Starting phenix.real_space_refine on Sat Nov 18 12:57:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/11_2023/8fma_29290.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/11_2023/8fma_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_29290/11_2023/8fma_29290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/11_2023/8fma_29290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/11_2023/8fma_29290.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fma_29290/11_2023/8fma_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-1.21rc1-5144/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: 26.49, 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: 37.86 Conformation dependent library (CDL) restraints added in 8.5 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: 5.19 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: 31.35 Time building geometry restraints manager: 40.25 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: 25014 14.18 - 28.37: 2266 28.37 - 42.55: 473 42.55 - 56.73: 88 56.73 - 70.91: 77 Dihedral angle restraints: 27918 sinusoidal: 11407 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 27915 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: 13.320 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: 1.130 Extract box with map and model: 41.070 Check model and map are aligned: 0.800 Set scattering table: 0.520 Process input model: 179.370 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 243.410 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.912 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 outliers start: 0 outliers final: 0 residues processed: 1113 average time/residue: 1.0004 time to fit residues: 1733.7086 Evaluate side-chains 786 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 786 time to evaluate : 4.906 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4116 ------------------------------------------------------------------------------- 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: 0.9990 chunk 560 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 340 optimal weight: 2.9990 chunk 417 optimal weight: 10.0000 chunk 649 optimal weight: 30.0000 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN F 320 ASN G 320 ASN H 122 ASN J 320 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 45067 Z= 0.191 Angle : 0.475 6.269 59631 Z= 0.256 Chirality : 0.045 0.151 4653 Planarity : 0.003 0.031 8844 Dihedral : 3.788 17.848 7546 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.50 % Allowed : 10.92 % Favored : 87.58 % 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: 1.68 (0.11), residues: 7095 helix: 2.78 (0.10), residues: 3069 sheet: -0.21 (0.17), residues: 1023 loop : -0.14 (0.12), residues: 3003 *********************** 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 860 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 810 time to evaluate : 4.864 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 outliers start: 50 outliers final: 35 residues processed: 825 average time/residue: 0.9011 time to fit residues: 1204.0756 Evaluate side-chains 781 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 746 time to evaluate : 5.052 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.6243 time to fit residues: 48.5714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 360 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 540 optimal weight: 0.9990 chunk 442 optimal weight: 50.0000 chunk 179 optimal weight: 0.9980 chunk 650 optimal weight: 1.9990 chunk 702 optimal weight: 50.0000 chunk 579 optimal weight: 20.0000 chunk 645 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 521 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.7250 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 45067 Z= 0.239 Angle : 0.466 5.976 59631 Z= 0.248 Chirality : 0.045 0.155 4653 Planarity : 0.003 0.029 8844 Dihedral : 3.783 19.107 7546 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.02 % Allowed : 11.97 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.11), residues: 7095 helix: 3.16 (0.10), residues: 2992 sheet: -0.25 (0.17), residues: 1012 loop : -0.11 (0.12), residues: 3091 *********************** 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 799 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 765 time to evaluate : 4.921 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 outliers start: 34 outliers final: 24 residues processed: 777 average time/residue: 0.8808 time to fit residues: 1099.3555 Evaluate side-chains 736 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 712 time to evaluate : 4.865 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5797 time to fit residues: 32.5933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 72 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 436 optimal weight: 30.0000 chunk 652 optimal weight: 8.9990 chunk 691 optimal weight: 0.0470 chunk 341 optimal weight: 4.9990 chunk 618 optimal weight: 0.0980 chunk 186 optimal weight: 0.7980 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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 G 320 ASN I 320 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 45067 Z= 0.141 Angle : 0.431 6.241 59631 Z= 0.227 Chirality : 0.044 0.141 4653 Planarity : 0.002 0.025 8844 Dihedral : 3.665 18.382 7546 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.96 % Allowed : 12.69 % Favored : 86.35 % 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: 2.06 (0.11), residues: 7095 helix: 3.33 (0.10), residues: 2992 sheet: -0.34 (0.16), residues: 1078 loop : 0.01 (0.12), residues: 3025 *********************** 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 783 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 751 time to evaluate : 5.053 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 outliers start: 32 outliers final: 28 residues processed: 755 average time/residue: 0.9328 time to fit residues: 1138.7661 Evaluate side-chains 735 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 707 time to evaluate : 4.937 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.6049 time to fit residues: 38.7493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 10 optimal weight: 1.9990 chunk 514 optimal weight: 30.0000 chunk 285 optimal weight: 0.8980 chunk 589 optimal weight: 10.0000 chunk 477 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 352 optimal weight: 20.0000 chunk 620 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN J 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 45067 Z= 0.220 Angle : 0.453 7.441 59631 Z= 0.238 Chirality : 0.045 0.159 4653 Planarity : 0.003 0.028 8844 Dihedral : 3.697 19.263 7546 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.69 % Allowed : 14.10 % Favored : 85.21 % 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: 2.14 (0.11), residues: 7095 helix: 3.41 (0.10), residues: 2992 sheet: -0.38 (0.16), residues: 1078 loop : 0.09 (0.12), residues: 3025 *********************** 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 773 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 750 time to evaluate : 4.974 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 outliers start: 23 outliers final: 19 residues processed: 757 average time/residue: 0.8823 time to fit residues: 1072.0586 Evaluate side-chains 723 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 704 time to evaluate : 4.953 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.6532 time to fit residues: 28.8593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 405 optimal weight: 40.0000 chunk 170 optimal weight: 2.9990 chunk 691 optimal weight: 5.9990 chunk 574 optimal weight: 40.0000 chunk 320 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 228 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** D 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** G 320 ASN ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** J 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN K 144 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN ** A 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 45067 Z= 0.480 Angle : 0.580 9.730 59631 Z= 0.313 Chirality : 0.050 0.226 4653 Planarity : 0.004 0.046 8844 Dihedral : 4.243 25.076 7546 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.25 % Allowed : 15.27 % Favored : 82.48 % 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: 1.69 (0.11), residues: 7095 helix: 3.03 (0.10), residues: 2992 sheet: -0.56 (0.18), residues: 957 loop : -0.22 (0.11), residues: 3146 *********************** 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 789 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 714 time to evaluate : 5.120 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 outliers start: 75 outliers final: 52 residues processed: 734 average time/residue: 0.9045 time to fit residues: 1061.9235 Evaluate side-chains 718 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 666 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 0.6726 time to fit residues: 70.9796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 666 optimal weight: 30.0000 chunk 77 optimal weight: 0.9980 chunk 394 optimal weight: 0.8980 chunk 505 optimal weight: 20.0000 chunk 391 optimal weight: 20.0000 chunk 582 optimal weight: 8.9990 chunk 386 optimal weight: 5.9990 chunk 689 optimal weight: 50.0000 chunk 431 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 318 optimal weight: 0.3980 overall best weight: 3.4584 ------------------------------------------------------------------------------- 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** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 ASN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 144 GLN ** 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: 0.7357 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 45067 Z= 0.504 Angle : 0.592 7.841 59631 Z= 0.320 Chirality : 0.051 0.207 4653 Planarity : 0.004 0.051 8844 Dihedral : 4.458 24.811 7546 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.32 % Allowed : 17.49 % Favored : 81.19 % 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: 1.37 (0.11), residues: 7095 helix: 2.91 (0.10), residues: 2926 sheet: -0.81 (0.17), residues: 968 loop : -0.43 (0.11), residues: 3201 *********************** 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 735 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 691 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: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 29 residues processed: 706 average time/residue: 0.9124 time to fit residues: 1019.0355 Evaluate side-chains 685 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 656 time to evaluate : 4.860 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.6148 time to fit residues: 39.2278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 411 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 133 optimal weight: 1.9990 chunk 438 optimal weight: 40.0000 chunk 469 optimal weight: 0.0070 chunk 340 optimal weight: 0.7980 chunk 64 optimal weight: 10.0000 chunk 541 optimal weight: 40.0000 overall best weight: 0.6402 ------------------------------------------------------------------------------- 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: 0.7294 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 45067 Z= 0.142 Angle : 0.460 9.166 59631 Z= 0.242 Chirality : 0.045 0.147 4653 Planarity : 0.003 0.030 8844 Dihedral : 3.976 21.814 7546 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.36 % Allowed : 18.84 % Favored : 80.80 % 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: 1.89 (0.11), residues: 7095 helix: 3.39 (0.10), residues: 2937 sheet: -0.69 (0.18), residues: 924 loop : -0.16 (0.11), residues: 3234 *********************** 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 748 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 736 time to evaluate : 5.053 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 outliers start: 12 outliers final: 7 residues processed: 736 average time/residue: 0.9149 time to fit residues: 1070.7516 Evaluate side-chains 699 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 692 time to evaluate : 5.001 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6480 time to fit residues: 14.6314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 626 optimal weight: 4.9990 chunk 660 optimal weight: 0.4980 chunk 602 optimal weight: 5.9990 chunk 642 optimal weight: 30.0000 chunk 386 optimal weight: 7.9990 chunk 279 optimal weight: 0.0870 chunk 504 optimal weight: 30.0000 chunk 197 optimal weight: 1.9990 chunk 580 optimal weight: 3.9990 chunk 607 optimal weight: 40.0000 chunk 639 optimal weight: 0.0270 overall best weight: 1.3220 ------------------------------------------------------------------------------- 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: 0.7312 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 45067 Z= 0.234 Angle : 0.472 8.459 59631 Z= 0.248 Chirality : 0.045 0.205 4653 Planarity : 0.003 0.031 8844 Dihedral : 3.926 20.837 7546 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.60 % Allowed : 19.44 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.11), residues: 7095 helix: 3.45 (0.10), residues: 2926 sheet: -0.78 (0.17), residues: 979 loop : -0.17 (0.11), residues: 3190 *********************** 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 717 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 697 time to evaluate : 5.880 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 outliers start: 20 outliers final: 15 residues processed: 701 average time/residue: 0.9182 time to fit residues: 1019.0893 Evaluate side-chains 700 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 685 time to evaluate : 4.924 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6139 time to fit residues: 23.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 421 optimal weight: 20.0000 chunk 679 optimal weight: 0.8980 chunk 414 optimal weight: 1.9990 chunk 322 optimal weight: 2.9990 chunk 472 optimal weight: 30.0000 chunk 712 optimal weight: 0.7980 chunk 655 optimal weight: 20.0000 chunk 567 optimal weight: 50.0000 chunk 58 optimal weight: 1.9990 chunk 438 optimal weight: 40.0000 chunk 347 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** ** D 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 148 ASN ** G 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4564 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= 0.254 Angle : 0.477 8.185 59631 Z= 0.251 Chirality : 0.045 0.170 4653 Planarity : 0.003 0.032 8844 Dihedral : 3.895 20.074 7546 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.36 % Allowed : 19.35 % Favored : 80.29 % 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: 1.89 (0.11), residues: 7095 helix: 3.47 (0.10), residues: 2926 sheet: -0.83 (0.17), residues: 979 loop : -0.16 (0.11), residues: 3190 ********************** 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 721 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 709 time to evaluate : 4.934 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 outliers start: 12 outliers final: 12 residues processed: 712 average time/residue: 0.9326 time to fit residues: 1053.2878 Evaluate side-chains 703 residues out of total 6380 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 691 time to evaluate : 4.910 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.5948 time to fit residues: 19.8524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 715 random chunks: chunk 450 optimal weight: 7.9990 chunk 604 optimal weight: 30.0000 chunk 173 optimal weight: 1.9990 chunk 523 optimal weight: 0.0000 chunk 83 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 568 optimal weight: 0.0000 chunk 237 optimal weight: 1.9990 chunk 583 optimal weight: 30.0000 chunk 71 optimal weight: 0.0370 chunk 104 optimal weight: 2.9990 overall best weight: 0.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 148 ASN A 320 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.204555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138265 restraints weight = 130467.918| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 3.35 r_work: 0.3495 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 45067 Z= 0.139 Angle : 0.438 7.750 59631 Z= 0.228 Chirality : 0.044 0.146 4653 Planarity : 0.003 0.031 8844 Dihedral : 3.712 20.069 7546 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.18 % Allowed : 19.56 % Favored : 80.26 % 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: 2.05 (0.11), residues: 7095 helix: 3.60 (0.10), residues: 2926 sheet: -0.78 (0.17), residues: 979 loop : -0.07 (0.12), residues: 3190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19359.87 seconds wall clock time: 334 minutes 17.52 seconds (20057.52 seconds total)