliers final: 69 residues processed: 758 average time/residue: 0.9556 time to fit residues: 1147.1631 Evaluate side-chains 782 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 706 time to evaluate : 5.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain C residue 108 ASP Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 353 SER Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain E residue 181 LEU Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 219 VAL Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 336 THR Chi-restraints excluded: chain F residue 161 ASP Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 210 SER Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 241 PHE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain G residue 210 SER Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain H residue 108 ASP Chi-restraints excluded: chain H residue 181 LEU Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 241 PHE Chi-restraints excluded: chain H residue 276 THR Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 325 SER Chi-restraints excluded: chain H residue 331 GLU Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 108 ASP Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain I residue 219 VAL Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 331 GLU Chi-restraints excluded: chain J residue 181 LEU Chi-restraints excluded: chain J residue 210 SER Chi-restraints excluded: chain J residue 219 VAL Chi-restraints excluded: chain J residue 282 ILE Chi-restraints excluded: chain J residue 313 LEU Chi-restraints excluded: chain J residue 314 GLU Chi-restraints excluded: chain J residue 331 GLU Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 108 ASP Chi-restraints excluded: chain K residue 195 ASP Chi-restraints excluded: chain K residue 210 SER Chi-restraints excluded: chain K residue 219 VAL Chi-restraints excluded: chain K residue 282 ILE Chi-restraints excluded: chain K residue 313 LEU Chi-restraints excluded: chain K residue 331 GLU Chi-restraints excluded: chain K residue 336 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain M residue 676 ASP Chi-restraints excluded: chain P residue 676 ASP Chi-restraints excluded: chain R residue 676 ASP Chi-restraints excluded: chain S residue 676 ASP Chi-restraints excluded: chain T residue 676 ASP Chi-restraints excluded: chain T residue 703 SER Chi-restraints excluded: chain U residue 676 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 450 optimal weight: 8.9990 chunk 604 optimal weight: 30.0000 chunk 173 optimal weight: 1.9990 chunk 523 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 chunk 568 optimal weight: 7.9990 chunk 237 optimal weight: 0.9980 chunk 583 optimal weight: 30.0000 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.200959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136956 restraints weight = 129552.143| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.90 r_work: 0.3483 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3349 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 45067 Z= 0.256 Angle : 0.471 7.871 59631 Z= 0.250 Chirality : 0.045 0.167 4653 Planarity : 0.003 0.035 8844 Dihedral : 3.905 19.088 7546 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 19.32 % Favored : 78.34 % 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: 1.87 (0.11), residues: 7095 helix: 3.41 (0.10), residues: 2937 sheet: -0.69 (0.17), residues: 957 loop : -0.22 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 240 HIS 0.004 0.001 HIS K 175 PHE 0.011 0.001 PHE K 198 TYR 0.028 0.002 TYR I 368 ARG 0.004 0.000 ARG F 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20158.78 seconds wall clock time: 347 minutes 28.49 seconds (20848.49 seconds total)