Starting phenix.real_space_refine on Thu Mar 21 04:38:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vjk_43284/03_2024/8vjk_43284_updated.pdb" } resolution = 2.92 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= 0.005 sd= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 32 5.49 5 S 960 5.16 5 C 91096 2.51 5 N 24576 2.21 5 O 26576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 141": "OD1" <-> "OD2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 386": "OD1" <-> "OD2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A ASP 1120": "OD1" <-> "OD2" Residue "A TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1457": "OD1" <-> "OD2" Residue "A ASP 1514": "OD1" <-> "OD2" Residue "A GLU 1544": "OE1" <-> "OE2" Residue "A TYR 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2005": "OE1" <-> "OE2" Residue "A ASP 2152": "OD1" <-> "OD2" Residue "A TYR 2239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3397": "OD1" <-> "OD2" Residue "A GLU 3441": "OE1" <-> "OE2" Residue "A GLU 3456": "OE1" <-> "OE2" Residue "A ASP 3532": "OD1" <-> "OD2" Residue "A PHE 3553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3586": "OD1" <-> "OD2" Residue "A PHE 3756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 3865": "OD1" <-> "OD2" Residue "A PHE 3954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4247": "OE1" <-> "OE2" Residue "A GLU 4674": "OE1" <-> "OE2" Residue "A ASP 4692": "OD1" <-> "OD2" Residue "A PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 4953": "OE1" <-> "OE2" Residue "A TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 5019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 42": "OD1" <-> "OD2" Residue "E GLU 62": "OE1" <-> "OE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 101": "OD1" <-> "OD2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 141": "OD1" <-> "OD2" Residue "B ASP 238": "OD1" <-> "OD2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 386": "OD1" <-> "OD2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "B GLU 945": "OE1" <-> "OE2" Residue "B ASP 1120": "OD1" <-> "OD2" Residue "B TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1457": "OD1" <-> "OD2" Residue "B ASP 1514": "OD1" <-> "OD2" Residue "B GLU 1544": "OE1" <-> "OE2" Residue "B TYR 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2005": "OE1" <-> "OE2" Residue "B ASP 2152": "OD1" <-> "OD2" Residue "B TYR 2239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3397": "OD1" <-> "OD2" Residue "B GLU 3441": "OE1" <-> "OE2" Residue "B GLU 3456": "OE1" <-> "OE2" Residue "B ASP 3532": "OD1" <-> "OD2" Residue "B PHE 3553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3586": "OD1" <-> "OD2" Residue "B PHE 3756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3865": "OD1" <-> "OD2" Residue "B PHE 3954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4247": "OE1" <-> "OE2" Residue "B GLU 4674": "OE1" <-> "OE2" Residue "B ASP 4692": "OD1" <-> "OD2" Residue "B PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 4953": "OE1" <-> "OE2" Residue "B TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 5019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 386": "OD1" <-> "OD2" Residue "C GLU 770": "OE1" <-> "OE2" Residue "C GLU 945": "OE1" <-> "OE2" Residue "C ASP 1120": "OD1" <-> "OD2" Residue "C TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1457": "OD1" <-> "OD2" Residue "C ASP 1514": "OD1" <-> "OD2" Residue "C GLU 1544": "OE1" <-> "OE2" Residue "C TYR 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2005": "OE1" <-> "OE2" Residue "C ASP 2152": "OD1" <-> "OD2" Residue "C TYR 2239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3397": "OD1" <-> "OD2" Residue "C GLU 3441": "OE1" <-> "OE2" Residue "C GLU 3456": "OE1" <-> "OE2" Residue "C ASP 3532": "OD1" <-> "OD2" Residue "C PHE 3553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3586": "OD1" <-> "OD2" Residue "C PHE 3756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 3865": "OD1" <-> "OD2" Residue "C PHE 3954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4247": "OE1" <-> "OE2" Residue "C GLU 4674": "OE1" <-> "OE2" Residue "C ASP 4692": "OD1" <-> "OD2" Residue "C PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 4953": "OE1" <-> "OE2" Residue "C TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 5019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 141": "OD1" <-> "OD2" Residue "D ASP 238": "OD1" <-> "OD2" Residue "D GLU 339": "OE1" <-> "OE2" Residue "D PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 386": "OD1" <-> "OD2" Residue "D GLU 770": "OE1" <-> "OE2" Residue "D GLU 945": "OE1" <-> "OE2" Residue "D ASP 1120": "OD1" <-> "OD2" Residue "D TYR 1434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1457": "OD1" <-> "OD2" Residue "D ASP 1514": "OD1" <-> "OD2" Residue "D GLU 1544": "OE1" <-> "OE2" Residue "D TYR 1713": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2005": "OE1" <-> "OE2" Residue "D ASP 2152": "OD1" <-> "OD2" Residue "D TYR 2239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3397": "OD1" <-> "OD2" Residue "D GLU 3441": "OE1" <-> "OE2" Residue "D GLU 3456": "OE1" <-> "OE2" Residue "D ASP 3532": "OD1" <-> "OD2" Residue "D PHE 3553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3586": "OD1" <-> "OD2" Residue "D PHE 3756": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 3865": "OD1" <-> "OD2" Residue "D PHE 3954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4247": "OE1" <-> "OE2" Residue "D GLU 4674": "OE1" <-> "OE2" Residue "D ASP 4692": "OD1" <-> "OD2" Residue "D PHE 4782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 4953": "OE1" <-> "OE2" Residue "D TYR 5012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 5019": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143248 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 34797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4373, 34797 Classifications: {'peptide': 4373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4150} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 829 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 34797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4373, 34797 Classifications: {'peptide': 4373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4150} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 34797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4373, 34797 Classifications: {'peptide': 4373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4150} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 34797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4373, 34797 Classifications: {'peptide': 4373} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 220, 'TRANS': 4150} Chain breaks: 13 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 186 Unusual residues: {' CA': 1, ' ZN': 1, 'ATP': 2, 'CFF': 1, 'PCW': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 34123 SG CYS A4956 169.706 171.769 88.072 1.00 79.97 S ATOM 34148 SG CYS A4959 169.940 174.432 90.815 1.00 78.21 S ATOM 72236 SG CYS B4956 194.766 169.718 88.079 1.00 79.97 S ATOM 72261 SG CYS B4959 192.103 169.952 90.822 1.00 78.21 S ATOM A05FD SG CYS C4956 196.810 194.759 88.076 1.00 79.97 S ATOM A05G2 SG CYS C4959 196.575 192.096 90.819 1.00 78.21 S ATOM A0W9Y SG CYS D4956 171.761 196.810 88.080 1.00 79.97 S ATOM A0WAN SG CYS D4959 174.423 196.576 90.823 1.00 78.21 S Time building chain proxies: 54.37, per 1000 atoms: 0.38 Number of scatterers: 143248 At special positions: 0 Unit cell: (367.353, 367.353, 208.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 960 16.00 P 32 15.00 O 26576 8.00 N 24576 7.00 C 91096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A3171 " - pdb=" SG CYS A3241 " distance=2.03 Simple disulfide: pdb=" SG CYS A4874 " - pdb=" SG CYS A4880 " distance=2.03 Simple disulfide: pdb=" SG CYS B3171 " - pdb=" SG CYS B3241 " distance=2.03 Simple disulfide: pdb=" SG CYS B4874 " - pdb=" SG CYS B4880 " distance=2.03 Simple disulfide: pdb=" SG CYS C3171 " - pdb=" SG CYS C3241 " distance=2.03 Simple disulfide: pdb=" SG CYS C4874 " - pdb=" SG CYS C4880 " distance=2.03 Simple disulfide: pdb=" SG CYS D3171 " - pdb=" SG CYS D3241 " distance=2.03 Simple disulfide: pdb=" SG CYS D4874 " - pdb=" SG CYS D4880 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.39 Conformation dependent library (CDL) restraints added in 19.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A8001 " pdb="ZN ZN A8001 " - pdb=" NE2 HIS A4976 " pdb="ZN ZN A8001 " - pdb=" ND1 HIS A4981 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4956 " pdb="ZN ZN A8001 " - pdb=" SG CYS A4959 " pdb=" ZN B8001 " pdb="ZN ZN B8001 " - pdb=" NE2 HIS B4976 " pdb="ZN ZN B8001 " - pdb=" ND1 HIS B4981 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4956 " pdb="ZN ZN B8001 " - pdb=" SG CYS B4959 " pdb=" ZN C8001 " pdb="ZN ZN C8001 " - pdb=" NE2 HIS C4976 " pdb="ZN ZN C8001 " - pdb=" ND1 HIS C4981 " pdb="ZN ZN C8001 " - pdb=" SG CYS C4956 " pdb="ZN ZN C8001 " - pdb=" SG CYS C4959 " pdb=" ZN D5102 " pdb="ZN ZN D5102 " - pdb=" NE2 HIS D4976 " pdb="ZN ZN D5102 " - pdb=" ND1 HIS D4981 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4956 " pdb="ZN ZN D5102 " - pdb=" SG CYS D4959 " Number of angles added : 4 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 33544 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 728 helices and 100 sheets defined 59.4% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 48.96 Creating SS restraints... Processing helix chain 'A' and resid 62 through 67 removed outlier: 4.089A pdb=" N CYS A 66 " --> pdb=" O ASP A 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 67' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 252 through 257 removed outlier: 5.150A pdb=" N ALA A 257 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 314 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 395 through 423 removed outlier: 3.723A pdb=" N PHE A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 454 Processing helix chain 'A' and resid 461 through 483 Processing helix chain 'A' and resid 484 through 498 removed outlier: 4.568A pdb=" N TYR A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 508 removed outlier: 3.787A pdb=" N PHE A 507 " --> pdb=" O HIS A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 4.190A pdb=" N SER A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LYS A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU A 518 " --> pdb=" O GLU A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.592A pdb=" N LEU A 540 " --> pdb=" O THR A 536 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER A 542 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 553 removed outlier: 3.984A pdb=" N LYS A 551 " --> pdb=" O TRP A 547 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 573 through 579 Processing helix chain 'A' and resid 580 through 594 Processing helix chain 'A' and resid 597 through 610 removed outlier: 3.666A pdb=" N LEU A 601 " --> pdb=" O ASN A 597 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 626 Processing helix chain 'A' and resid 811 through 816 removed outlier: 4.453A pdb=" N ALA A 815 " --> pdb=" O PRO A 811 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL A 816 " --> pdb=" O CYS A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 816' Processing helix chain 'A' and resid 848 through 854 removed outlier: 4.027A pdb=" N PHE A 852 " --> pdb=" O SER A 848 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 853 " --> pdb=" O HIS A 849 " (cutoff:3.500A) Proline residue: A 854 - end of helix No H-bonds generated for 'chain 'A' and resid 848 through 854' Processing helix chain 'A' and resid 866 through 891 removed outlier: 3.514A pdb=" N LYS A 874 " --> pdb=" O ARG A 870 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU A 877 " --> pdb=" O GLU A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 936 removed outlier: 3.658A pdb=" N LEU A 930 " --> pdb=" O SER A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 951 removed outlier: 4.572A pdb=" N GLU A 948 " --> pdb=" O ASP A 944 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 962 removed outlier: 5.030A pdb=" N MET A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1005 Processing helix chain 'A' and resid 1029 through 1051 Processing helix chain 'A' and resid 1068 through 1073 removed outlier: 3.808A pdb=" N ALA A1073 " --> pdb=" O ARG A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 7.060A pdb=" N GLU A1222 " --> pdb=" O CYS A1218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A1223 " --> pdb=" O GLY A1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1218 through 1223' Processing helix chain 'A' and resid 1424 through 1431 removed outlier: 3.692A pdb=" N LEU A1429 " --> pdb=" O PRO A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1450 removed outlier: 3.978A pdb=" N VAL A1449 " --> pdb=" O GLU A1445 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP A1450 " --> pdb=" O PRO A1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1445 through 1450' Processing helix chain 'A' and resid 1497 through 1503 removed outlier: 3.985A pdb=" N PHE A1501 " --> pdb=" O TRP A1497 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A1503 " --> pdb=" O GLY A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1581 removed outlier: 3.853A pdb=" N ALA A1579 " --> pdb=" O PRO A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1658 removed outlier: 4.294A pdb=" N LEU A1654 " --> pdb=" O ASP A1650 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER A1655 " --> pdb=" O ILE A1651 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU A1656 " --> pdb=" O LEU A1652 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1658 " --> pdb=" O LEU A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1659 through 1676 Processing helix chain 'A' and resid 1679 through 1690 removed outlier: 3.799A pdb=" N SER A1688 " --> pdb=" O HIS A1684 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS A1689 " --> pdb=" O ALA A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1691 through 1701 Processing helix chain 'A' and resid 1705 through 1720 Processing helix chain 'A' and resid 1721 through 1733 removed outlier: 4.220A pdb=" N SER A1733 " --> pdb=" O ARG A1729 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1747 removed outlier: 5.781A pdb=" N THR A1747 " --> pdb=" O THR A1743 " (cutoff:3.500A) Processing helix chain 'A' and resid 1805 through 1827 Processing helix chain 'A' and resid 1835 through 1854 Proline residue: A1842 - end of helix Processing helix chain 'A' and resid 1857 through 1869 Processing helix chain 'A' and resid 1926 through 1931 removed outlier: 3.795A pdb=" N MET A1930 " --> pdb=" O GLY A1926 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS A1931 " --> pdb=" O LEU A1927 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1926 through 1931' Processing helix chain 'A' and resid 1933 through 1985 removed outlier: 5.162A pdb=" N PHE A1985 " --> pdb=" O LEU A1981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1988 through 2001 removed outlier: 4.174A pdb=" N GLU A1998 " --> pdb=" O ARG A1994 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A1999 " --> pdb=" O ARG A1995 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2012 Processing helix chain 'A' and resid 2018 through 2023 Proline residue: A2023 - end of helix Processing helix chain 'A' and resid 2025 through 2044 Processing helix chain 'A' and resid 2094 through 2110 Processing helix chain 'A' and resid 2114 through 2131 Processing helix chain 'A' and resid 2132 through 2143 Proline residue: A2140 - end of helix removed outlier: 5.300A pdb=" N TYR A2143 " --> pdb=" O LEU A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2146 through 2170 removed outlier: 3.835A pdb=" N VAL A2150 " --> pdb=" O SER A2146 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU A2151 " --> pdb=" O VAL A2147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP A2152 " --> pdb=" O SER A2148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A2167 " --> pdb=" O ILE A2163 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE A2168 " --> pdb=" O ARG A2164 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL A2169 " --> pdb=" O SER A2165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN A2170 " --> pdb=" O LEU A2166 " (cutoff:3.500A) Processing helix chain 'A' and resid 2172 through 2189 Processing helix chain 'A' and resid 2190 through 2195 Processing helix chain 'A' and resid 2196 through 2203 Processing helix chain 'A' and resid 2204 through 2220 removed outlier: 5.249A pdb=" N GLY A2219 " --> pdb=" O VAL A2215 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A2220 " --> pdb=" O LEU A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2226 through 2245 removed outlier: 3.890A pdb=" N SER A2244 " --> pdb=" O PHE A2240 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG A2245 " --> pdb=" O CYS A2241 " (cutoff:3.500A) Processing helix chain 'A' and resid 2246 through 2256 removed outlier: 3.945A pdb=" N HIS A2254 " --> pdb=" O SER A2250 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU A2255 " --> pdb=" O MET A2251 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER A2256 " --> pdb=" O PHE A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2257 through 2263 removed outlier: 4.182A pdb=" N GLY A2263 " --> pdb=" O LEU A2259 " (cutoff:3.500A) Processing helix chain 'A' and resid 2272 through 2282 removed outlier: 3.592A pdb=" N VAL A2281 " --> pdb=" O ALA A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2284 through 2291 Processing helix chain 'A' and resid 2292 through 2309 Processing helix chain 'A' and resid 2311 through 2318 Processing helix chain 'A' and resid 2325 through 2341 Processing helix chain 'A' and resid 2347 through 2362 Proline residue: A2362 - end of helix Processing helix chain 'A' and resid 2376 through 2391 Proline residue: A2391 - end of helix Processing helix chain 'A' and resid 2418 through 2438 removed outlier: 3.506A pdb=" N MET A2424 " --> pdb=" O GLY A2420 " (cutoff:3.500A) Processing helix chain 'A' and resid 2440 through 2447 Processing helix chain 'A' and resid 2448 through 2463 Proline residue: A2463 - end of helix Processing helix chain 'A' and resid 2464 through 2473 Processing helix chain 'A' and resid 2496 through 2510 removed outlier: 3.816A pdb=" N LYS A2500 " --> pdb=" O VAL A2496 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A2503 " --> pdb=" O HIS A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2515 through 2526 Processing helix chain 'A' and resid 2527 through 2539 removed outlier: 3.680A pdb=" N ASP A2538 " --> pdb=" O ALA A2534 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR A2539 " --> pdb=" O ALA A2535 " (cutoff:3.500A) Processing helix chain 'A' and resid 2545 through 2567 removed outlier: 5.251A pdb=" N LEU A2560 " --> pdb=" O CYS A2556 " (cutoff:3.500A) Proline residue: A2561 - end of helix Processing helix chain 'A' and resid 2576 through 2593 Processing helix chain 'A' and resid 2597 through 2615 removed outlier: 3.652A pdb=" N TYR A2614 " --> pdb=" O ALA A2610 " (cutoff:3.500A) Processing helix chain 'A' and resid 2616 through 2631 removed outlier: 3.605A pdb=" N LEU A2620 " --> pdb=" O ARG A2616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN A2621 " --> pdb=" O PRO A2617 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS A2622 " --> pdb=" O SER A2618 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU A2623 " --> pdb=" O MET A2619 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A2629 " --> pdb=" O ARG A2625 " (cutoff:3.500A) Processing helix chain 'A' and resid 2637 through 2653 Proline residue: A2641 - end of helix Processing helix chain 'A' and resid 2669 through 2690 Processing helix chain 'A' and resid 2694 through 2712 removed outlier: 3.528A pdb=" N MET A2701 " --> pdb=" O TYR A2697 " (cutoff:3.500A) Proline residue: A2702 - end of helix Proline residue: A2712 - end of helix Processing helix chain 'A' and resid 2742 through 2747 removed outlier: 3.872A pdb=" N VAL A2746 " --> pdb=" O GLU A2742 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE A2747 " --> pdb=" O THR A2743 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2742 through 2747' Processing helix chain 'A' and resid 2749 through 2775 Processing helix chain 'A' and resid 2801 through 2820 Proline residue: A2809 - end of helix Processing helix chain 'A' and resid 2869 through 2899 Processing helix chain 'A' and resid 2908 through 2913 removed outlier: 5.216A pdb=" N THR A2913 " --> pdb=" O TYR A2909 " (cutoff:3.500A) Processing helix chain 'A' and resid 2918 through 2935 removed outlier: 4.362A pdb=" N LYS A2923 " --> pdb=" O ARG A2919 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A2924 " --> pdb=" O ASP A2920 " (cutoff:3.500A) Processing helix chain 'A' and resid 2942 through 2948 Processing helix chain 'A' and resid 2950 through 2955 Processing helix chain 'A' and resid 2956 through 2983 Processing helix chain 'A' and resid 2992 through 3015 removed outlier: 3.702A pdb=" N LEU A3003 " --> pdb=" O PHE A2999 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A3004 " --> pdb=" O ALA A3000 " (cutoff:3.500A) Proline residue: A3005 - end of helix removed outlier: 3.850A pdb=" N CYS A3015 " --> pdb=" O PHE A3011 " (cutoff:3.500A) Processing helix chain 'A' and resid 3033 through 3052 Processing helix chain 'A' and resid 3054 through 3059 Processing helix chain 'A' and resid 3061 through 3076 Processing helix chain 'A' and resid 3077 through 3084 removed outlier: 4.147A pdb=" N VAL A3081 " --> pdb=" O ASP A3077 " (cutoff:3.500A) Processing helix chain 'A' and resid 3086 through 3113 Processing helix chain 'A' and resid 3124 through 3152 removed outlier: 5.105A pdb=" N LEU A3138 " --> pdb=" O THR A3134 " (cutoff:3.500A) Proline residue: A3139 - end of helix Processing helix chain 'A' and resid 3160 through 3180 removed outlier: 3.540A pdb=" N THR A3178 " --> pdb=" O TYR A3174 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR A3179 " --> pdb=" O SER A3175 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG A3180 " --> pdb=" O LEU A3176 " (cutoff:3.500A) Processing helix chain 'A' and resid 3181 through 3202 Proline residue: A3189 - end of helix Processing helix chain 'A' and resid 3208 through 3216 removed outlier: 4.513A pdb=" N ASN A3212 " --> pdb=" O GLU A3208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU A3213 " --> pdb=" O PRO A3209 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR A3214 " --> pdb=" O GLU A3210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A3215 " --> pdb=" O LEU A3211 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA A3216 " --> pdb=" O ASN A3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3208 through 3216' Processing helix chain 'A' and resid 3218 through 3223 Processing helix chain 'A' and resid 3224 through 3232 removed outlier: 4.154A pdb=" N ARG A3228 " --> pdb=" O SER A3224 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA A3229 " --> pdb=" O PRO A3225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A3230 " --> pdb=" O ARG A3226 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A3231 " --> pdb=" O GLU A3227 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY A3232 " --> pdb=" O ARG A3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3224 through 3232' Processing helix chain 'A' and resid 3236 through 3242 removed outlier: 3.546A pdb=" N MET A3240 " --> pdb=" O SER A3236 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS A3241 " --> pdb=" O VAL A3237 " (cutoff:3.500A) Proline residue: A3242 - end of helix No H-bonds generated for 'chain 'A' and resid 3236 through 3242' Processing helix chain 'A' and resid 3246 through 3261 Processing helix chain 'A' and resid 3263 through 3268 removed outlier: 3.591A pdb=" N MET A3267 " --> pdb=" O ARG A3263 " (cutoff:3.500A) Proline residue: A3268 - end of helix No H-bonds generated for 'chain 'A' and resid 3263 through 3268' Processing helix chain 'A' and resid 3269 through 3289 removed outlier: 4.526A pdb=" N LEU A3275 " --> pdb=" O ILE A3271 " (cutoff:3.500A) Proline residue: A3276 - end of helix Proline residue: A3283 - end of helix removed outlier: 3.545A pdb=" N ARG A3288 " --> pdb=" O ARG A3284 " (cutoff:3.500A) Processing helix chain 'A' and resid 3309 through 3328 removed outlier: 3.591A pdb=" N LEU A3313 " --> pdb=" O THR A3309 " (cutoff:3.500A) Processing helix chain 'A' and resid 3334 through 3348 removed outlier: 4.322A pdb=" N ARG A3338 " --> pdb=" O SER A3334 " (cutoff:3.500A) Proline residue: A3345 - end of helix removed outlier: 4.211A pdb=" N SER A3348 " --> pdb=" O GLN A3344 " (cutoff:3.500A) Processing helix chain 'A' and resid 3351 through 3384 removed outlier: 4.479A pdb=" N LEU A3355 " --> pdb=" O ARG A3351 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG A3356 " --> pdb=" O PRO A3352 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE A3360 " --> pdb=" O ARG A3356 " (cutoff:3.500A) Proline residue: A3361 - end of helix removed outlier: 4.408A pdb=" N ALA A3384 " --> pdb=" O LEU A3380 " (cutoff:3.500A) Processing helix chain 'A' and resid 3389 through 3414 removed outlier: 4.394A pdb=" N LEU A3393 " --> pdb=" O GLU A3389 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU A3394 " --> pdb=" O GLU A3390 " (cutoff:3.500A) Proline residue: A3411 - end of helix Processing helix chain 'A' and resid 3420 through 3428 Proline residue: A3428 - end of helix Processing helix chain 'A' and resid 3429 through 3450 removed outlier: 5.080A pdb=" N HIS A3450 " --> pdb=" O TRP A3446 " (cutoff:3.500A) Processing helix chain 'A' and resid 3451 through 3464 Processing helix chain 'A' and resid 3466 through 3472 Processing helix chain 'A' and resid 3505 through 3510 removed outlier: 5.608A pdb=" N LEU A3510 " --> pdb=" O VAL A3506 " (cutoff:3.500A) Processing helix chain 'A' and resid 3511 through 3527 removed outlier: 3.727A pdb=" N LEU A3515 " --> pdb=" O ILE A3511 " (cutoff:3.500A) Proline residue: A3520 - end of helix removed outlier: 5.001A pdb=" N ALA A3527 " --> pdb=" O LEU A3523 " (cutoff:3.500A) Processing helix chain 'A' and resid 3530 through 3544 Processing helix chain 'A' and resid 3546 through 3558 Processing helix chain 'A' and resid 3563 through 3568 removed outlier: 3.817A pdb=" N SER A3567 " --> pdb=" O LYS A3563 " (cutoff:3.500A) Proline residue: A3568 - end of helix No H-bonds generated for 'chain 'A' and resid 3563 through 3568' Processing helix chain 'A' and resid 3569 through 3581 removed outlier: 3.574A pdb=" N LEU A3576 " --> pdb=" O TRP A3572 " (cutoff:3.500A) Proline residue: A3581 - end of helix Processing helix chain 'A' and resid 3582 through 3587 removed outlier: 4.658A pdb=" N ASP A3586 " --> pdb=" O GLY A3582 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A3587 " --> pdb=" O ARG A3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3582 through 3587' Processing helix chain 'A' and resid 3589 through 3613 Proline residue: A3613 - end of helix Processing helix chain 'A' and resid 3641 through 3646 removed outlier: 4.134A pdb=" N LEU A3645 " --> pdb=" O PRO A3641 " (cutoff:3.500A) Proline residue: A3646 - end of helix No H-bonds generated for 'chain 'A' and resid 3641 through 3646' Processing helix chain 'A' and resid 3647 through 3662 Processing helix chain 'A' and resid 3670 through 3681 removed outlier: 5.515A pdb=" N ALA A3681 " --> pdb=" O ASP A3677 " (cutoff:3.500A) Processing helix chain 'A' and resid 3683 through 3688 Processing helix chain 'A' and resid 3697 through 3712 Processing helix chain 'A' and resid 3720 through 3735 removed outlier: 3.655A pdb=" N CYS A3734 " --> pdb=" O MET A3730 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS A3735 " --> pdb=" O ALA A3731 " (cutoff:3.500A) Processing helix chain 'A' and resid 3755 through 3775 removed outlier: 3.751A pdb=" N LEU A3773 " --> pdb=" O GLN A3769 " (cutoff:3.500A) Processing helix chain 'A' and resid 3777 through 3790 removed outlier: 3.993A pdb=" N LYS A3790 " --> pdb=" O ILE A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3794 through 3809 Processing helix chain 'A' and resid 3812 through 3827 Processing helix chain 'A' and resid 3829 through 3842 Processing helix chain 'A' and resid 3846 through 3860 removed outlier: 4.900A pdb=" N GLY A3860 " --> pdb=" O ALA A3856 " (cutoff:3.500A) Processing helix chain 'A' and resid 3864 through 3869 removed outlier: 5.143A pdb=" N ILE A3869 " --> pdb=" O ASP A3865 " (cutoff:3.500A) Processing helix chain 'A' and resid 3880 through 3896 removed outlier: 3.664A pdb=" N CYS A3895 " --> pdb=" O LEU A3891 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3908 removed outlier: 4.295A pdb=" N ARG A3907 " --> pdb=" O GLN A3903 " (cutoff:3.500A) Processing helix chain 'A' and resid 3917 through 3942 removed outlier: 4.550A pdb=" N GLY A3942 " --> pdb=" O TRP A3938 " (cutoff:3.500A) Processing helix chain 'A' and resid 3947 through 3973 Processing helix chain 'A' and resid 3976 through 3986 Processing helix chain 'A' and resid 3987 through 4010 removed outlier: 3.914A pdb=" N ASP A4009 " --> pdb=" O LYS A4005 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER A4010 " --> pdb=" O LEU A4006 " (cutoff:3.500A) Processing helix chain 'A' and resid 4011 through 4035 removed outlier: 5.791A pdb=" N LEU A4015 " --> pdb=" O SER A4011 " (cutoff:3.500A) Processing helix chain 'A' and resid 4041 through 4055 Processing helix chain 'A' and resid 4056 through 4078 removed outlier: 3.909A pdb=" N GLY A4076 " --> pdb=" O LYS A4072 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A4077 " --> pdb=" O ASP A4073 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU A4078 " --> pdb=" O ILE A4074 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4085 removed outlier: 4.775A pdb=" N THR A4085 " --> pdb=" O GLN A4081 " (cutoff:3.500A) Processing helix chain 'A' and resid 4092 through 4104 Processing helix chain 'A' and resid 4107 through 4119 removed outlier: 4.307A pdb=" N GLU A4119 " --> pdb=" O LEU A4115 " (cutoff:3.500A) Processing helix chain 'A' and resid 4127 through 4140 removed outlier: 4.837A pdb=" N PHE A4135 " --> pdb=" O PHE A4131 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN A4136 " --> pdb=" O ALA A4132 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU A4137 " --> pdb=" O ASN A4133 " (cutoff:3.500A) Proline residue: A4138 - end of helix Processing helix chain 'A' and resid 4141 through 4158 Proline residue: A4158 - end of helix Processing helix chain 'A' and resid 4160 through 4171 removed outlier: 3.707A pdb=" N ARG A4164 " --> pdb=" O ASP A4160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN A4165 " --> pdb=" O PRO A4161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE A4166 " --> pdb=" O ARG A4162 " (cutoff:3.500A) Processing helix chain 'A' and resid 4172 through 4178 Processing helix chain 'A' and resid 4201 through 4210 Processing helix chain 'A' and resid 4211 through 4227 Processing helix chain 'A' and resid 4232 through 4255 Processing helix chain 'A' and resid 4538 through 4557 Processing helix chain 'A' and resid 4558 through 4578 removed outlier: 4.267A pdb=" N PHE A4577 " --> pdb=" O PHE A4573 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR A4578 " --> pdb=" O ILE A4574 " (cutoff:3.500A) Processing helix chain 'A' and resid 4638 through 4681 removed outlier: 4.163A pdb=" N VAL A4664 " --> pdb=" O ASN A4660 " (cutoff:3.500A) Proline residue: A4665 - end of helix Processing helix chain 'A' and resid 4694 through 4707 removed outlier: 3.536A pdb=" N ARG A4701 " --> pdb=" O GLY A4697 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU A4702 " --> pdb=" O GLN A4698 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL A4703 " --> pdb=" O TRP A4699 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A4704 " --> pdb=" O ASP A4700 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN A4705 " --> pdb=" O ARG A4701 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR A4706 " --> pdb=" O LEU A4702 " (cutoff:3.500A) Proline residue: A4707 - end of helix Processing helix chain 'A' and resid 4717 through 4727 Processing helix chain 'A' and resid 4731 through 4740 Processing helix chain 'A' and resid 4742 through 4752 removed outlier: 3.609A pdb=" N ALA A4750 " --> pdb=" O LEU A4746 " (cutoff:3.500A) Processing helix chain 'A' and resid 4761 through 4769 Processing helix chain 'A' and resid 4770 through 4785 removed outlier: 3.558A pdb=" N ASP A4784 " --> pdb=" O VAL A4780 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN A4785 " --> pdb=" O ILE A4781 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4803 removed outlier: 3.711A pdb=" N HIS A4801 " --> pdb=" O SER A4797 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A4802 " --> pdb=" O LEU A4798 " (cutoff:3.500A) Processing helix chain 'A' and resid 4804 through 4818 removed outlier: 4.657A pdb=" N ALA A4808 " --> pdb=" O ASN A4804 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA A4809 " --> pdb=" O PHE A4805 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS A4810 " --> pdb=" O PHE A4806 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU A4811 " --> pdb=" O PHE A4807 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A4812 " --> pdb=" O ALA A4808 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP A4813 " --> pdb=" O ALA A4809 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE A4814 " --> pdb=" O HIS A4810 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA A4815 " --> pdb=" O LEU A4811 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A4816 " --> pdb=" O LEU A4812 " (cutoff:3.500A) Processing helix chain 'A' and resid 4819 through 4830 removed outlier: 3.607A pdb=" N VAL A4828 " --> pdb=" O ILE A4824 " (cutoff:3.500A) Processing helix chain 'A' and resid 4831 through 4856 Processing helix chain 'A' and resid 4857 through 4862 removed outlier: 4.206A pdb=" N TYR A4861 " --> pdb=" O PHE A4857 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN A4862 " --> pdb=" O ARG A4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4857 through 4862' Processing helix chain 'A' and resid 4876 through 4891 removed outlier: 4.460A pdb=" N VAL A4889 " --> pdb=" O MET A4885 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A4890 " --> pdb=" O TYR A4886 " (cutoff:3.500A) Processing helix chain 'A' and resid 4894 through 4899 removed outlier: 4.176A pdb=" N GLU A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4907 through 4922 Processing helix chain 'A' and resid 4926 through 4954 Processing helix chain 'A' and resid 4962 through 4968 removed outlier: 3.758A pdb=" N PHE A4966 " --> pdb=" O GLY A4962 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A4968 " --> pdb=" O ASP A4964 " (cutoff:3.500A) Processing helix chain 'A' and resid 4971 through 4979 Processing helix chain 'A' and resid 4982 through 4996 Processing helix chain 'A' and resid 5002 through 5015 Processing helix chain 'A' and resid 5025 through 5031 Processing helix chain 'A' and resid 323 through 328 removed outlier: 4.480A pdb=" N VAL A 326 " --> pdb=" O LYS A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix Processing helix chain 'A' and resid 3153 through 3158 removed outlier: 4.459A pdb=" N ILE A3158 " --> pdb=" O PHE A3153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3153 through 3158' Processing helix chain 'A' and resid 4683 through 4688 Processing helix chain 'B' and resid 62 through 67 removed outlier: 4.089A pdb=" N CYS B 66 " --> pdb=" O ASP B 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 67' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 252 through 257 removed outlier: 5.150A pdb=" N ALA B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 314 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 395 through 423 removed outlier: 3.722A pdb=" N PHE B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 454 Processing helix chain 'B' and resid 461 through 483 Processing helix chain 'B' and resid 484 through 498 removed outlier: 4.568A pdb=" N TYR B 498 " --> pdb=" O ARG B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 508 removed outlier: 3.788A pdb=" N PHE B 507 " --> pdb=" O HIS B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 532 removed outlier: 4.190A pdb=" N SER B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 545 removed outlier: 3.592A pdb=" N LEU B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE B 541 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER B 542 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ASN B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 553 removed outlier: 3.984A pdb=" N LYS B 551 " --> pdb=" O TRP B 547 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP B 553 " --> pdb=" O VAL B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 573 through 579 Processing helix chain 'B' and resid 580 through 594 Processing helix chain 'B' and resid 597 through 610 removed outlier: 3.666A pdb=" N LEU B 601 " --> pdb=" O ASN B 597 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N CYS B 610 " --> pdb=" O SER B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 626 Processing helix chain 'B' and resid 811 through 816 removed outlier: 4.453A pdb=" N ALA B 815 " --> pdb=" O PRO B 811 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL B 816 " --> pdb=" O CYS B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 811 through 816' Processing helix chain 'B' and resid 848 through 854 removed outlier: 4.027A pdb=" N PHE B 852 " --> pdb=" O SER B 848 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 853 " --> pdb=" O HIS B 849 " (cutoff:3.500A) Proline residue: B 854 - end of helix No H-bonds generated for 'chain 'B' and resid 848 through 854' Processing helix chain 'B' and resid 866 through 891 removed outlier: 3.515A pdb=" N LYS B 874 " --> pdb=" O ARG B 870 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 936 removed outlier: 3.658A pdb=" N LEU B 930 " --> pdb=" O SER B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 944 through 951 removed outlier: 4.572A pdb=" N GLU B 948 " --> pdb=" O ASP B 944 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP B 949 " --> pdb=" O GLU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 962 removed outlier: 5.029A pdb=" N MET B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1005 Processing helix chain 'B' and resid 1029 through 1051 Processing helix chain 'B' and resid 1068 through 1073 removed outlier: 3.808A pdb=" N ALA B1073 " --> pdb=" O ARG B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1218 through 1223 removed outlier: 7.060A pdb=" N GLU B1222 " --> pdb=" O CYS B1218 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY B1223 " --> pdb=" O GLY B1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1218 through 1223' Processing helix chain 'B' and resid 1424 through 1431 removed outlier: 3.692A pdb=" N LEU B1429 " --> pdb=" O PRO B1425 " (cutoff:3.500A) Processing helix chain 'B' and resid 1445 through 1450 removed outlier: 3.979A pdb=" N VAL B1449 " --> pdb=" O GLU B1445 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP B1450 " --> pdb=" O PRO B1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1445 through 1450' Processing helix chain 'B' and resid 1497 through 1503 removed outlier: 3.985A pdb=" N PHE B1501 " --> pdb=" O TRP B1497 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER B1503 " --> pdb=" O GLY B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1575 through 1581 removed outlier: 3.853A pdb=" N ALA B1579 " --> pdb=" O PRO B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1650 through 1658 removed outlier: 4.294A pdb=" N LEU B1654 " --> pdb=" O ASP B1650 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER B1655 " --> pdb=" O ILE B1651 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU B1656 " --> pdb=" O LEU B1652 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B1658 " --> pdb=" O LEU B1654 " (cutoff:3.500A) Processing helix chain 'B' and resid 1659 through 1676 Processing helix chain 'B' and resid 1679 through 1690 removed outlier: 3.799A pdb=" N SER B1688 " --> pdb=" O HIS B1684 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS B1689 " --> pdb=" O ALA B1685 " (cutoff:3.500A) Processing helix chain 'B' and resid 1691 through 1701 Processing helix chain 'B' and resid 1705 through 1720 Processing helix chain 'B' and resid 1721 through 1733 removed outlier: 4.221A pdb=" N SER B1733 " --> pdb=" O ARG B1729 " (cutoff:3.500A) Processing helix chain 'B' and resid 1740 through 1747 removed outlier: 5.781A pdb=" N THR B1747 " --> pdb=" O THR B1743 " (cutoff:3.500A) Processing helix chain 'B' and resid 1805 through 1827 Processing helix chain 'B' and resid 1835 through 1854 Proline residue: B1842 - end of helix Processing helix chain 'B' and resid 1857 through 1869 Processing helix chain 'B' and resid 1926 through 1931 removed outlier: 3.796A pdb=" N MET B1930 " --> pdb=" O GLY B1926 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS B1931 " --> pdb=" O LEU B1927 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1926 through 1931' Processing helix chain 'B' and resid 1933 through 1985 removed outlier: 5.161A pdb=" N PHE B1985 " --> pdb=" O LEU B1981 " (cutoff:3.500A) Processing helix chain 'B' and resid 1988 through 2001 removed outlier: 4.174A pdb=" N GLU B1998 " --> pdb=" O ARG B1994 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE B1999 " --> pdb=" O ARG B1995 " (cutoff:3.500A) Processing helix chain 'B' and resid 2002 through 2012 Processing helix chain 'B' and resid 2018 through 2023 Proline residue: B2023 - end of helix Processing helix chain 'B' and resid 2025 through 2044 Processing helix chain 'B' and resid 2094 through 2110 Processing helix chain 'B' and resid 2114 through 2131 Processing helix chain 'B' and resid 2132 through 2143 Proline residue: B2140 - end of helix removed outlier: 5.300A pdb=" N TYR B2143 " --> pdb=" O LEU B2139 " (cutoff:3.500A) Processing helix chain 'B' and resid 2146 through 2170 removed outlier: 3.835A pdb=" N VAL B2150 " --> pdb=" O SER B2146 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N GLU B2151 " --> pdb=" O VAL B2147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP B2152 " --> pdb=" O SER B2148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B2167 " --> pdb=" O ILE B2163 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE B2168 " --> pdb=" O ARG B2164 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B2169 " --> pdb=" O SER B2165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN B2170 " --> pdb=" O LEU B2166 " (cutoff:3.500A) Processing helix chain 'B' and resid 2172 through 2189 Processing helix chain 'B' and resid 2190 through 2195 Processing helix chain 'B' and resid 2196 through 2203 Processing helix chain 'B' and resid 2204 through 2220 removed outlier: 5.250A pdb=" N GLY B2219 " --> pdb=" O VAL B2215 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU B2220 " --> pdb=" O LEU B2216 " (cutoff:3.500A) Processing helix chain 'B' and resid 2226 through 2245 removed outlier: 3.891A pdb=" N SER B2244 " --> pdb=" O PHE B2240 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG B2245 " --> pdb=" O CYS B2241 " (cutoff:3.500A) Processing helix chain 'B' and resid 2246 through 2256 removed outlier: 3.945A pdb=" N HIS B2254 " --> pdb=" O SER B2250 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU B2255 " --> pdb=" O MET B2251 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER B2256 " --> pdb=" O PHE B2252 " (cutoff:3.500A) Processing helix chain 'B' and resid 2257 through 2263 removed outlier: 4.183A pdb=" N GLY B2263 " --> pdb=" O LEU B2259 " (cutoff:3.500A) Processing helix chain 'B' and resid 2272 through 2282 removed outlier: 3.592A pdb=" N VAL B2281 " --> pdb=" O ALA B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2284 through 2291 Processing helix chain 'B' and resid 2292 through 2309 Processing helix chain 'B' and resid 2311 through 2318 Processing helix chain 'B' and resid 2325 through 2341 Processing helix chain 'B' and resid 2347 through 2362 Proline residue: B2362 - end of helix Processing helix chain 'B' and resid 2376 through 2391 Proline residue: B2391 - end of helix Processing helix chain 'B' and resid 2418 through 2438 removed outlier: 3.507A pdb=" N MET B2424 " --> pdb=" O GLY B2420 " (cutoff:3.500A) Processing helix chain 'B' and resid 2440 through 2447 Processing helix chain 'B' and resid 2448 through 2463 Proline residue: B2463 - end of helix Processing helix chain 'B' and resid 2464 through 2473 Processing helix chain 'B' and resid 2496 through 2510 removed outlier: 3.816A pdb=" N LYS B2500 " --> pdb=" O VAL B2496 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET B2503 " --> pdb=" O HIS B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2515 through 2526 Processing helix chain 'B' and resid 2527 through 2539 removed outlier: 3.680A pdb=" N ASP B2538 " --> pdb=" O ALA B2534 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR B2539 " --> pdb=" O ALA B2535 " (cutoff:3.500A) Processing helix chain 'B' and resid 2545 through 2567 removed outlier: 5.251A pdb=" N LEU B2560 " --> pdb=" O CYS B2556 " (cutoff:3.500A) Proline residue: B2561 - end of helix Processing helix chain 'B' and resid 2576 through 2593 Processing helix chain 'B' and resid 2597 through 2615 removed outlier: 3.652A pdb=" N TYR B2614 " --> pdb=" O ALA B2610 " (cutoff:3.500A) Processing helix chain 'B' and resid 2616 through 2631 removed outlier: 3.605A pdb=" N LEU B2620 " --> pdb=" O ARG B2616 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN B2621 " --> pdb=" O PRO B2617 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS B2622 " --> pdb=" O SER B2618 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU B2623 " --> pdb=" O MET B2619 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B2629 " --> pdb=" O ARG B2625 " (cutoff:3.500A) Processing helix chain 'B' and resid 2637 through 2653 Proline residue: B2641 - end of helix Processing helix chain 'B' and resid 2669 through 2690 Processing helix chain 'B' and resid 2694 through 2712 removed outlier: 3.529A pdb=" N MET B2701 " --> pdb=" O TYR B2697 " (cutoff:3.500A) Proline residue: B2702 - end of helix Proline residue: B2712 - end of helix Processing helix chain 'B' and resid 2742 through 2747 removed outlier: 3.872A pdb=" N VAL B2746 " --> pdb=" O GLU B2742 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE B2747 " --> pdb=" O THR B2743 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2742 through 2747' Processing helix chain 'B' and resid 2749 through 2775 Processing helix chain 'B' and resid 2801 through 2820 Proline residue: B2809 - end of helix Processing helix chain 'B' and resid 2869 through 2899 Processing helix chain 'B' and resid 2908 through 2913 removed outlier: 5.215A pdb=" N THR B2913 " --> pdb=" O TYR B2909 " (cutoff:3.500A) Processing helix chain 'B' and resid 2918 through 2935 removed outlier: 4.362A pdb=" N LYS B2923 " --> pdb=" O ARG B2919 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA B2924 " --> pdb=" O ASP B2920 " (cutoff:3.500A) Processing helix chain 'B' and resid 2942 through 2948 Processing helix chain 'B' and resid 2950 through 2955 Processing helix chain 'B' and resid 2956 through 2983 Processing helix chain 'B' and resid 2992 through 3015 removed outlier: 3.702A pdb=" N LEU B3003 " --> pdb=" O PHE B2999 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU B3004 " --> pdb=" O ALA B3000 " (cutoff:3.500A) Proline residue: B3005 - end of helix removed outlier: 3.850A pdb=" N CYS B3015 " --> pdb=" O PHE B3011 " (cutoff:3.500A) Processing helix chain 'B' and resid 3033 through 3052 Processing helix chain 'B' and resid 3054 through 3059 Processing helix chain 'B' and resid 3061 through 3076 Processing helix chain 'B' and resid 3077 through 3084 removed outlier: 4.147A pdb=" N VAL B3081 " --> pdb=" O ASP B3077 " (cutoff:3.500A) Processing helix chain 'B' and resid 3086 through 3113 Processing helix chain 'B' and resid 3124 through 3152 removed outlier: 5.106A pdb=" N LEU B3138 " --> pdb=" O THR B3134 " (cutoff:3.500A) Proline residue: B3139 - end of helix Processing helix chain 'B' and resid 3160 through 3180 removed outlier: 3.540A pdb=" N THR B3178 " --> pdb=" O TYR B3174 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B3179 " --> pdb=" O SER B3175 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG B3180 " --> pdb=" O LEU B3176 " (cutoff:3.500A) Processing helix chain 'B' and resid 3181 through 3202 Proline residue: B3189 - end of helix Processing helix chain 'B' and resid 3208 through 3216 removed outlier: 4.513A pdb=" N ASN B3212 " --> pdb=" O GLU B3208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU B3213 " --> pdb=" O PRO B3209 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR B3214 " --> pdb=" O GLU B3210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN B3215 " --> pdb=" O LEU B3211 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA B3216 " --> pdb=" O ASN B3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3208 through 3216' Processing helix chain 'B' and resid 3218 through 3223 Processing helix chain 'B' and resid 3224 through 3232 removed outlier: 4.153A pdb=" N ARG B3228 " --> pdb=" O SER B3224 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ALA B3229 " --> pdb=" O PRO B3225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE B3230 " --> pdb=" O ARG B3226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B3231 " --> pdb=" O GLU B3227 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N GLY B3232 " --> pdb=" O ARG B3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3224 through 3232' Processing helix chain 'B' and resid 3236 through 3242 removed outlier: 3.545A pdb=" N MET B3240 " --> pdb=" O SER B3236 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS B3241 " --> pdb=" O VAL B3237 " (cutoff:3.500A) Proline residue: B3242 - end of helix No H-bonds generated for 'chain 'B' and resid 3236 through 3242' Processing helix chain 'B' and resid 3246 through 3261 Processing helix chain 'B' and resid 3263 through 3268 removed outlier: 3.591A pdb=" N MET B3267 " --> pdb=" O ARG B3263 " (cutoff:3.500A) Proline residue: B3268 - end of helix No H-bonds generated for 'chain 'B' and resid 3263 through 3268' Processing helix chain 'B' and resid 3269 through 3289 removed outlier: 4.526A pdb=" N LEU B3275 " --> pdb=" O ILE B3271 " (cutoff:3.500A) Proline residue: B3276 - end of helix Proline residue: B3283 - end of helix removed outlier: 3.545A pdb=" N ARG B3288 " --> pdb=" O ARG B3284 " (cutoff:3.500A) Processing helix chain 'B' and resid 3309 through 3328 removed outlier: 3.590A pdb=" N LEU B3313 " --> pdb=" O THR B3309 " (cutoff:3.500A) Processing helix chain 'B' and resid 3334 through 3348 removed outlier: 4.322A pdb=" N ARG B3338 " --> pdb=" O SER B3334 " (cutoff:3.500A) Proline residue: B3345 - end of helix removed outlier: 4.211A pdb=" N SER B3348 " --> pdb=" O GLN B3344 " (cutoff:3.500A) Processing helix chain 'B' and resid 3351 through 3384 removed outlier: 4.479A pdb=" N LEU B3355 " --> pdb=" O ARG B3351 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG B3356 " --> pdb=" O PRO B3352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE B3360 " --> pdb=" O ARG B3356 " (cutoff:3.500A) Proline residue: B3361 - end of helix removed outlier: 4.408A pdb=" N ALA B3384 " --> pdb=" O LEU B3380 " (cutoff:3.500A) Processing helix chain 'B' and resid 3389 through 3414 removed outlier: 4.394A pdb=" N LEU B3393 " --> pdb=" O GLU B3389 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B3394 " --> pdb=" O GLU B3390 " (cutoff:3.500A) Proline residue: B3411 - end of helix Processing helix chain 'B' and resid 3420 through 3428 Proline residue: B3428 - end of helix Processing helix chain 'B' and resid 3429 through 3450 removed outlier: 5.080A pdb=" N HIS B3450 " --> pdb=" O TRP B3446 " (cutoff:3.500A) Processing helix chain 'B' and resid 3451 through 3464 Processing helix chain 'B' and resid 3466 through 3472 Processing helix chain 'B' and resid 3505 through 3510 removed outlier: 5.608A pdb=" N LEU B3510 " --> pdb=" O VAL B3506 " (cutoff:3.500A) Processing helix chain 'B' and resid 3511 through 3527 removed outlier: 3.727A pdb=" N LEU B3515 " --> pdb=" O ILE B3511 " (cutoff:3.500A) Proline residue: B3520 - end of helix removed outlier: 5.002A pdb=" N ALA B3527 " --> pdb=" O LEU B3523 " (cutoff:3.500A) Processing helix chain 'B' and resid 3530 through 3544 Processing helix chain 'B' and resid 3546 through 3558 Processing helix chain 'B' and resid 3563 through 3568 removed outlier: 3.817A pdb=" N SER B3567 " --> pdb=" O LYS B3563 " (cutoff:3.500A) Proline residue: B3568 - end of helix No H-bonds generated for 'chain 'B' and resid 3563 through 3568' Processing helix chain 'B' and resid 3569 through 3581 removed outlier: 3.574A pdb=" N LEU B3576 " --> pdb=" O TRP B3572 " (cutoff:3.500A) Proline residue: B3581 - end of helix Processing helix chain 'B' and resid 3582 through 3587 removed outlier: 4.658A pdb=" N ASP B3586 " --> pdb=" O GLY B3582 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA B3587 " --> pdb=" O ARG B3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3582 through 3587' Processing helix chain 'B' and resid 3589 through 3613 Proline residue: B3613 - end of helix Processing helix chain 'B' and resid 3641 through 3646 removed outlier: 4.134A pdb=" N LEU B3645 " --> pdb=" O PRO B3641 " (cutoff:3.500A) Proline residue: B3646 - end of helix No H-bonds generated for 'chain 'B' and resid 3641 through 3646' Processing helix chain 'B' and resid 3647 through 3662 Processing helix chain 'B' and resid 3670 through 3681 removed outlier: 5.516A pdb=" N ALA B3681 " --> pdb=" O ASP B3677 " (cutoff:3.500A) Processing helix chain 'B' and resid 3683 through 3688 Processing helix chain 'B' and resid 3697 through 3712 Processing helix chain 'B' and resid 3720 through 3735 removed outlier: 3.655A pdb=" N CYS B3734 " --> pdb=" O MET B3730 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS B3735 " --> pdb=" O ALA B3731 " (cutoff:3.500A) Processing helix chain 'B' and resid 3755 through 3775 removed outlier: 3.751A pdb=" N LEU B3773 " --> pdb=" O GLN B3769 " (cutoff:3.500A) Processing helix chain 'B' and resid 3777 through 3790 removed outlier: 3.993A pdb=" N LYS B3790 " --> pdb=" O ILE B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3794 through 3809 Processing helix chain 'B' and resid 3812 through 3827 Processing helix chain 'B' and resid 3829 through 3842 Processing helix chain 'B' and resid 3846 through 3860 removed outlier: 4.900A pdb=" N GLY B3860 " --> pdb=" O ALA B3856 " (cutoff:3.500A) Processing helix chain 'B' and resid 3864 through 3869 removed outlier: 5.143A pdb=" N ILE B3869 " --> pdb=" O ASP B3865 " (cutoff:3.500A) Processing helix chain 'B' and resid 3880 through 3896 removed outlier: 3.664A pdb=" N CYS B3895 " --> pdb=" O LEU B3891 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3908 removed outlier: 4.295A pdb=" N ARG B3907 " --> pdb=" O GLN B3903 " (cutoff:3.500A) Processing helix chain 'B' and resid 3917 through 3942 removed outlier: 4.550A pdb=" N GLY B3942 " --> pdb=" O TRP B3938 " (cutoff:3.500A) Processing helix chain 'B' and resid 3947 through 3973 Processing helix chain 'B' and resid 3976 through 3986 Processing helix chain 'B' and resid 3987 through 4010 removed outlier: 3.914A pdb=" N ASP B4009 " --> pdb=" O LYS B4005 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER B4010 " --> pdb=" O LEU B4006 " (cutoff:3.500A) Processing helix chain 'B' and resid 4011 through 4035 removed outlier: 5.791A pdb=" N LEU B4015 " --> pdb=" O SER B4011 " (cutoff:3.500A) Processing helix chain 'B' and resid 4041 through 4055 Processing helix chain 'B' and resid 4056 through 4078 removed outlier: 3.909A pdb=" N GLY B4076 " --> pdb=" O LYS B4072 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER B4077 " --> pdb=" O ASP B4073 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU B4078 " --> pdb=" O ILE B4074 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4085 removed outlier: 4.775A pdb=" N THR B4085 " --> pdb=" O GLN B4081 " (cutoff:3.500A) Processing helix chain 'B' and resid 4092 through 4104 Processing helix chain 'B' and resid 4107 through 4119 removed outlier: 4.306A pdb=" N GLU B4119 " --> pdb=" O LEU B4115 " (cutoff:3.500A) Processing helix chain 'B' and resid 4127 through 4140 removed outlier: 4.838A pdb=" N PHE B4135 " --> pdb=" O PHE B4131 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN B4136 " --> pdb=" O ALA B4132 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU B4137 " --> pdb=" O ASN B4133 " (cutoff:3.500A) Proline residue: B4138 - end of helix Processing helix chain 'B' and resid 4141 through 4158 Proline residue: B4158 - end of helix Processing helix chain 'B' and resid 4160 through 4171 removed outlier: 3.707A pdb=" N ARG B4164 " --> pdb=" O ASP B4160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN B4165 " --> pdb=" O PRO B4161 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B4166 " --> pdb=" O ARG B4162 " (cutoff:3.500A) Processing helix chain 'B' and resid 4172 through 4178 Processing helix chain 'B' and resid 4201 through 4210 Processing helix chain 'B' and resid 4211 through 4227 Processing helix chain 'B' and resid 4232 through 4255 Processing helix chain 'B' and resid 4538 through 4557 Processing helix chain 'B' and resid 4558 through 4578 removed outlier: 4.266A pdb=" N PHE B4577 " --> pdb=" O PHE B4573 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR B4578 " --> pdb=" O ILE B4574 " (cutoff:3.500A) Processing helix chain 'B' and resid 4638 through 4681 removed outlier: 4.162A pdb=" N VAL B4664 " --> pdb=" O ASN B4660 " (cutoff:3.500A) Proline residue: B4665 - end of helix Processing helix chain 'B' and resid 4694 through 4707 removed outlier: 3.536A pdb=" N ARG B4701 " --> pdb=" O GLY B4697 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU B4702 " --> pdb=" O GLN B4698 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL B4703 " --> pdb=" O TRP B4699 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B4704 " --> pdb=" O ASP B4700 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN B4705 " --> pdb=" O ARG B4701 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR B4706 " --> pdb=" O LEU B4702 " (cutoff:3.500A) Proline residue: B4707 - end of helix Processing helix chain 'B' and resid 4717 through 4727 Processing helix chain 'B' and resid 4731 through 4740 Processing helix chain 'B' and resid 4742 through 4752 removed outlier: 3.609A pdb=" N ALA B4750 " --> pdb=" O LEU B4746 " (cutoff:3.500A) Processing helix chain 'B' and resid 4761 through 4769 Processing helix chain 'B' and resid 4770 through 4785 removed outlier: 3.558A pdb=" N ASP B4784 " --> pdb=" O VAL B4780 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN B4785 " --> pdb=" O ILE B4781 " (cutoff:3.500A) Processing helix chain 'B' and resid 4786 through 4803 removed outlier: 3.711A pdb=" N HIS B4801 " --> pdb=" O SER B4797 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR B4802 " --> pdb=" O LEU B4798 " (cutoff:3.500A) Processing helix chain 'B' and resid 4804 through 4818 removed outlier: 4.657A pdb=" N ALA B4808 " --> pdb=" O ASN B4804 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA B4809 " --> pdb=" O PHE B4805 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N HIS B4810 " --> pdb=" O PHE B4806 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU B4811 " --> pdb=" O PHE B4807 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU B4812 " --> pdb=" O ALA B4808 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP B4813 " --> pdb=" O ALA B4809 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ILE B4814 " --> pdb=" O HIS B4810 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA B4815 " --> pdb=" O LEU B4811 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET B4816 " --> pdb=" O LEU B4812 " (cutoff:3.500A) Processing helix chain 'B' and resid 4819 through 4830 removed outlier: 3.607A pdb=" N VAL B4828 " --> pdb=" O ILE B4824 " (cutoff:3.500A) Processing helix chain 'B' and resid 4831 through 4856 Processing helix chain 'B' and resid 4857 through 4862 removed outlier: 4.206A pdb=" N TYR B4861 " --> pdb=" O PHE B4857 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN B4862 " --> pdb=" O ARG B4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4857 through 4862' Processing helix chain 'B' and resid 4876 through 4891 removed outlier: 4.460A pdb=" N VAL B4889 " --> pdb=" O MET B4885 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG B4890 " --> pdb=" O TYR B4886 " (cutoff:3.500A) Processing helix chain 'B' and resid 4894 through 4899 removed outlier: 4.176A pdb=" N GLU B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4907 through 4922 Processing helix chain 'B' and resid 4926 through 4954 Processing helix chain 'B' and resid 4962 through 4968 removed outlier: 3.758A pdb=" N PHE B4966 " --> pdb=" O GLY B4962 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B4968 " --> pdb=" O ASP B4964 " (cutoff:3.500A) Processing helix chain 'B' and resid 4971 through 4979 Processing helix chain 'B' and resid 4982 through 4996 Processing helix chain 'B' and resid 5002 through 5015 Processing helix chain 'B' and resid 5025 through 5031 Processing helix chain 'B' and resid 323 through 328 removed outlier: 4.481A pdb=" N VAL B 326 " --> pdb=" O LYS B 323 " (cutoff:3.500A) Proline residue: B 328 - end of helix Processing helix chain 'B' and resid 3153 through 3158 removed outlier: 4.459A pdb=" N ILE B3158 " --> pdb=" O PHE B3153 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3153 through 3158' Processing helix chain 'B' and resid 4683 through 4688 Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.089A pdb=" N CYS C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N CYS C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 252 through 257 removed outlier: 5.150A pdb=" N ALA C 257 " --> pdb=" O VAL C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 314 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 395 through 423 removed outlier: 3.723A pdb=" N PHE C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 454 Processing helix chain 'C' and resid 461 through 483 Processing helix chain 'C' and resid 484 through 498 removed outlier: 4.568A pdb=" N TYR C 498 " --> pdb=" O ARG C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 508 removed outlier: 3.788A pdb=" N PHE C 507 " --> pdb=" O HIS C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 4.191A pdb=" N SER C 515 " --> pdb=" O GLU C 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N GLU C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 545 removed outlier: 3.592A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE C 541 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N SER C 542 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 553 removed outlier: 3.984A pdb=" N LYS C 551 " --> pdb=" O TRP C 547 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 552 " --> pdb=" O LEU C 548 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP C 553 " --> pdb=" O VAL C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 573 through 579 Processing helix chain 'C' and resid 580 through 594 Processing helix chain 'C' and resid 597 through 610 removed outlier: 3.666A pdb=" N LEU C 601 " --> pdb=" O ASN C 597 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS C 610 " --> pdb=" O SER C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 626 Processing helix chain 'C' and resid 811 through 816 removed outlier: 4.453A pdb=" N ALA C 815 " --> pdb=" O PRO C 811 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL C 816 " --> pdb=" O CYS C 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 811 through 816' Processing helix chain 'C' and resid 848 through 854 removed outlier: 4.027A pdb=" N PHE C 852 " --> pdb=" O SER C 848 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL C 853 " --> pdb=" O HIS C 849 " (cutoff:3.500A) Proline residue: C 854 - end of helix No H-bonds generated for 'chain 'C' and resid 848 through 854' Processing helix chain 'C' and resid 866 through 891 removed outlier: 3.515A pdb=" N LYS C 874 " --> pdb=" O ARG C 870 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 936 removed outlier: 3.658A pdb=" N LEU C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 951 removed outlier: 4.571A pdb=" N GLU C 948 " --> pdb=" O ASP C 944 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP C 949 " --> pdb=" O GLU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 962 removed outlier: 5.030A pdb=" N MET C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 1005 Processing helix chain 'C' and resid 1029 through 1051 Processing helix chain 'C' and resid 1068 through 1073 removed outlier: 3.808A pdb=" N ALA C1073 " --> pdb=" O ARG C1069 " (cutoff:3.500A) Processing helix chain 'C' and resid 1218 through 1223 removed outlier: 7.060A pdb=" N GLU C1222 " --> pdb=" O CYS C1218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1223 " --> pdb=" O GLY C1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1218 through 1223' Processing helix chain 'C' and resid 1424 through 1431 removed outlier: 3.692A pdb=" N LEU C1429 " --> pdb=" O PRO C1425 " (cutoff:3.500A) Processing helix chain 'C' and resid 1445 through 1450 removed outlier: 3.979A pdb=" N VAL C1449 " --> pdb=" O GLU C1445 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP C1450 " --> pdb=" O PRO C1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1445 through 1450' Processing helix chain 'C' and resid 1497 through 1503 removed outlier: 3.985A pdb=" N PHE C1501 " --> pdb=" O TRP C1497 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER C1503 " --> pdb=" O GLY C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1575 through 1581 removed outlier: 3.853A pdb=" N ALA C1579 " --> pdb=" O PRO C1575 " (cutoff:3.500A) Processing helix chain 'C' and resid 1650 through 1658 removed outlier: 4.294A pdb=" N LEU C1654 " --> pdb=" O ASP C1650 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER C1655 " --> pdb=" O ILE C1651 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLU C1656 " --> pdb=" O LEU C1652 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU C1658 " --> pdb=" O LEU C1654 " (cutoff:3.500A) Processing helix chain 'C' and resid 1659 through 1676 Processing helix chain 'C' and resid 1679 through 1690 removed outlier: 3.799A pdb=" N SER C1688 " --> pdb=" O HIS C1684 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS C1689 " --> pdb=" O ALA C1685 " (cutoff:3.500A) Processing helix chain 'C' and resid 1691 through 1701 Processing helix chain 'C' and resid 1705 through 1720 Processing helix chain 'C' and resid 1721 through 1733 removed outlier: 4.221A pdb=" N SER C1733 " --> pdb=" O ARG C1729 " (cutoff:3.500A) Processing helix chain 'C' and resid 1740 through 1747 removed outlier: 5.781A pdb=" N THR C1747 " --> pdb=" O THR C1743 " (cutoff:3.500A) Processing helix chain 'C' and resid 1805 through 1827 Processing helix chain 'C' and resid 1835 through 1854 Proline residue: C1842 - end of helix Processing helix chain 'C' and resid 1857 through 1869 Processing helix chain 'C' and resid 1926 through 1931 removed outlier: 3.794A pdb=" N MET C1930 " --> pdb=" O GLY C1926 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS C1931 " --> pdb=" O LEU C1927 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1926 through 1931' Processing helix chain 'C' and resid 1933 through 1985 removed outlier: 5.161A pdb=" N PHE C1985 " --> pdb=" O LEU C1981 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 2001 removed outlier: 4.174A pdb=" N GLU C1998 " --> pdb=" O ARG C1994 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C1999 " --> pdb=" O ARG C1995 " (cutoff:3.500A) Processing helix chain 'C' and resid 2002 through 2012 Processing helix chain 'C' and resid 2018 through 2023 Proline residue: C2023 - end of helix Processing helix chain 'C' and resid 2025 through 2044 Processing helix chain 'C' and resid 2094 through 2110 Processing helix chain 'C' and resid 2114 through 2131 Processing helix chain 'C' and resid 2132 through 2143 Proline residue: C2140 - end of helix removed outlier: 5.300A pdb=" N TYR C2143 " --> pdb=" O LEU C2139 " (cutoff:3.500A) Processing helix chain 'C' and resid 2146 through 2170 removed outlier: 3.835A pdb=" N VAL C2150 " --> pdb=" O SER C2146 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU C2151 " --> pdb=" O VAL C2147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP C2152 " --> pdb=" O SER C2148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C2167 " --> pdb=" O ILE C2163 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C2168 " --> pdb=" O ARG C2164 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL C2169 " --> pdb=" O SER C2165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN C2170 " --> pdb=" O LEU C2166 " (cutoff:3.500A) Processing helix chain 'C' and resid 2172 through 2189 Processing helix chain 'C' and resid 2190 through 2195 Processing helix chain 'C' and resid 2196 through 2203 Processing helix chain 'C' and resid 2204 through 2220 removed outlier: 5.249A pdb=" N GLY C2219 " --> pdb=" O VAL C2215 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLU C2220 " --> pdb=" O LEU C2216 " (cutoff:3.500A) Processing helix chain 'C' and resid 2226 through 2245 removed outlier: 3.890A pdb=" N SER C2244 " --> pdb=" O PHE C2240 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ARG C2245 " --> pdb=" O CYS C2241 " (cutoff:3.500A) Processing helix chain 'C' and resid 2246 through 2256 removed outlier: 3.945A pdb=" N HIS C2254 " --> pdb=" O SER C2250 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU C2255 " --> pdb=" O MET C2251 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER C2256 " --> pdb=" O PHE C2252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2257 through 2263 removed outlier: 4.182A pdb=" N GLY C2263 " --> pdb=" O LEU C2259 " (cutoff:3.500A) Processing helix chain 'C' and resid 2272 through 2282 removed outlier: 3.591A pdb=" N VAL C2281 " --> pdb=" O ALA C2277 " (cutoff:3.500A) Processing helix chain 'C' and resid 2284 through 2291 Processing helix chain 'C' and resid 2292 through 2309 Processing helix chain 'C' and resid 2311 through 2318 Processing helix chain 'C' and resid 2325 through 2341 Processing helix chain 'C' and resid 2347 through 2362 Proline residue: C2362 - end of helix Processing helix chain 'C' and resid 2376 through 2391 Proline residue: C2391 - end of helix Processing helix chain 'C' and resid 2418 through 2438 removed outlier: 3.506A pdb=" N MET C2424 " --> pdb=" O GLY C2420 " (cutoff:3.500A) Processing helix chain 'C' and resid 2440 through 2447 Processing helix chain 'C' and resid 2448 through 2463 Proline residue: C2463 - end of helix Processing helix chain 'C' and resid 2464 through 2473 Processing helix chain 'C' and resid 2496 through 2510 removed outlier: 3.815A pdb=" N LYS C2500 " --> pdb=" O VAL C2496 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET C2503 " --> pdb=" O HIS C2499 " (cutoff:3.500A) Processing helix chain 'C' and resid 2515 through 2526 Processing helix chain 'C' and resid 2527 through 2539 removed outlier: 3.679A pdb=" N ASP C2538 " --> pdb=" O ALA C2534 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR C2539 " --> pdb=" O ALA C2535 " (cutoff:3.500A) Processing helix chain 'C' and resid 2545 through 2567 removed outlier: 5.252A pdb=" N LEU C2560 " --> pdb=" O CYS C2556 " (cutoff:3.500A) Proline residue: C2561 - end of helix Processing helix chain 'C' and resid 2576 through 2593 Processing helix chain 'C' and resid 2597 through 2615 removed outlier: 3.652A pdb=" N TYR C2614 " --> pdb=" O ALA C2610 " (cutoff:3.500A) Processing helix chain 'C' and resid 2616 through 2631 removed outlier: 3.605A pdb=" N LEU C2620 " --> pdb=" O ARG C2616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN C2621 " --> pdb=" O PRO C2617 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS C2622 " --> pdb=" O SER C2618 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU C2623 " --> pdb=" O MET C2619 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C2629 " --> pdb=" O ARG C2625 " (cutoff:3.500A) Processing helix chain 'C' and resid 2637 through 2653 Proline residue: C2641 - end of helix Processing helix chain 'C' and resid 2669 through 2690 Processing helix chain 'C' and resid 2694 through 2712 removed outlier: 3.528A pdb=" N MET C2701 " --> pdb=" O TYR C2697 " (cutoff:3.500A) Proline residue: C2702 - end of helix Proline residue: C2712 - end of helix Processing helix chain 'C' and resid 2742 through 2747 removed outlier: 3.872A pdb=" N VAL C2746 " --> pdb=" O GLU C2742 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE C2747 " --> pdb=" O THR C2743 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2742 through 2747' Processing helix chain 'C' and resid 2749 through 2775 Processing helix chain 'C' and resid 2801 through 2820 Proline residue: C2809 - end of helix Processing helix chain 'C' and resid 2869 through 2899 Processing helix chain 'C' and resid 2908 through 2913 removed outlier: 5.216A pdb=" N THR C2913 " --> pdb=" O TYR C2909 " (cutoff:3.500A) Processing helix chain 'C' and resid 2918 through 2935 removed outlier: 4.363A pdb=" N LYS C2923 " --> pdb=" O ARG C2919 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA C2924 " --> pdb=" O ASP C2920 " (cutoff:3.500A) Processing helix chain 'C' and resid 2942 through 2948 Processing helix chain 'C' and resid 2950 through 2955 Processing helix chain 'C' and resid 2956 through 2983 Processing helix chain 'C' and resid 2992 through 3015 removed outlier: 3.702A pdb=" N LEU C3003 " --> pdb=" O PHE C2999 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C3004 " --> pdb=" O ALA C3000 " (cutoff:3.500A) Proline residue: C3005 - end of helix removed outlier: 3.851A pdb=" N CYS C3015 " --> pdb=" O PHE C3011 " (cutoff:3.500A) Processing helix chain 'C' and resid 3033 through 3052 Processing helix chain 'C' and resid 3054 through 3059 Processing helix chain 'C' and resid 3061 through 3076 Processing helix chain 'C' and resid 3077 through 3084 removed outlier: 4.147A pdb=" N VAL C3081 " --> pdb=" O ASP C3077 " (cutoff:3.500A) Processing helix chain 'C' and resid 3086 through 3113 Processing helix chain 'C' and resid 3124 through 3152 removed outlier: 5.105A pdb=" N LEU C3138 " --> pdb=" O THR C3134 " (cutoff:3.500A) Proline residue: C3139 - end of helix Processing helix chain 'C' and resid 3160 through 3180 removed outlier: 3.540A pdb=" N THR C3178 " --> pdb=" O TYR C3174 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C3179 " --> pdb=" O SER C3175 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG C3180 " --> pdb=" O LEU C3176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3181 through 3202 Proline residue: C3189 - end of helix Processing helix chain 'C' and resid 3208 through 3216 removed outlier: 4.513A pdb=" N ASN C3212 " --> pdb=" O GLU C3208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU C3213 " --> pdb=" O PRO C3209 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR C3214 " --> pdb=" O GLU C3210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN C3215 " --> pdb=" O LEU C3211 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ALA C3216 " --> pdb=" O ASN C3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3208 through 3216' Processing helix chain 'C' and resid 3218 through 3223 Processing helix chain 'C' and resid 3224 through 3232 removed outlier: 4.153A pdb=" N ARG C3228 " --> pdb=" O SER C3224 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA C3229 " --> pdb=" O PRO C3225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE C3230 " --> pdb=" O ARG C3226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU C3231 " --> pdb=" O GLU C3227 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY C3232 " --> pdb=" O ARG C3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3224 through 3232' Processing helix chain 'C' and resid 3236 through 3242 removed outlier: 3.545A pdb=" N MET C3240 " --> pdb=" O SER C3236 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS C3241 " --> pdb=" O VAL C3237 " (cutoff:3.500A) Proline residue: C3242 - end of helix No H-bonds generated for 'chain 'C' and resid 3236 through 3242' Processing helix chain 'C' and resid 3246 through 3261 Processing helix chain 'C' and resid 3263 through 3268 removed outlier: 3.591A pdb=" N MET C3267 " --> pdb=" O ARG C3263 " (cutoff:3.500A) Proline residue: C3268 - end of helix No H-bonds generated for 'chain 'C' and resid 3263 through 3268' Processing helix chain 'C' and resid 3269 through 3289 removed outlier: 4.526A pdb=" N LEU C3275 " --> pdb=" O ILE C3271 " (cutoff:3.500A) Proline residue: C3276 - end of helix Proline residue: C3283 - end of helix removed outlier: 3.544A pdb=" N ARG C3288 " --> pdb=" O ARG C3284 " (cutoff:3.500A) Processing helix chain 'C' and resid 3309 through 3328 removed outlier: 3.591A pdb=" N LEU C3313 " --> pdb=" O THR C3309 " (cutoff:3.500A) Processing helix chain 'C' and resid 3334 through 3348 removed outlier: 4.321A pdb=" N ARG C3338 " --> pdb=" O SER C3334 " (cutoff:3.500A) Proline residue: C3345 - end of helix removed outlier: 4.211A pdb=" N SER C3348 " --> pdb=" O GLN C3344 " (cutoff:3.500A) Processing helix chain 'C' and resid 3351 through 3384 removed outlier: 4.478A pdb=" N LEU C3355 " --> pdb=" O ARG C3351 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG C3356 " --> pdb=" O PRO C3352 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE C3360 " --> pdb=" O ARG C3356 " (cutoff:3.500A) Proline residue: C3361 - end of helix removed outlier: 4.409A pdb=" N ALA C3384 " --> pdb=" O LEU C3380 " (cutoff:3.500A) Processing helix chain 'C' and resid 3389 through 3414 removed outlier: 4.394A pdb=" N LEU C3393 " --> pdb=" O GLU C3389 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU C3394 " --> pdb=" O GLU C3390 " (cutoff:3.500A) Proline residue: C3411 - end of helix Processing helix chain 'C' and resid 3420 through 3428 Proline residue: C3428 - end of helix Processing helix chain 'C' and resid 3429 through 3450 removed outlier: 5.082A pdb=" N HIS C3450 " --> pdb=" O TRP C3446 " (cutoff:3.500A) Processing helix chain 'C' and resid 3451 through 3464 Processing helix chain 'C' and resid 3466 through 3472 Processing helix chain 'C' and resid 3505 through 3510 removed outlier: 5.608A pdb=" N LEU C3510 " --> pdb=" O VAL C3506 " (cutoff:3.500A) Processing helix chain 'C' and resid 3511 through 3527 removed outlier: 3.727A pdb=" N LEU C3515 " --> pdb=" O ILE C3511 " (cutoff:3.500A) Proline residue: C3520 - end of helix removed outlier: 5.000A pdb=" N ALA C3527 " --> pdb=" O LEU C3523 " (cutoff:3.500A) Processing helix chain 'C' and resid 3530 through 3544 Processing helix chain 'C' and resid 3546 through 3558 Processing helix chain 'C' and resid 3563 through 3568 removed outlier: 3.817A pdb=" N SER C3567 " --> pdb=" O LYS C3563 " (cutoff:3.500A) Proline residue: C3568 - end of helix No H-bonds generated for 'chain 'C' and resid 3563 through 3568' Processing helix chain 'C' and resid 3569 through 3581 removed outlier: 3.574A pdb=" N LEU C3576 " --> pdb=" O TRP C3572 " (cutoff:3.500A) Proline residue: C3581 - end of helix Processing helix chain 'C' and resid 3582 through 3587 removed outlier: 4.657A pdb=" N ASP C3586 " --> pdb=" O GLY C3582 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA C3587 " --> pdb=" O ARG C3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3582 through 3587' Processing helix chain 'C' and resid 3589 through 3613 Proline residue: C3613 - end of helix Processing helix chain 'C' and resid 3641 through 3646 removed outlier: 4.133A pdb=" N LEU C3645 " --> pdb=" O PRO C3641 " (cutoff:3.500A) Proline residue: C3646 - end of helix No H-bonds generated for 'chain 'C' and resid 3641 through 3646' Processing helix chain 'C' and resid 3647 through 3662 Processing helix chain 'C' and resid 3670 through 3681 removed outlier: 5.515A pdb=" N ALA C3681 " --> pdb=" O ASP C3677 " (cutoff:3.500A) Processing helix chain 'C' and resid 3683 through 3688 Processing helix chain 'C' and resid 3697 through 3712 Processing helix chain 'C' and resid 3720 through 3735 removed outlier: 3.655A pdb=" N CYS C3734 " --> pdb=" O MET C3730 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS C3735 " --> pdb=" O ALA C3731 " (cutoff:3.500A) Processing helix chain 'C' and resid 3755 through 3775 removed outlier: 3.750A pdb=" N LEU C3773 " --> pdb=" O GLN C3769 " (cutoff:3.500A) Processing helix chain 'C' and resid 3777 through 3790 removed outlier: 3.993A pdb=" N LYS C3790 " --> pdb=" O ILE C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3794 through 3809 Processing helix chain 'C' and resid 3812 through 3827 Processing helix chain 'C' and resid 3829 through 3842 Processing helix chain 'C' and resid 3846 through 3860 removed outlier: 4.901A pdb=" N GLY C3860 " --> pdb=" O ALA C3856 " (cutoff:3.500A) Processing helix chain 'C' and resid 3864 through 3869 removed outlier: 5.143A pdb=" N ILE C3869 " --> pdb=" O ASP C3865 " (cutoff:3.500A) Processing helix chain 'C' and resid 3880 through 3896 removed outlier: 3.663A pdb=" N CYS C3895 " --> pdb=" O LEU C3891 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3908 removed outlier: 4.295A pdb=" N ARG C3907 " --> pdb=" O GLN C3903 " (cutoff:3.500A) Processing helix chain 'C' and resid 3917 through 3942 removed outlier: 4.549A pdb=" N GLY C3942 " --> pdb=" O TRP C3938 " (cutoff:3.500A) Processing helix chain 'C' and resid 3947 through 3973 Processing helix chain 'C' and resid 3976 through 3986 Processing helix chain 'C' and resid 3987 through 4010 removed outlier: 3.914A pdb=" N ASP C4009 " --> pdb=" O LYS C4005 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N SER C4010 " --> pdb=" O LEU C4006 " (cutoff:3.500A) Processing helix chain 'C' and resid 4011 through 4035 removed outlier: 5.791A pdb=" N LEU C4015 " --> pdb=" O SER C4011 " (cutoff:3.500A) Processing helix chain 'C' and resid 4041 through 4055 Processing helix chain 'C' and resid 4056 through 4078 removed outlier: 3.909A pdb=" N GLY C4076 " --> pdb=" O LYS C4072 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER C4077 " --> pdb=" O ASP C4073 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU C4078 " --> pdb=" O ILE C4074 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4085 removed outlier: 4.775A pdb=" N THR C4085 " --> pdb=" O GLN C4081 " (cutoff:3.500A) Processing helix chain 'C' and resid 4092 through 4104 Processing helix chain 'C' and resid 4107 through 4119 removed outlier: 4.307A pdb=" N GLU C4119 " --> pdb=" O LEU C4115 " (cutoff:3.500A) Processing helix chain 'C' and resid 4127 through 4140 removed outlier: 4.838A pdb=" N PHE C4135 " --> pdb=" O PHE C4131 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN C4136 " --> pdb=" O ALA C4132 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU C4137 " --> pdb=" O ASN C4133 " (cutoff:3.500A) Proline residue: C4138 - end of helix Processing helix chain 'C' and resid 4141 through 4158 Proline residue: C4158 - end of helix Processing helix chain 'C' and resid 4160 through 4171 removed outlier: 3.707A pdb=" N ARG C4164 " --> pdb=" O ASP C4160 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C4165 " --> pdb=" O PRO C4161 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C4166 " --> pdb=" O ARG C4162 " (cutoff:3.500A) Processing helix chain 'C' and resid 4172 through 4178 Processing helix chain 'C' and resid 4201 through 4210 Processing helix chain 'C' and resid 4211 through 4227 Processing helix chain 'C' and resid 4232 through 4255 Processing helix chain 'C' and resid 4538 through 4557 Processing helix chain 'C' and resid 4558 through 4578 removed outlier: 4.267A pdb=" N PHE C4577 " --> pdb=" O PHE C4573 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR C4578 " --> pdb=" O ILE C4574 " (cutoff:3.500A) Processing helix chain 'C' and resid 4638 through 4681 removed outlier: 4.163A pdb=" N VAL C4664 " --> pdb=" O ASN C4660 " (cutoff:3.500A) Proline residue: C4665 - end of helix Processing helix chain 'C' and resid 4694 through 4707 removed outlier: 3.535A pdb=" N ARG C4701 " --> pdb=" O GLY C4697 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU C4702 " --> pdb=" O GLN C4698 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL C4703 " --> pdb=" O TRP C4699 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU C4704 " --> pdb=" O ASP C4700 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASN C4705 " --> pdb=" O ARG C4701 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR C4706 " --> pdb=" O LEU C4702 " (cutoff:3.500A) Proline residue: C4707 - end of helix Processing helix chain 'C' and resid 4717 through 4727 Processing helix chain 'C' and resid 4731 through 4740 Processing helix chain 'C' and resid 4742 through 4752 removed outlier: 3.609A pdb=" N ALA C4750 " --> pdb=" O LEU C4746 " (cutoff:3.500A) Processing helix chain 'C' and resid 4761 through 4769 Processing helix chain 'C' and resid 4770 through 4785 removed outlier: 3.558A pdb=" N ASP C4784 " --> pdb=" O VAL C4780 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN C4785 " --> pdb=" O ILE C4781 " (cutoff:3.500A) Processing helix chain 'C' and resid 4786 through 4803 removed outlier: 3.711A pdb=" N HIS C4801 " --> pdb=" O SER C4797 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C4802 " --> pdb=" O LEU C4798 " (cutoff:3.500A) Processing helix chain 'C' and resid 4804 through 4818 removed outlier: 4.657A pdb=" N ALA C4808 " --> pdb=" O ASN C4804 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA C4809 " --> pdb=" O PHE C4805 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS C4810 " --> pdb=" O PHE C4806 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU C4811 " --> pdb=" O PHE C4807 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU C4812 " --> pdb=" O ALA C4808 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP C4813 " --> pdb=" O ALA C4809 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE C4814 " --> pdb=" O HIS C4810 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA C4815 " --> pdb=" O LEU C4811 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET C4816 " --> pdb=" O LEU C4812 " (cutoff:3.500A) Processing helix chain 'C' and resid 4819 through 4830 removed outlier: 3.607A pdb=" N VAL C4828 " --> pdb=" O ILE C4824 " (cutoff:3.500A) Processing helix chain 'C' and resid 4831 through 4856 Processing helix chain 'C' and resid 4857 through 4862 removed outlier: 4.206A pdb=" N TYR C4861 " --> pdb=" O PHE C4857 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN C4862 " --> pdb=" O ARG C4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4857 through 4862' Processing helix chain 'C' and resid 4876 through 4891 removed outlier: 4.460A pdb=" N VAL C4889 " --> pdb=" O MET C4885 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG C4890 " --> pdb=" O TYR C4886 " (cutoff:3.500A) Processing helix chain 'C' and resid 4894 through 4899 removed outlier: 4.176A pdb=" N GLU C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4907 through 4922 Processing helix chain 'C' and resid 4926 through 4954 Processing helix chain 'C' and resid 4962 through 4968 removed outlier: 3.758A pdb=" N PHE C4966 " --> pdb=" O GLY C4962 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C4968 " --> pdb=" O ASP C4964 " (cutoff:3.500A) Processing helix chain 'C' and resid 4971 through 4979 Processing helix chain 'C' and resid 4982 through 4996 Processing helix chain 'C' and resid 5002 through 5015 Processing helix chain 'C' and resid 5025 through 5031 Processing helix chain 'C' and resid 323 through 328 removed outlier: 4.480A pdb=" N VAL C 326 " --> pdb=" O LYS C 323 " (cutoff:3.500A) Proline residue: C 328 - end of helix Processing helix chain 'C' and resid 3153 through 3158 removed outlier: 4.458A pdb=" N ILE C3158 " --> pdb=" O PHE C3153 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3153 through 3158' Processing helix chain 'C' and resid 4683 through 4688 Processing helix chain 'D' and resid 62 through 67 removed outlier: 4.089A pdb=" N CYS D 66 " --> pdb=" O ASP D 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N CYS D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 67' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 252 through 257 removed outlier: 5.150A pdb=" N ALA D 257 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 314 Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 395 through 423 removed outlier: 3.723A pdb=" N PHE D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 454 Processing helix chain 'D' and resid 461 through 483 Processing helix chain 'D' and resid 484 through 498 removed outlier: 4.568A pdb=" N TYR D 498 " --> pdb=" O ARG D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 508 removed outlier: 3.787A pdb=" N PHE D 507 " --> pdb=" O HIS D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 532 removed outlier: 4.190A pdb=" N SER D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TRP D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS D 517 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 545 removed outlier: 3.592A pdb=" N LEU D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N PHE D 541 " --> pdb=" O ASN D 537 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N SER D 542 " --> pdb=" O CYS D 538 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ASN D 544 " --> pdb=" O LEU D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 553 removed outlier: 3.984A pdb=" N LYS D 551 " --> pdb=" O TRP D 547 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP D 553 " --> pdb=" O VAL D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 572 Processing helix chain 'D' and resid 573 through 579 Processing helix chain 'D' and resid 580 through 594 Processing helix chain 'D' and resid 597 through 610 removed outlier: 3.666A pdb=" N LEU D 601 " --> pdb=" O ASN D 597 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N CYS D 610 " --> pdb=" O SER D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 626 Processing helix chain 'D' and resid 811 through 816 removed outlier: 4.452A pdb=" N ALA D 815 " --> pdb=" O PRO D 811 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D 816 " --> pdb=" O CYS D 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 811 through 816' Processing helix chain 'D' and resid 848 through 854 removed outlier: 4.028A pdb=" N PHE D 852 " --> pdb=" O SER D 848 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL D 853 " --> pdb=" O HIS D 849 " (cutoff:3.500A) Proline residue: D 854 - end of helix No H-bonds generated for 'chain 'D' and resid 848 through 854' Processing helix chain 'D' and resid 866 through 891 removed outlier: 3.515A pdb=" N LYS D 874 " --> pdb=" O ARG D 870 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU D 877 " --> pdb=" O GLU D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 936 removed outlier: 3.658A pdb=" N LEU D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 951 removed outlier: 4.571A pdb=" N GLU D 948 " --> pdb=" O ASP D 944 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP D 949 " --> pdb=" O GLU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 957 through 962 removed outlier: 5.029A pdb=" N MET D 962 " --> pdb=" O LYS D 958 " (cutoff:3.500A) Processing helix chain 'D' and resid 979 through 1005 Processing helix chain 'D' and resid 1029 through 1051 Processing helix chain 'D' and resid 1068 through 1073 removed outlier: 3.808A pdb=" N ALA D1073 " --> pdb=" O ARG D1069 " (cutoff:3.500A) Processing helix chain 'D' and resid 1218 through 1223 removed outlier: 7.060A pdb=" N GLU D1222 " --> pdb=" O CYS D1218 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY D1223 " --> pdb=" O GLY D1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1218 through 1223' Processing helix chain 'D' and resid 1424 through 1431 removed outlier: 3.692A pdb=" N LEU D1429 " --> pdb=" O PRO D1425 " (cutoff:3.500A) Processing helix chain 'D' and resid 1445 through 1450 removed outlier: 3.978A pdb=" N VAL D1449 " --> pdb=" O GLU D1445 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N TRP D1450 " --> pdb=" O PRO D1446 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1445 through 1450' Processing helix chain 'D' and resid 1497 through 1503 removed outlier: 3.985A pdb=" N PHE D1501 " --> pdb=" O TRP D1497 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER D1503 " --> pdb=" O GLY D1499 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1581 removed outlier: 3.853A pdb=" N ALA D1579 " --> pdb=" O PRO D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1650 through 1658 removed outlier: 4.294A pdb=" N LEU D1654 " --> pdb=" O ASP D1650 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER D1655 " --> pdb=" O ILE D1651 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU D1656 " --> pdb=" O LEU D1652 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU D1658 " --> pdb=" O LEU D1654 " (cutoff:3.500A) Processing helix chain 'D' and resid 1659 through 1676 Processing helix chain 'D' and resid 1679 through 1690 removed outlier: 3.799A pdb=" N SER D1688 " --> pdb=" O HIS D1684 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N HIS D1689 " --> pdb=" O ALA D1685 " (cutoff:3.500A) Processing helix chain 'D' and resid 1691 through 1701 Processing helix chain 'D' and resid 1705 through 1720 Processing helix chain 'D' and resid 1721 through 1733 removed outlier: 4.221A pdb=" N SER D1733 " --> pdb=" O ARG D1729 " (cutoff:3.500A) Processing helix chain 'D' and resid 1740 through 1747 removed outlier: 5.781A pdb=" N THR D1747 " --> pdb=" O THR D1743 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1827 Processing helix chain 'D' and resid 1835 through 1854 Proline residue: D1842 - end of helix Processing helix chain 'D' and resid 1857 through 1869 Processing helix chain 'D' and resid 1926 through 1931 removed outlier: 3.796A pdb=" N MET D1930 " --> pdb=" O GLY D1926 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS D1931 " --> pdb=" O LEU D1927 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1926 through 1931' Processing helix chain 'D' and resid 1933 through 1985 removed outlier: 5.162A pdb=" N PHE D1985 " --> pdb=" O LEU D1981 " (cutoff:3.500A) Processing helix chain 'D' and resid 1988 through 2001 removed outlier: 4.174A pdb=" N GLU D1998 " --> pdb=" O ARG D1994 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE D1999 " --> pdb=" O ARG D1995 " (cutoff:3.500A) Processing helix chain 'D' and resid 2002 through 2012 Processing helix chain 'D' and resid 2018 through 2023 Proline residue: D2023 - end of helix Processing helix chain 'D' and resid 2025 through 2044 Processing helix chain 'D' and resid 2094 through 2110 Processing helix chain 'D' and resid 2114 through 2131 Processing helix chain 'D' and resid 2132 through 2143 Proline residue: D2140 - end of helix removed outlier: 5.300A pdb=" N TYR D2143 " --> pdb=" O LEU D2139 " (cutoff:3.500A) Processing helix chain 'D' and resid 2146 through 2170 removed outlier: 3.835A pdb=" N VAL D2150 " --> pdb=" O SER D2146 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLU D2151 " --> pdb=" O VAL D2147 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP D2152 " --> pdb=" O SER D2148 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D2167 " --> pdb=" O ILE D2163 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE D2168 " --> pdb=" O ARG D2164 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL D2169 " --> pdb=" O SER D2165 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLN D2170 " --> pdb=" O LEU D2166 " (cutoff:3.500A) Processing helix chain 'D' and resid 2172 through 2189 Processing helix chain 'D' and resid 2190 through 2195 Processing helix chain 'D' and resid 2196 through 2203 Processing helix chain 'D' and resid 2204 through 2220 removed outlier: 5.249A pdb=" N GLY D2219 " --> pdb=" O VAL D2215 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU D2220 " --> pdb=" O LEU D2216 " (cutoff:3.500A) Processing helix chain 'D' and resid 2226 through 2245 removed outlier: 3.890A pdb=" N SER D2244 " --> pdb=" O PHE D2240 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ARG D2245 " --> pdb=" O CYS D2241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2246 through 2256 removed outlier: 3.944A pdb=" N HIS D2254 " --> pdb=" O SER D2250 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D2255 " --> pdb=" O MET D2251 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER D2256 " --> pdb=" O PHE D2252 " (cutoff:3.500A) Processing helix chain 'D' and resid 2257 through 2263 removed outlier: 4.183A pdb=" N GLY D2263 " --> pdb=" O LEU D2259 " (cutoff:3.500A) Processing helix chain 'D' and resid 2272 through 2282 removed outlier: 3.592A pdb=" N VAL D2281 " --> pdb=" O ALA D2277 " (cutoff:3.500A) Processing helix chain 'D' and resid 2284 through 2291 Processing helix chain 'D' and resid 2292 through 2309 Processing helix chain 'D' and resid 2311 through 2318 Processing helix chain 'D' and resid 2325 through 2341 Processing helix chain 'D' and resid 2347 through 2362 Proline residue: D2362 - end of helix Processing helix chain 'D' and resid 2376 through 2391 Proline residue: D2391 - end of helix Processing helix chain 'D' and resid 2418 through 2438 removed outlier: 3.506A pdb=" N MET D2424 " --> pdb=" O GLY D2420 " (cutoff:3.500A) Processing helix chain 'D' and resid 2440 through 2447 Processing helix chain 'D' and resid 2448 through 2463 Proline residue: D2463 - end of helix Processing helix chain 'D' and resid 2464 through 2473 Processing helix chain 'D' and resid 2496 through 2510 removed outlier: 3.816A pdb=" N LYS D2500 " --> pdb=" O VAL D2496 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET D2503 " --> pdb=" O HIS D2499 " (cutoff:3.500A) Processing helix chain 'D' and resid 2515 through 2526 Processing helix chain 'D' and resid 2527 through 2539 removed outlier: 3.681A pdb=" N ASP D2538 " --> pdb=" O ALA D2534 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N THR D2539 " --> pdb=" O ALA D2535 " (cutoff:3.500A) Processing helix chain 'D' and resid 2545 through 2567 removed outlier: 5.251A pdb=" N LEU D2560 " --> pdb=" O CYS D2556 " (cutoff:3.500A) Proline residue: D2561 - end of helix Processing helix chain 'D' and resid 2576 through 2593 Processing helix chain 'D' and resid 2597 through 2615 removed outlier: 3.653A pdb=" N TYR D2614 " --> pdb=" O ALA D2610 " (cutoff:3.500A) Processing helix chain 'D' and resid 2616 through 2631 removed outlier: 3.604A pdb=" N LEU D2620 " --> pdb=" O ARG D2616 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLN D2621 " --> pdb=" O PRO D2617 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N HIS D2622 " --> pdb=" O SER D2618 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LEU D2623 " --> pdb=" O MET D2619 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D2629 " --> pdb=" O ARG D2625 " (cutoff:3.500A) Processing helix chain 'D' and resid 2637 through 2653 Proline residue: D2641 - end of helix Processing helix chain 'D' and resid 2669 through 2690 Processing helix chain 'D' and resid 2694 through 2712 removed outlier: 3.528A pdb=" N MET D2701 " --> pdb=" O TYR D2697 " (cutoff:3.500A) Proline residue: D2702 - end of helix Proline residue: D2712 - end of helix Processing helix chain 'D' and resid 2742 through 2747 removed outlier: 3.872A pdb=" N VAL D2746 " --> pdb=" O GLU D2742 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE D2747 " --> pdb=" O THR D2743 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2742 through 2747' Processing helix chain 'D' and resid 2749 through 2775 Processing helix chain 'D' and resid 2801 through 2820 Proline residue: D2809 - end of helix Processing helix chain 'D' and resid 2869 through 2899 Processing helix chain 'D' and resid 2908 through 2913 removed outlier: 5.216A pdb=" N THR D2913 " --> pdb=" O TYR D2909 " (cutoff:3.500A) Processing helix chain 'D' and resid 2918 through 2935 removed outlier: 4.362A pdb=" N LYS D2923 " --> pdb=" O ARG D2919 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA D2924 " --> pdb=" O ASP D2920 " (cutoff:3.500A) Processing helix chain 'D' and resid 2942 through 2948 Processing helix chain 'D' and resid 2950 through 2955 Processing helix chain 'D' and resid 2956 through 2983 Processing helix chain 'D' and resid 2992 through 3015 removed outlier: 3.702A pdb=" N LEU D3003 " --> pdb=" O PHE D2999 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D3004 " --> pdb=" O ALA D3000 " (cutoff:3.500A) Proline residue: D3005 - end of helix removed outlier: 3.850A pdb=" N CYS D3015 " --> pdb=" O PHE D3011 " (cutoff:3.500A) Processing helix chain 'D' and resid 3033 through 3052 Processing helix chain 'D' and resid 3054 through 3059 Processing helix chain 'D' and resid 3061 through 3076 Processing helix chain 'D' and resid 3077 through 3084 removed outlier: 4.148A pdb=" N VAL D3081 " --> pdb=" O ASP D3077 " (cutoff:3.500A) Processing helix chain 'D' and resid 3086 through 3113 Processing helix chain 'D' and resid 3124 through 3152 removed outlier: 5.105A pdb=" N LEU D3138 " --> pdb=" O THR D3134 " (cutoff:3.500A) Proline residue: D3139 - end of helix Processing helix chain 'D' and resid 3160 through 3180 removed outlier: 3.540A pdb=" N THR D3178 " --> pdb=" O TYR D3174 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR D3179 " --> pdb=" O SER D3175 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ARG D3180 " --> pdb=" O LEU D3176 " (cutoff:3.500A) Processing helix chain 'D' and resid 3181 through 3202 Proline residue: D3189 - end of helix Processing helix chain 'D' and resid 3208 through 3216 removed outlier: 4.513A pdb=" N ASN D3212 " --> pdb=" O GLU D3208 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU D3213 " --> pdb=" O PRO D3209 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TYR D3214 " --> pdb=" O GLU D3210 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN D3215 " --> pdb=" O LEU D3211 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ALA D3216 " --> pdb=" O ASN D3212 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3208 through 3216' Processing helix chain 'D' and resid 3218 through 3223 Processing helix chain 'D' and resid 3224 through 3232 removed outlier: 4.154A pdb=" N ARG D3228 " --> pdb=" O SER D3224 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA D3229 " --> pdb=" O PRO D3225 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE D3230 " --> pdb=" O ARG D3226 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU D3231 " --> pdb=" O GLU D3227 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLY D3232 " --> pdb=" O ARG D3228 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3224 through 3232' Processing helix chain 'D' and resid 3236 through 3242 removed outlier: 3.547A pdb=" N MET D3240 " --> pdb=" O SER D3236 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N CYS D3241 " --> pdb=" O VAL D3237 " (cutoff:3.500A) Proline residue: D3242 - end of helix No H-bonds generated for 'chain 'D' and resid 3236 through 3242' Processing helix chain 'D' and resid 3246 through 3261 Processing helix chain 'D' and resid 3263 through 3268 removed outlier: 3.590A pdb=" N MET D3267 " --> pdb=" O ARG D3263 " (cutoff:3.500A) Proline residue: D3268 - end of helix No H-bonds generated for 'chain 'D' and resid 3263 through 3268' Processing helix chain 'D' and resid 3269 through 3289 removed outlier: 4.526A pdb=" N LEU D3275 " --> pdb=" O ILE D3271 " (cutoff:3.500A) Proline residue: D3276 - end of helix Proline residue: D3283 - end of helix removed outlier: 3.545A pdb=" N ARG D3288 " --> pdb=" O ARG D3284 " (cutoff:3.500A) Processing helix chain 'D' and resid 3309 through 3328 removed outlier: 3.590A pdb=" N LEU D3313 " --> pdb=" O THR D3309 " (cutoff:3.500A) Processing helix chain 'D' and resid 3334 through 3348 removed outlier: 4.322A pdb=" N ARG D3338 " --> pdb=" O SER D3334 " (cutoff:3.500A) Proline residue: D3345 - end of helix removed outlier: 4.212A pdb=" N SER D3348 " --> pdb=" O GLN D3344 " (cutoff:3.500A) Processing helix chain 'D' and resid 3351 through 3384 removed outlier: 4.478A pdb=" N LEU D3355 " --> pdb=" O ARG D3351 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ARG D3356 " --> pdb=" O PRO D3352 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE D3360 " --> pdb=" O ARG D3356 " (cutoff:3.500A) Proline residue: D3361 - end of helix removed outlier: 4.407A pdb=" N ALA D3384 " --> pdb=" O LEU D3380 " (cutoff:3.500A) Processing helix chain 'D' and resid 3389 through 3414 removed outlier: 4.394A pdb=" N LEU D3393 " --> pdb=" O GLU D3389 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU D3394 " --> pdb=" O GLU D3390 " (cutoff:3.500A) Proline residue: D3411 - end of helix Processing helix chain 'D' and resid 3420 through 3428 Proline residue: D3428 - end of helix Processing helix chain 'D' and resid 3429 through 3450 removed outlier: 5.081A pdb=" N HIS D3450 " --> pdb=" O TRP D3446 " (cutoff:3.500A) Processing helix chain 'D' and resid 3451 through 3464 Processing helix chain 'D' and resid 3466 through 3472 Processing helix chain 'D' and resid 3505 through 3510 removed outlier: 5.608A pdb=" N LEU D3510 " --> pdb=" O VAL D3506 " (cutoff:3.500A) Processing helix chain 'D' and resid 3511 through 3527 removed outlier: 3.727A pdb=" N LEU D3515 " --> pdb=" O ILE D3511 " (cutoff:3.500A) Proline residue: D3520 - end of helix removed outlier: 5.000A pdb=" N ALA D3527 " --> pdb=" O LEU D3523 " (cutoff:3.500A) Processing helix chain 'D' and resid 3530 through 3544 Processing helix chain 'D' and resid 3546 through 3558 Processing helix chain 'D' and resid 3563 through 3568 removed outlier: 3.817A pdb=" N SER D3567 " --> pdb=" O LYS D3563 " (cutoff:3.500A) Proline residue: D3568 - end of helix No H-bonds generated for 'chain 'D' and resid 3563 through 3568' Processing helix chain 'D' and resid 3569 through 3581 removed outlier: 3.574A pdb=" N LEU D3576 " --> pdb=" O TRP D3572 " (cutoff:3.500A) Proline residue: D3581 - end of helix Processing helix chain 'D' and resid 3582 through 3587 removed outlier: 4.658A pdb=" N ASP D3586 " --> pdb=" O GLY D3582 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA D3587 " --> pdb=" O ARG D3583 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3582 through 3587' Processing helix chain 'D' and resid 3589 through 3613 Proline residue: D3613 - end of helix Processing helix chain 'D' and resid 3641 through 3646 removed outlier: 4.134A pdb=" N LEU D3645 " --> pdb=" O PRO D3641 " (cutoff:3.500A) Proline residue: D3646 - end of helix No H-bonds generated for 'chain 'D' and resid 3641 through 3646' Processing helix chain 'D' and resid 3647 through 3662 Processing helix chain 'D' and resid 3670 through 3681 removed outlier: 5.515A pdb=" N ALA D3681 " --> pdb=" O ASP D3677 " (cutoff:3.500A) Processing helix chain 'D' and resid 3683 through 3688 Processing helix chain 'D' and resid 3697 through 3712 Processing helix chain 'D' and resid 3720 through 3735 removed outlier: 3.655A pdb=" N CYS D3734 " --> pdb=" O MET D3730 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N HIS D3735 " --> pdb=" O ALA D3731 " (cutoff:3.500A) Processing helix chain 'D' and resid 3755 through 3775 removed outlier: 3.751A pdb=" N LEU D3773 " --> pdb=" O GLN D3769 " (cutoff:3.500A) Processing helix chain 'D' and resid 3777 through 3790 removed outlier: 3.993A pdb=" N LYS D3790 " --> pdb=" O ILE D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3794 through 3809 Processing helix chain 'D' and resid 3812 through 3827 Processing helix chain 'D' and resid 3829 through 3842 Processing helix chain 'D' and resid 3846 through 3860 removed outlier: 4.901A pdb=" N GLY D3860 " --> pdb=" O ALA D3856 " (cutoff:3.500A) Processing helix chain 'D' and resid 3864 through 3869 removed outlier: 5.143A pdb=" N ILE D3869 " --> pdb=" O ASP D3865 " (cutoff:3.500A) Processing helix chain 'D' and resid 3880 through 3896 removed outlier: 3.664A pdb=" N CYS D3895 " --> pdb=" O LEU D3891 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3908 removed outlier: 4.296A pdb=" N ARG D3907 " --> pdb=" O GLN D3903 " (cutoff:3.500A) Processing helix chain 'D' and resid 3917 through 3942 removed outlier: 4.551A pdb=" N GLY D3942 " --> pdb=" O TRP D3938 " (cutoff:3.500A) Processing helix chain 'D' and resid 3947 through 3973 Processing helix chain 'D' and resid 3976 through 3986 Processing helix chain 'D' and resid 3987 through 4010 removed outlier: 3.915A pdb=" N ASP D4009 " --> pdb=" O LYS D4005 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER D4010 " --> pdb=" O LEU D4006 " (cutoff:3.500A) Processing helix chain 'D' and resid 4011 through 4035 removed outlier: 5.791A pdb=" N LEU D4015 " --> pdb=" O SER D4011 " (cutoff:3.500A) Processing helix chain 'D' and resid 4041 through 4055 Processing helix chain 'D' and resid 4056 through 4078 removed outlier: 3.909A pdb=" N GLY D4076 " --> pdb=" O LYS D4072 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D4077 " --> pdb=" O ASP D4073 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU D4078 " --> pdb=" O ILE D4074 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4085 removed outlier: 4.775A pdb=" N THR D4085 " --> pdb=" O GLN D4081 " (cutoff:3.500A) Processing helix chain 'D' and resid 4092 through 4104 Processing helix chain 'D' and resid 4107 through 4119 removed outlier: 4.307A pdb=" N GLU D4119 " --> pdb=" O LEU D4115 " (cutoff:3.500A) Processing helix chain 'D' and resid 4127 through 4140 removed outlier: 4.837A pdb=" N PHE D4135 " --> pdb=" O PHE D4131 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN D4136 " --> pdb=" O ALA D4132 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU D4137 " --> pdb=" O ASN D4133 " (cutoff:3.500A) Proline residue: D4138 - end of helix Processing helix chain 'D' and resid 4141 through 4158 Proline residue: D4158 - end of helix Processing helix chain 'D' and resid 4160 through 4171 removed outlier: 3.707A pdb=" N ARG D4164 " --> pdb=" O ASP D4160 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN D4165 " --> pdb=" O PRO D4161 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE D4166 " --> pdb=" O ARG D4162 " (cutoff:3.500A) Processing helix chain 'D' and resid 4172 through 4178 Processing helix chain 'D' and resid 4201 through 4210 Processing helix chain 'D' and resid 4211 through 4227 Processing helix chain 'D' and resid 4232 through 4255 Processing helix chain 'D' and resid 4538 through 4557 Processing helix chain 'D' and resid 4558 through 4578 removed outlier: 4.266A pdb=" N PHE D4577 " --> pdb=" O PHE D4573 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TYR D4578 " --> pdb=" O ILE D4574 " (cutoff:3.500A) Processing helix chain 'D' and resid 4638 through 4681 removed outlier: 4.163A pdb=" N VAL D4664 " --> pdb=" O ASN D4660 " (cutoff:3.500A) Proline residue: D4665 - end of helix Processing helix chain 'D' and resid 4694 through 4707 removed outlier: 3.535A pdb=" N ARG D4701 " --> pdb=" O GLY D4697 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU D4702 " --> pdb=" O GLN D4698 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N VAL D4703 " --> pdb=" O TRP D4699 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D4704 " --> pdb=" O ASP D4700 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ASN D4705 " --> pdb=" O ARG D4701 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR D4706 " --> pdb=" O LEU D4702 " (cutoff:3.500A) Proline residue: D4707 - end of helix Processing helix chain 'D' and resid 4717 through 4727 Processing helix chain 'D' and resid 4731 through 4740 Processing helix chain 'D' and resid 4742 through 4752 removed outlier: 3.609A pdb=" N ALA D4750 " --> pdb=" O LEU D4746 " (cutoff:3.500A) Processing helix chain 'D' and resid 4761 through 4769 Processing helix chain 'D' and resid 4770 through 4785 removed outlier: 3.558A pdb=" N ASP D4784 " --> pdb=" O VAL D4780 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASN D4785 " --> pdb=" O ILE D4781 " (cutoff:3.500A) Processing helix chain 'D' and resid 4786 through 4803 removed outlier: 3.711A pdb=" N HIS D4801 " --> pdb=" O SER D4797 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D4802 " --> pdb=" O LEU D4798 " (cutoff:3.500A) Processing helix chain 'D' and resid 4804 through 4818 removed outlier: 4.657A pdb=" N ALA D4808 " --> pdb=" O ASN D4804 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA D4809 " --> pdb=" O PHE D4805 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N HIS D4810 " --> pdb=" O PHE D4806 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU D4811 " --> pdb=" O PHE D4807 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D4812 " --> pdb=" O ALA D4808 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP D4813 " --> pdb=" O ALA D4809 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE D4814 " --> pdb=" O HIS D4810 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA D4815 " --> pdb=" O LEU D4811 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET D4816 " --> pdb=" O LEU D4812 " (cutoff:3.500A) Processing helix chain 'D' and resid 4819 through 4830 removed outlier: 3.607A pdb=" N VAL D4828 " --> pdb=" O ILE D4824 " (cutoff:3.500A) Processing helix chain 'D' and resid 4831 through 4856 Processing helix chain 'D' and resid 4857 through 4862 removed outlier: 4.205A pdb=" N TYR D4861 " --> pdb=" O PHE D4857 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ASN D4862 " --> pdb=" O ARG D4858 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4857 through 4862' Processing helix chain 'D' and resid 4876 through 4891 removed outlier: 4.460A pdb=" N VAL D4889 " --> pdb=" O MET D4885 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG D4890 " --> pdb=" O TYR D4886 " (cutoff:3.500A) Processing helix chain 'D' and resid 4894 through 4899 removed outlier: 4.176A pdb=" N GLU D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4907 through 4922 Processing helix chain 'D' and resid 4926 through 4954 Processing helix chain 'D' and resid 4962 through 4968 removed outlier: 3.757A pdb=" N PHE D4966 " --> pdb=" O GLY D4962 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR D4968 " --> pdb=" O ASP D4964 " (cutoff:3.500A) Processing helix chain 'D' and resid 4971 through 4979 Processing helix chain 'D' and resid 4982 through 4996 Processing helix chain 'D' and resid 5002 through 5015 Processing helix chain 'D' and resid 5025 through 5031 Processing helix chain 'D' and resid 323 through 328 removed outlier: 4.480A pdb=" N VAL D 326 " --> pdb=" O LYS D 323 " (cutoff:3.500A) Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 3153 through 3158 removed outlier: 4.460A pdb=" N ILE D3158 " --> pdb=" O PHE D3153 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3153 through 3158' Processing helix chain 'D' and resid 4683 through 4688 Processing helix chain 'E' and resid 39 through 44 removed outlier: 3.838A pdb=" N ARG E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.180A pdb=" N SER E 68 " --> pdb=" O VAL E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.996A pdb=" N TYR E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 removed outlier: 3.839A pdb=" N ARG F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.186A pdb=" N SER F 68 " --> pdb=" O VAL F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.968A pdb=" N TYR F 83 " --> pdb=" O SER F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 removed outlier: 3.835A pdb=" N ARG G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.184A pdb=" N SER G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.965A pdb=" N TYR G 83 " --> pdb=" O SER G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 removed outlier: 3.824A pdb=" N ARG H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.179A pdb=" N SER H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.967A pdb=" N TYR H 83 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 48 through 53 removed outlier: 6.505A pdb=" N LYS A 35 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU A 23 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ALA A 40 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL A 21 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 113 removed outlier: 5.301A pdb=" N LEU A 110 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET A 117 " --> pdb=" O HIS A 112 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 149 through 153 Processing sheet with id= 4, first strand: chain 'A' and resid 182 through 185 Processing sheet with id= 5, first strand: chain 'A' and resid 219 through 222 removed outlier: 4.107A pdb=" N HIS A 219 " --> pdb=" O LEU A 263 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU A 260 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE A 283 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 231 through 234 removed outlier: 5.246A pdb=" N VAL A 246 " --> pdb=" O ALA A 377 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'A' and resid 315 through 319 Processing sheet with id= 8, first strand: chain 'A' and resid 682 through 687 removed outlier: 5.348A pdb=" N HIS A 682 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A1647 " --> pdb=" O ILE A1642 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 754 through 760 removed outlier: 3.785A pdb=" N ASP A 743 " --> pdb=" O VAL A 669 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS A 789 " --> pdb=" O ASP A 670 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY A1626 " --> pdb=" O ALA A1621 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'A' and resid 767 through 770 Processing sheet with id= 11, first strand: chain 'A' and resid 830 through 834 removed outlier: 4.646A pdb=" N TYR A 830 " --> pdb=" O VAL A 841 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY A 837 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU A1203 " --> pdb=" O PRO A 838 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN A1199 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A1200 " --> pdb=" O VAL A1096 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY A1087 " --> pdb=" O LEU A1156 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP A1148 " --> pdb=" O ALA A1095 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 897 through 900 removed outlier: 6.592A pdb=" N ARG A 898 " --> pdb=" O HIS A 905 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS A 905 " --> pdb=" O ARG A 898 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP A 900 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'A' and resid 937 through 942 removed outlier: 7.851A pdb=" N GLY A 937 " --> pdb=" O PRO A1057 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS A 939 " --> pdb=" O GLU A1055 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1006 through 1009 Processing sheet with id= 15, first strand: chain 'A' and resid 1135 through 1139 removed outlier: 7.364A pdb=" N LEU A1121 " --> pdb=" O ARG A1107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A1127 " --> pdb=" O MET A1101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET A1101 " --> pdb=" O GLY A1127 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU A1100 " --> pdb=" O GLY A1196 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A1075 " --> pdb=" O SER A1240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR A1236 " --> pdb=" O GLU A1079 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR A1237 " --> pdb=" O MET A1609 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1244 through 1247 removed outlier: 6.859A pdb=" N GLU A1597 " --> pdb=" O SER A1293 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE A1289 " --> pdb=" O LEU A1601 " (cutoff:3.500A) removed outlier: 14.028A pdb=" N MET A1287 " --> pdb=" O PRO A1603 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR A1547 " --> pdb=" O PHE A1298 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1268 through 1274 removed outlier: 3.886A pdb=" N VAL A1563 " --> pdb=" O LEU A1273 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL A1562 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY A1568 " --> pdb=" O TYR A1435 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR A1435 " --> pdb=" O GLY A1568 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR A1432 " --> pdb=" O LEU A1523 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A1527 " --> pdb=" O ASP A1522 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY A1526 " --> pdb=" O VAL A1543 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2478 through 2481 Processing sheet with id= 19, first strand: chain 'A' and resid 2776 through 2779 Processing sheet with id= 20, first strand: chain 'A' and resid 2822 through 2826 Processing sheet with id= 21, first strand: chain 'A' and resid 4180 through 4187 removed outlier: 4.842A pdb=" N TYR A4180 " --> pdb=" O ILE A4200 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'A' and resid 4579 through 4582 Processing sheet with id= 23, first strand: chain 'A' and resid 1088 through 1091 Processing sheet with id= 24, first strand: chain 'B' and resid 48 through 53 removed outlier: 6.505A pdb=" N LYS B 35 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 23 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ALA B 40 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL B 21 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'B' and resid 110 through 113 removed outlier: 5.300A pdb=" N LEU B 110 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET B 117 " --> pdb=" O HIS B 112 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'B' and resid 149 through 153 Processing sheet with id= 27, first strand: chain 'B' and resid 182 through 185 Processing sheet with id= 28, first strand: chain 'B' and resid 219 through 222 removed outlier: 4.106A pdb=" N HIS B 219 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LEU B 260 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 283 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 231 through 234 removed outlier: 5.245A pdb=" N VAL B 246 " --> pdb=" O ALA B 377 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 315 through 319 Processing sheet with id= 31, first strand: chain 'B' and resid 682 through 687 removed outlier: 5.348A pdb=" N HIS B 682 " --> pdb=" O SER B 785 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG B1647 " --> pdb=" O ILE B1642 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 754 through 760 removed outlier: 3.785A pdb=" N ASP B 743 " --> pdb=" O VAL B 669 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 789 " --> pdb=" O ASP B 670 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY B1626 " --> pdb=" O ALA B1621 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 767 through 770 Processing sheet with id= 34, first strand: chain 'B' and resid 830 through 834 removed outlier: 4.645A pdb=" N TYR B 830 " --> pdb=" O VAL B 841 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 837 " --> pdb=" O GLY B 834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU B1203 " --> pdb=" O PRO B 838 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN B1199 " --> pdb=" O GLY B 842 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B1200 " --> pdb=" O VAL B1096 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY B1087 " --> pdb=" O LEU B1156 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP B1148 " --> pdb=" O ALA B1095 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 897 through 900 removed outlier: 6.592A pdb=" N ARG B 898 " --> pdb=" O HIS B 905 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS B 905 " --> pdb=" O ARG B 898 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP B 900 " --> pdb=" O ARG B 903 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 937 through 942 removed outlier: 7.851A pdb=" N GLY B 937 " --> pdb=" O PRO B1057 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 939 " --> pdb=" O GLU B1055 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1006 through 1009 Processing sheet with id= 38, first strand: chain 'B' and resid 1135 through 1139 removed outlier: 7.364A pdb=" N LEU B1121 " --> pdb=" O ARG B1107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B1127 " --> pdb=" O MET B1101 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET B1101 " --> pdb=" O GLY B1127 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU B1100 " --> pdb=" O GLY B1196 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE B1075 " --> pdb=" O SER B1240 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N THR B1236 " --> pdb=" O GLU B1079 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR B1237 " --> pdb=" O MET B1609 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 1244 through 1247 removed outlier: 6.860A pdb=" N GLU B1597 " --> pdb=" O SER B1293 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N PHE B1289 " --> pdb=" O LEU B1601 " (cutoff:3.500A) removed outlier: 14.028A pdb=" N MET B1287 " --> pdb=" O PRO B1603 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B1547 " --> pdb=" O PHE B1298 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 1268 through 1274 removed outlier: 3.886A pdb=" N VAL B1563 " --> pdb=" O LEU B1273 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL B1562 " --> pdb=" O PHE B1441 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY B1568 " --> pdb=" O TYR B1435 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR B1435 " --> pdb=" O GLY B1568 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR B1432 " --> pdb=" O LEU B1523 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B1527 " --> pdb=" O ASP B1522 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY B1526 " --> pdb=" O VAL B1543 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 2478 through 2481 Processing sheet with id= 42, first strand: chain 'B' and resid 2776 through 2779 Processing sheet with id= 43, first strand: chain 'B' and resid 2822 through 2826 Processing sheet with id= 44, first strand: chain 'B' and resid 4180 through 4187 removed outlier: 4.842A pdb=" N TYR B4180 " --> pdb=" O ILE B4200 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'B' and resid 4579 through 4582 Processing sheet with id= 46, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id= 47, first strand: chain 'C' and resid 48 through 53 removed outlier: 6.505A pdb=" N LYS C 35 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU C 23 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ALA C 40 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL C 21 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 110 through 113 removed outlier: 5.301A pdb=" N LEU C 110 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET C 117 " --> pdb=" O HIS C 112 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'C' and resid 149 through 153 Processing sheet with id= 50, first strand: chain 'C' and resid 182 through 185 Processing sheet with id= 51, first strand: chain 'C' and resid 219 through 222 removed outlier: 4.107A pdb=" N HIS C 219 " --> pdb=" O LEU C 263 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU C 260 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 283 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'C' and resid 231 through 234 removed outlier: 5.245A pdb=" N VAL C 246 " --> pdb=" O ALA C 377 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 315 through 319 Processing sheet with id= 54, first strand: chain 'C' and resid 682 through 687 removed outlier: 5.348A pdb=" N HIS C 682 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C1647 " --> pdb=" O ILE C1642 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'C' and resid 754 through 760 removed outlier: 3.784A pdb=" N ASP C 743 " --> pdb=" O VAL C 669 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS C 789 " --> pdb=" O ASP C 670 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY C1626 " --> pdb=" O ALA C1621 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 767 through 770 Processing sheet with id= 57, first strand: chain 'C' and resid 830 through 834 removed outlier: 4.645A pdb=" N TYR C 830 " --> pdb=" O VAL C 841 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 837 " --> pdb=" O GLY C 834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU C1203 " --> pdb=" O PRO C 838 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN C1199 " --> pdb=" O GLY C 842 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL C1200 " --> pdb=" O VAL C1096 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY C1087 " --> pdb=" O LEU C1156 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP C1148 " --> pdb=" O ALA C1095 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 897 through 900 removed outlier: 6.592A pdb=" N ARG C 898 " --> pdb=" O HIS C 905 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS C 905 " --> pdb=" O ARG C 898 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N ASP C 900 " --> pdb=" O ARG C 903 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 937 through 942 removed outlier: 7.851A pdb=" N GLY C 937 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS C 939 " --> pdb=" O GLU C1055 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 1006 through 1009 Processing sheet with id= 61, first strand: chain 'C' and resid 1135 through 1139 removed outlier: 7.364A pdb=" N LEU C1121 " --> pdb=" O ARG C1107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY C1127 " --> pdb=" O MET C1101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET C1101 " --> pdb=" O GLY C1127 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU C1100 " --> pdb=" O GLY C1196 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE C1075 " --> pdb=" O SER C1240 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR C1236 " --> pdb=" O GLU C1079 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THR C1237 " --> pdb=" O MET C1609 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 1244 through 1247 removed outlier: 6.860A pdb=" N GLU C1597 " --> pdb=" O SER C1293 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE C1289 " --> pdb=" O LEU C1601 " (cutoff:3.500A) removed outlier: 14.028A pdb=" N MET C1287 " --> pdb=" O PRO C1603 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR C1547 " --> pdb=" O PHE C1298 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 1268 through 1274 removed outlier: 3.886A pdb=" N VAL C1563 " --> pdb=" O LEU C1273 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL C1562 " --> pdb=" O PHE C1441 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY C1568 " --> pdb=" O TYR C1435 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR C1435 " --> pdb=" O GLY C1568 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR C1432 " --> pdb=" O LEU C1523 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C1527 " --> pdb=" O ASP C1522 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N GLY C1526 " --> pdb=" O VAL C1543 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'C' and resid 2478 through 2481 Processing sheet with id= 65, first strand: chain 'C' and resid 2776 through 2779 Processing sheet with id= 66, first strand: chain 'C' and resid 2822 through 2826 Processing sheet with id= 67, first strand: chain 'C' and resid 4180 through 4187 removed outlier: 4.841A pdb=" N TYR C4180 " --> pdb=" O ILE C4200 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'C' and resid 4579 through 4582 Processing sheet with id= 69, first strand: chain 'C' and resid 1088 through 1091 Processing sheet with id= 70, first strand: chain 'D' and resid 48 through 53 removed outlier: 6.505A pdb=" N LYS D 35 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LEU D 23 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 10.253A pdb=" N ALA D 40 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 13.179A pdb=" N VAL D 21 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 110 through 113 removed outlier: 5.301A pdb=" N LEU D 110 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N MET D 117 " --> pdb=" O HIS D 112 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 149 through 153 Processing sheet with id= 73, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 74, first strand: chain 'D' and resid 219 through 222 removed outlier: 4.107A pdb=" N HIS D 219 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N LEU D 260 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE D 283 " --> pdb=" O LEU D 292 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 231 through 234 removed outlier: 5.246A pdb=" N VAL D 246 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'D' and resid 315 through 319 Processing sheet with id= 77, first strand: chain 'D' and resid 682 through 687 removed outlier: 5.348A pdb=" N HIS D 682 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D1647 " --> pdb=" O ILE D1642 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 754 through 760 removed outlier: 3.784A pdb=" N ASP D 743 " --> pdb=" O VAL D 669 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS D 789 " --> pdb=" O ASP D 670 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY D1626 " --> pdb=" O ALA D1621 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 767 through 770 Processing sheet with id= 80, first strand: chain 'D' and resid 830 through 834 removed outlier: 4.646A pdb=" N TYR D 830 " --> pdb=" O VAL D 841 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY D 837 " --> pdb=" O GLY D 834 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU D1203 " --> pdb=" O PRO D 838 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLN D1199 " --> pdb=" O GLY D 842 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D1200 " --> pdb=" O VAL D1096 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY D1087 " --> pdb=" O LEU D1156 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASP D1148 " --> pdb=" O ALA D1095 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 897 through 900 removed outlier: 6.591A pdb=" N ARG D 898 " --> pdb=" O HIS D 905 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N HIS D 905 " --> pdb=" O ARG D 898 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP D 900 " --> pdb=" O ARG D 903 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'D' and resid 937 through 942 removed outlier: 7.851A pdb=" N GLY D 937 " --> pdb=" O PRO D1057 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS D 939 " --> pdb=" O GLU D1055 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 1006 through 1009 Processing sheet with id= 84, first strand: chain 'D' and resid 1135 through 1139 removed outlier: 7.364A pdb=" N LEU D1121 " --> pdb=" O ARG D1107 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY D1127 " --> pdb=" O MET D1101 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N MET D1101 " --> pdb=" O GLY D1127 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLU D1100 " --> pdb=" O GLY D1196 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE D1075 " --> pdb=" O SER D1240 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N THR D1236 " --> pdb=" O GLU D1079 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N THR D1237 " --> pdb=" O MET D1609 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'D' and resid 1244 through 1247 removed outlier: 6.860A pdb=" N GLU D1597 " --> pdb=" O SER D1293 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N PHE D1289 " --> pdb=" O LEU D1601 " (cutoff:3.500A) removed outlier: 14.028A pdb=" N MET D1287 " --> pdb=" O PRO D1603 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR D1547 " --> pdb=" O PHE D1298 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'D' and resid 1268 through 1274 removed outlier: 3.886A pdb=" N VAL D1563 " --> pdb=" O LEU D1273 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N VAL D1562 " --> pdb=" O PHE D1441 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY D1568 " --> pdb=" O TYR D1435 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TYR D1435 " --> pdb=" O GLY D1568 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N THR D1432 " --> pdb=" O LEU D1523 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU D1527 " --> pdb=" O ASP D1522 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N GLY D1526 " --> pdb=" O VAL D1543 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'D' and resid 2478 through 2481 Processing sheet with id= 88, first strand: chain 'D' and resid 2776 through 2779 Processing sheet with id= 89, first strand: chain 'D' and resid 2822 through 2826 Processing sheet with id= 90, first strand: chain 'D' and resid 4180 through 4187 removed outlier: 4.842A pdb=" N TYR D4180 " --> pdb=" O ILE D4200 " (cutoff:3.500A) Processing sheet with id= 91, first strand: chain 'D' and resid 4579 through 4582 Processing sheet with id= 92, first strand: chain 'D' and resid 1088 through 1091 Processing sheet with id= 93, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.754A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'E' and resid 22 through 25 removed outlier: 3.694A pdb=" N LYS E 106 " --> pdb=" O VAL E 24 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'F' and resid 3 through 8 removed outlier: 6.777A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'F' and resid 22 through 25 removed outlier: 3.670A pdb=" N LYS F 106 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.756A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'G' and resid 22 through 25 removed outlier: 3.659A pdb=" N LYS G 106 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'H' and resid 3 through 8 removed outlier: 6.756A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.675A pdb=" N LYS H 106 " --> pdb=" O VAL H 24 " (cutoff:3.500A) 7704 hydrogen bonds defined for protein. 22968 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: 117.02 Time building geometry restraints manager: 45.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 23984 1.31 - 1.44: 38368 1.44 - 1.57: 82539 1.57 - 1.69: 73 1.69 - 1.82: 1516 Bond restraints: 146480 Sorted by residual: bond pdb=" C11 PCW B8006 " pdb=" O3 PCW B8006 " ideal model delta sigma weight residual 1.326 1.422 -0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C11 PCW A8006 " pdb=" O3 PCW A8006 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11 PCW C8006 " pdb=" O3 PCW C8006 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11 PCW D5107 " pdb=" O3 PCW D5107 " ideal model delta sigma weight residual 1.326 1.421 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" C11 PCW D5101 " pdb=" O3 PCW D5101 " ideal model delta sigma weight residual 1.326 1.417 -0.091 2.00e-02 2.50e+03 2.08e+01 ... (remaining 146475 not shown) Histogram of bond angle deviations from ideal: 93.92 - 105.91: 3999 105.91 - 117.90: 107012 117.90 - 129.90: 86305 129.90 - 141.89: 1052 141.89 - 153.89: 8 Bond angle restraints: 198376 Sorted by residual: angle pdb=" C5 PCW C8007 " pdb=" N PCW C8007 " pdb=" C7 PCW C8007 " ideal model delta sigma weight residual 107.31 140.35 -33.04 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C5 PCW A8007 " pdb=" N PCW A8007 " pdb=" C7 PCW A8007 " ideal model delta sigma weight residual 107.31 140.33 -33.02 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C5 PCW D5101 " pdb=" N PCW D5101 " pdb=" C7 PCW D5101 " ideal model delta sigma weight residual 107.31 140.32 -33.01 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C5 PCW B8007 " pdb=" N PCW B8007 " pdb=" C7 PCW B8007 " ideal model delta sigma weight residual 107.31 140.29 -32.98 3.00e+00 1.11e-01 1.21e+02 angle pdb=" C6 PCW B8006 " pdb=" N PCW B8006 " pdb=" C8 PCW B8006 " ideal model delta sigma weight residual 109.11 141.14 -32.03 3.00e+00 1.11e-01 1.14e+02 ... (remaining 198371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 80311 17.69 - 35.37: 6503 35.37 - 53.06: 1146 53.06 - 70.75: 432 70.75 - 88.43: 172 Dihedral angle restraints: 88564 sinusoidal: 36604 harmonic: 51960 Sorted by residual: dihedral pdb=" CB CYS D3171 " pdb=" SG CYS D3171 " pdb=" SG CYS D3241 " pdb=" CB CYS D3241 " ideal model delta sinusoidal sigma weight residual -86.00 -132.00 46.00 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS C3171 " pdb=" SG CYS C3171 " pdb=" SG CYS C3241 " pdb=" CB CYS C3241 " ideal model delta sinusoidal sigma weight residual -86.00 -132.00 46.00 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS A3171 " pdb=" SG CYS A3171 " pdb=" SG CYS A3241 " pdb=" CB CYS A3241 " ideal model delta sinusoidal sigma weight residual -86.00 -132.00 46.00 1 1.00e+01 1.00e-02 2.93e+01 ... (remaining 88561 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 19290 0.058 - 0.116: 2242 0.116 - 0.174: 188 0.174 - 0.232: 12 0.232 - 0.290: 12 Chirality restraints: 21744 Sorted by residual: chirality pdb=" C2' ATP A8005 " pdb=" C1' ATP A8005 " pdb=" C3' ATP A8005 " pdb=" O2' ATP A8005 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' ATP C8005 " pdb=" C1' ATP C8005 " pdb=" C3' ATP C8005 " pdb=" O2' ATP C8005 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2' ATP D5106 " pdb=" C1' ATP D5106 " pdb=" C3' ATP D5106 " pdb=" O2' ATP D5106 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 21741 not shown) Planarity restraints: 25732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D1055 " -0.022 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C GLU D1055 " 0.075 2.00e-02 2.50e+03 pdb=" O GLU D1055 " -0.027 2.00e-02 2.50e+03 pdb=" N PRO D1056 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1055 " 0.022 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C GLU B1055 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU B1055 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B1056 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1055 " 0.022 2.00e-02 2.50e+03 4.31e-02 1.85e+01 pdb=" C GLU A1055 " -0.075 2.00e-02 2.50e+03 pdb=" O GLU A1055 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO A1056 " 0.025 2.00e-02 2.50e+03 ... (remaining 25729 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 750 2.54 - 3.13: 114642 3.13 - 3.72: 231974 3.72 - 4.31: 325072 4.31 - 4.90: 542636 Nonbonded interactions: 1215074 Sorted by model distance: nonbonded pdb=" OE2 GLU D3456 " pdb=" OG SER D3509 " model vdw 1.955 2.440 nonbonded pdb=" OE2 GLU A3456 " pdb=" OG SER A3509 " model vdw 1.956 2.440 nonbonded pdb=" OE2 GLU C3456 " pdb=" OG SER C3509 " model vdw 1.956 2.440 nonbonded pdb=" OE2 GLU B3456 " pdb=" OG SER B3509 " model vdw 1.957 2.440 nonbonded pdb=" OE2 GLU D3208 " pdb=" OG1 THR D3306 " model vdw 1.968 2.440 ... (remaining 1215069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 5035 or resid 8007)) selection = (chain 'B' and (resid 11 through 5035 or resid 8007)) selection = (chain 'C' and (resid 11 through 5035 or resid 8007)) selection = (chain 'D' and (resid 11 through 5035 or resid 5107)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 30.340 Check model and map are aligned: 1.570 Set scattering table: 1.010 Process input model: 408.000 Find NCS groups from input model: 11.000 Set up NCS constraints: 0.890 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 470.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.003 0.096 146480 Z= 0.206 Angle : 0.691 33.044 198376 Z= 0.351 Chirality : 0.037 0.290 21744 Planarity : 0.004 0.068 25732 Dihedral : 14.127 88.435 54996 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.05 % Allowed : 0.17 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 2.22 (0.06), residues: 17800 helix: 2.48 (0.05), residues: 9368 sheet: 0.41 (0.13), residues: 1784 loop : 0.39 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP B1144 HIS 0.012 0.001 HIS D2884 PHE 0.029 0.001 PHE A2798 TYR 0.019 0.001 TYR D2257 ARG 0.017 0.000 ARG C3349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1122 time to evaluate : 12.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2945 MET cc_start: 0.6764 (mpp) cc_final: 0.6311 (ptp) REVERT: A 3466 ASN cc_start: 0.8452 (t0) cc_final: 0.7906 (t0) REVERT: A 3558 LEU cc_start: 0.8145 (pt) cc_final: 0.7877 (pp) REVERT: A 3656 GLU cc_start: 0.8055 (tp30) cc_final: 0.7826 (tp30) REVERT: B 2178 LEU cc_start: 0.9210 (tp) cc_final: 0.9005 (tp) REVERT: B 2945 MET cc_start: 0.6720 (mpp) cc_final: 0.6290 (ptp) REVERT: B 3466 ASN cc_start: 0.8386 (t0) cc_final: 0.7848 (t0) REVERT: B 3558 LEU cc_start: 0.8112 (pt) cc_final: 0.7838 (pp) REVERT: B 4691 GLU cc_start: 0.8051 (tp30) cc_final: 0.7497 (tm-30) REVERT: C 2945 MET cc_start: 0.6789 (mpp) cc_final: 0.6320 (ptp) REVERT: C 3466 ASN cc_start: 0.8401 (t0) cc_final: 0.7864 (t0) REVERT: C 3558 LEU cc_start: 0.8195 (pt) cc_final: 0.7926 (pp) REVERT: C 3656 GLU cc_start: 0.8064 (tp30) cc_final: 0.7836 (tp30) REVERT: D 2945 MET cc_start: 0.6782 (mpp) cc_final: 0.6338 (ptp) REVERT: D 3466 ASN cc_start: 0.8415 (t0) cc_final: 0.7868 (t0) REVERT: D 3656 GLU cc_start: 0.8062 (tp30) cc_final: 0.7834 (tp30) outliers start: 8 outliers final: 0 residues processed: 1126 average time/residue: 2.2647 time to fit residues: 3576.8882 Evaluate side-chains 888 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 888 time to evaluate : 11.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1509 optimal weight: 10.0000 chunk 1355 optimal weight: 8.9990 chunk 751 optimal weight: 7.9990 chunk 462 optimal weight: 9.9990 chunk 914 optimal weight: 10.0000 chunk 724 optimal weight: 2.9990 chunk 1401 optimal weight: 6.9990 chunk 542 optimal weight: 3.9990 chunk 852 optimal weight: 3.9990 chunk 1043 optimal weight: 7.9990 chunk 1623 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 682 HIS A 825 GLN A 905 HIS A 920 ASN A1245 GLN A1275 HIS A1421 ASN A2521 HIS A2764 HIS A3070 HIS ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3873 ASN A3898 HIS A4226 ASN B 682 HIS B 736 GLN B 825 GLN B 905 HIS B 920 ASN B1245 GLN B1275 HIS B1421 ASN B1430 ASN B2521 HIS B2764 HIS B3070 HIS ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3873 ASN B3898 HIS B4226 ASN C 682 HIS C 905 HIS C 920 ASN C1245 GLN C1275 HIS C1421 ASN C2521 HIS C2764 HIS C3070 HIS ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3873 ASN C3898 HIS C4226 ASN D 682 HIS D 825 GLN D 905 HIS D 920 ASN D1245 GLN D1275 HIS D1421 ASN D2521 HIS D2764 HIS D3070 HIS D3344 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3873 ASN D3898 HIS D4226 ASN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 146480 Z= 0.499 Angle : 0.618 11.227 198376 Z= 0.313 Chirality : 0.044 0.223 21744 Planarity : 0.005 0.072 25732 Dihedral : 6.808 89.176 20100 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.04 % Favored : 97.93 % Rotamer: Outliers : 0.94 % Allowed : 5.07 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 2.00 (0.06), residues: 17800 helix: 2.27 (0.05), residues: 9376 sheet: 0.40 (0.12), residues: 1736 loop : 0.30 (0.08), residues: 6688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D1144 HIS 0.013 0.001 HIS B 682 PHE 0.031 0.002 PHE A2974 TYR 0.025 0.002 TYR C2554 ARG 0.013 0.001 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 906 time to evaluate : 10.884 Fit side-chains revert: symmetry clash REVERT: A 2875 MET cc_start: 0.7834 (mpp) cc_final: 0.7568 (mpt) REVERT: A 2945 MET cc_start: 0.6487 (mpp) cc_final: 0.5991 (ptp) REVERT: A 3466 ASN cc_start: 0.8359 (t0) cc_final: 0.7729 (t0) REVERT: A 3543 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8902 (mp) REVERT: A 3656 GLU cc_start: 0.8143 (tp30) cc_final: 0.7904 (tp30) REVERT: A 3683 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7439 (tm-30) REVERT: A 3878 MET cc_start: 0.8992 (mmt) cc_final: 0.8775 (mmt) REVERT: A 4691 GLU cc_start: 0.8086 (tp30) cc_final: 0.7601 (tm-30) REVERT: A 4730 PHE cc_start: 0.8302 (t80) cc_final: 0.8077 (t80) REVERT: E 58 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8191 (ttp80) REVERT: F 58 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8179 (ttp80) REVERT: G 58 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8211 (ttp80) REVERT: H 58 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8211 (ttp80) REVERT: B 1171 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8151 (mtm) REVERT: B 2178 LEU cc_start: 0.9231 (tp) cc_final: 0.9030 (tp) REVERT: B 2945 MET cc_start: 0.6600 (mpp) cc_final: 0.6089 (ptp) REVERT: B 3466 ASN cc_start: 0.8349 (t0) cc_final: 0.7680 (t0) REVERT: B 3543 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8942 (mp) REVERT: B 3878 MET cc_start: 0.9015 (mmt) cc_final: 0.8652 (mmt) REVERT: B 4235 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8292 (tt0) REVERT: B 4691 GLU cc_start: 0.8122 (tp30) cc_final: 0.7577 (tm-30) REVERT: B 4730 PHE cc_start: 0.8267 (t80) cc_final: 0.8055 (t80) REVERT: C 1171 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: C 2178 LEU cc_start: 0.9236 (tp) cc_final: 0.9034 (tp) REVERT: C 2875 MET cc_start: 0.7936 (mpp) cc_final: 0.7643 (mpt) REVERT: C 2945 MET cc_start: 0.6572 (mpp) cc_final: 0.6095 (ptp) REVERT: C 3466 ASN cc_start: 0.8381 (t0) cc_final: 0.7728 (t0) REVERT: C 3543 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8892 (mp) REVERT: C 3656 GLU cc_start: 0.8171 (tp30) cc_final: 0.7927 (tp30) REVERT: C 3683 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7438 (tm-30) REVERT: C 3878 MET cc_start: 0.8995 (mmt) cc_final: 0.8770 (mmt) REVERT: C 4691 GLU cc_start: 0.8103 (tp30) cc_final: 0.7597 (tm-30) REVERT: C 4730 PHE cc_start: 0.8297 (t80) cc_final: 0.8069 (t80) REVERT: D 1171 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8145 (mtm) REVERT: D 2875 MET cc_start: 0.7897 (mpp) cc_final: 0.7609 (mpt) REVERT: D 2945 MET cc_start: 0.6572 (mpp) cc_final: 0.6139 (ptp) REVERT: D 3466 ASN cc_start: 0.8378 (t0) cc_final: 0.7713 (t0) REVERT: D 3543 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8922 (mp) REVERT: D 3656 GLU cc_start: 0.8161 (tp30) cc_final: 0.7916 (tp30) REVERT: D 3683 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7437 (tm-30) REVERT: D 3878 MET cc_start: 0.9021 (mmt) cc_final: 0.8664 (mmt) REVERT: D 4691 GLU cc_start: 0.8090 (tp30) cc_final: 0.7599 (tm-30) REVERT: D 4730 PHE cc_start: 0.8298 (t80) cc_final: 0.8072 (t80) outliers start: 147 outliers final: 43 residues processed: 968 average time/residue: 2.2973 time to fit residues: 3230.5585 Evaluate side-chains 929 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 874 time to evaluate : 11.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 989 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 3394 LEU Chi-restraints excluded: chain A residue 3543 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 1047 LEU Chi-restraints excluded: chain B residue 1171 MET Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 2229 MET Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 3184 VAL Chi-restraints excluded: chain B residue 3394 LEU Chi-restraints excluded: chain B residue 3543 LEU Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 1171 MET Chi-restraints excluded: chain C residue 1429 LEU Chi-restraints excluded: chain C residue 3394 LEU Chi-restraints excluded: chain C residue 3543 LEU Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 1171 MET Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 3184 VAL Chi-restraints excluded: chain D residue 3394 LEU Chi-restraints excluded: chain D residue 3543 LEU Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 902 optimal weight: 3.9990 chunk 503 optimal weight: 3.9990 chunk 1351 optimal weight: 10.0000 chunk 1105 optimal weight: 0.9990 chunk 447 optimal weight: 7.9990 chunk 1626 optimal weight: 4.9990 chunk 1757 optimal weight: 10.0000 chunk 1448 optimal weight: 0.8980 chunk 1613 optimal weight: 50.0000 chunk 554 optimal weight: 5.9990 chunk 1304 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A2934 ASN A3344 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A3930 GLN A4037 ASN A4226 ASN B 309 HIS B 736 GLN ** B 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3344 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4037 ASN B4226 ASN C 309 HIS C 825 GLN ** C 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C2934 ASN C3344 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4037 ASN C4226 ASN D 309 HIS D1421 ASN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4037 ASN D4226 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 146480 Z= 0.235 Angle : 0.502 11.515 198376 Z= 0.257 Chirality : 0.038 0.164 21744 Planarity : 0.004 0.050 25732 Dihedral : 6.550 86.505 20100 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.68 % Favored : 98.30 % Rotamer: Outliers : 0.75 % Allowed : 6.76 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 2.13 (0.06), residues: 17800 helix: 2.41 (0.05), residues: 9400 sheet: 0.35 (0.12), residues: 1724 loop : 0.33 (0.08), residues: 6676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D3572 HIS 0.006 0.001 HIS D3774 PHE 0.032 0.001 PHE C2974 TYR 0.021 0.001 TYR B 894 ARG 0.014 0.000 ARG G 14 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 892 time to evaluate : 12.224 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: A 378 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7957 (ppp) REVERT: A 2945 MET cc_start: 0.6422 (mpp) cc_final: 0.5823 (ptp) REVERT: A 3466 ASN cc_start: 0.8382 (t0) cc_final: 0.7705 (t0) REVERT: A 3656 GLU cc_start: 0.8142 (tp30) cc_final: 0.7897 (tp30) REVERT: A 3878 MET cc_start: 0.8801 (mmt) cc_final: 0.8587 (mmt) REVERT: A 4691 GLU cc_start: 0.8070 (tp30) cc_final: 0.7597 (tm-30) REVERT: E 60 TRP cc_start: 0.9352 (OUTLIER) cc_final: 0.8710 (m100) REVERT: F 60 TRP cc_start: 0.9350 (OUTLIER) cc_final: 0.8697 (m100) REVERT: G 60 TRP cc_start: 0.9358 (OUTLIER) cc_final: 0.8705 (m100) REVERT: H 60 TRP cc_start: 0.9356 (OUTLIER) cc_final: 0.8682 (m100) REVERT: B 378 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.7970 (ppp) REVERT: B 2178 LEU cc_start: 0.9212 (tp) cc_final: 0.8861 (mm) REVERT: B 2503 MET cc_start: 0.8960 (mmt) cc_final: 0.8632 (mmt) REVERT: B 2945 MET cc_start: 0.6562 (mpp) cc_final: 0.6004 (ptp) REVERT: B 3466 ASN cc_start: 0.8358 (t0) cc_final: 0.7656 (t0) REVERT: B 3878 MET cc_start: 0.8825 (mmt) cc_final: 0.8589 (mmt) REVERT: B 4691 GLU cc_start: 0.8096 (tp30) cc_final: 0.7600 (tm-30) REVERT: C 378 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7966 (ppp) REVERT: C 2178 LEU cc_start: 0.9216 (tp) cc_final: 0.8864 (mm) REVERT: C 2945 MET cc_start: 0.6550 (mpp) cc_final: 0.5969 (ptp) REVERT: C 3466 ASN cc_start: 0.8379 (t0) cc_final: 0.7696 (t0) REVERT: C 3656 GLU cc_start: 0.8144 (tp30) cc_final: 0.7915 (tp30) REVERT: C 3878 MET cc_start: 0.8794 (mmt) cc_final: 0.8580 (mmt) REVERT: C 4691 GLU cc_start: 0.8085 (tp30) cc_final: 0.7601 (tm-30) REVERT: D 378 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7976 (ppp) REVERT: D 2945 MET cc_start: 0.6504 (mpp) cc_final: 0.5941 (ptp) REVERT: D 3466 ASN cc_start: 0.8363 (t0) cc_final: 0.7669 (t0) REVERT: D 3656 GLU cc_start: 0.8141 (tp30) cc_final: 0.7896 (tp30) REVERT: D 3878 MET cc_start: 0.8822 (mmt) cc_final: 0.8583 (mmt) REVERT: D 4691 GLU cc_start: 0.8085 (tp30) cc_final: 0.7606 (tm-30) outliers start: 117 outliers final: 35 residues processed: 946 average time/residue: 2.1304 time to fit residues: 2902.1086 Evaluate side-chains 908 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 865 time to evaluate : 11.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 3184 VAL Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 3184 VAL Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1607 optimal weight: 50.0000 chunk 1222 optimal weight: 10.0000 chunk 844 optimal weight: 3.9990 chunk 180 optimal weight: 30.0000 chunk 776 optimal weight: 6.9990 chunk 1092 optimal weight: 6.9990 chunk 1632 optimal weight: 3.9990 chunk 1728 optimal weight: 0.9990 chunk 852 optimal weight: 6.9990 chunk 1547 optimal weight: 0.9980 chunk 465 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A1430 ASN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN ** B 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2934 ASN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C1430 ASN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C3930 GLN C4226 ASN ** D 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D2934 ASN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 146480 Z= 0.347 Angle : 0.534 13.217 198376 Z= 0.270 Chirality : 0.040 0.174 21744 Planarity : 0.004 0.061 25732 Dihedral : 6.442 85.230 20100 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.00 % Favored : 97.98 % Rotamer: Outliers : 1.05 % Allowed : 7.50 % Favored : 91.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 2.04 (0.06), residues: 17800 helix: 2.35 (0.05), residues: 9420 sheet: 0.34 (0.12), residues: 1664 loop : 0.25 (0.08), residues: 6716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3572 HIS 0.009 0.001 HIS D3700 PHE 0.031 0.001 PHE D2974 TYR 0.017 0.001 TYR C 894 ARG 0.014 0.000 ARG A1997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1058 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 894 time to evaluate : 12.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 378 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7944 (ppp) REVERT: A 2875 MET cc_start: 0.7942 (tpp) cc_final: 0.6922 (mpp) REVERT: A 2945 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.5821 (ptp) REVERT: A 3454 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.8077 (ptm160) REVERT: A 3466 ASN cc_start: 0.8391 (t0) cc_final: 0.7712 (t0) REVERT: A 3543 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 3656 GLU cc_start: 0.8176 (tp30) cc_final: 0.7916 (tp30) REVERT: A 3861 MET cc_start: 0.2902 (OUTLIER) cc_final: 0.1124 (tpt) REVERT: A 4235 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: A 4691 GLU cc_start: 0.8071 (tp30) cc_final: 0.7576 (tm-30) REVERT: E 60 TRP cc_start: 0.9403 (OUTLIER) cc_final: 0.8716 (m100) REVERT: F 60 TRP cc_start: 0.9413 (OUTLIER) cc_final: 0.8662 (m100) REVERT: G 60 TRP cc_start: 0.9413 (OUTLIER) cc_final: 0.8657 (m100) REVERT: H 60 TRP cc_start: 0.9411 (OUTLIER) cc_final: 0.8738 (m100) REVERT: B 378 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.7952 (ppp) REVERT: B 2178 LEU cc_start: 0.9217 (tp) cc_final: 0.8896 (mm) REVERT: B 3454 ARG cc_start: 0.8311 (ttp-110) cc_final: 0.8061 (ptm160) REVERT: B 3462 GLN cc_start: 0.8422 (mp10) cc_final: 0.8208 (mp10) REVERT: B 3466 ASN cc_start: 0.8367 (t0) cc_final: 0.7644 (t0) REVERT: B 3543 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8825 (mp) REVERT: B 3861 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.1156 (tpt) REVERT: B 4235 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: B 4691 GLU cc_start: 0.8095 (tp30) cc_final: 0.7593 (tm-30) REVERT: C 378 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.7950 (ppp) REVERT: C 2875 MET cc_start: 0.7988 (tpp) cc_final: 0.6952 (mpp) REVERT: C 3454 ARG cc_start: 0.8343 (ttp-110) cc_final: 0.8083 (ptm160) REVERT: C 3462 GLN cc_start: 0.8411 (mp10) cc_final: 0.8208 (mp10) REVERT: C 3466 ASN cc_start: 0.8368 (t0) cc_final: 0.7658 (t0) REVERT: C 3543 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8819 (mp) REVERT: C 3656 GLU cc_start: 0.8193 (tp30) cc_final: 0.7946 (tp30) REVERT: C 3861 MET cc_start: 0.2904 (OUTLIER) cc_final: 0.1189 (tpt) REVERT: C 4235 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: C 4691 GLU cc_start: 0.8082 (tp30) cc_final: 0.7580 (tm-30) REVERT: D 2875 MET cc_start: 0.7952 (tpp) cc_final: 0.6900 (mpp) REVERT: D 3466 ASN cc_start: 0.8354 (t0) cc_final: 0.7641 (t0) REVERT: D 3543 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8827 (mp) REVERT: D 3656 GLU cc_start: 0.8190 (tp30) cc_final: 0.7928 (tp30) REVERT: D 3861 MET cc_start: 0.2884 (OUTLIER) cc_final: 0.1158 (tpt) REVERT: D 4235 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: D 4691 GLU cc_start: 0.8079 (tp30) cc_final: 0.7576 (tm-30) outliers start: 164 outliers final: 55 residues processed: 1005 average time/residue: 2.1182 time to fit residues: 3079.0170 Evaluate side-chains 958 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 883 time to evaluate : 11.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3543 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3861 MET Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4235 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3543 LEU Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1071 ASP Chi-restraints excluded: chain C residue 1429 LEU Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3543 LEU Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4235 GLU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3543 LEU Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4235 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1439 optimal weight: 9.9990 chunk 981 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 1286 optimal weight: 5.9990 chunk 713 optimal weight: 0.9980 chunk 1474 optimal weight: 7.9990 chunk 1194 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 882 optimal weight: 0.9990 chunk 1551 optimal weight: 10.0000 chunk 436 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN B 736 GLN ** B 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 HIS ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C3609 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4226 ASN ** D 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D1430 ASN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 146480 Z= 0.393 Angle : 0.549 13.650 198376 Z= 0.278 Chirality : 0.041 0.182 21744 Planarity : 0.004 0.064 25732 Dihedral : 6.404 85.430 20100 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.88 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 8.22 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.97 (0.06), residues: 17800 helix: 2.31 (0.05), residues: 9396 sheet: 0.30 (0.13), residues: 1640 loop : 0.20 (0.08), residues: 6764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3572 HIS 0.010 0.001 HIS B3700 PHE 0.030 0.002 PHE C2974 TYR 0.016 0.001 TYR A 894 ARG 0.014 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 911 time to evaluate : 12.183 Fit side-chains revert: symmetry clash REVERT: A 221 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 378 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8016 (ppp) REVERT: A 2875 MET cc_start: 0.7966 (tpp) cc_final: 0.6909 (mpp) REVERT: A 2945 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5740 (ptp) REVERT: A 3208 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8717 (pt0) REVERT: A 3356 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7652 (tpp80) REVERT: A 3454 ARG cc_start: 0.8365 (ttp-110) cc_final: 0.8087 (ptm160) REVERT: A 3466 ASN cc_start: 0.8378 (t0) cc_final: 0.7730 (t0) REVERT: A 3543 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8807 (mp) REVERT: A 3656 GLU cc_start: 0.8208 (tp30) cc_final: 0.7930 (tp30) REVERT: A 3861 MET cc_start: 0.2841 (OUTLIER) cc_final: 0.1074 (mmm) REVERT: A 4235 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8268 (tt0) REVERT: A 4691 GLU cc_start: 0.8146 (tp30) cc_final: 0.7597 (tm-30) REVERT: E 7 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.9086 (t) REVERT: E 60 TRP cc_start: 0.9401 (OUTLIER) cc_final: 0.8604 (m100) REVERT: H 60 TRP cc_start: 0.9408 (OUTLIER) cc_final: 0.8621 (m100) REVERT: B 221 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8781 (pp) REVERT: B 378 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8020 (ppp) REVERT: B 2875 MET cc_start: 0.7670 (mmm) cc_final: 0.6510 (mpp) REVERT: B 2945 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.5863 (ptp) REVERT: B 3167 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8146 (m-80) REVERT: B 3208 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8743 (pt0) REVERT: B 3356 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7702 (tpp80) REVERT: B 3454 ARG cc_start: 0.8356 (ttp-110) cc_final: 0.8079 (ptm160) REVERT: B 3462 GLN cc_start: 0.8443 (mp10) cc_final: 0.8211 (mp10) REVERT: B 3466 ASN cc_start: 0.8361 (t0) cc_final: 0.7662 (t0) REVERT: B 3543 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8805 (mp) REVERT: B 3861 MET cc_start: 0.2882 (OUTLIER) cc_final: 0.1081 (mmm) REVERT: B 4235 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8281 (tt0) REVERT: C 378 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.8021 (ppp) REVERT: C 2875 MET cc_start: 0.7995 (tpp) cc_final: 0.6958 (mpp) REVERT: C 2945 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5797 (ptp) REVERT: C 3208 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: C 3356 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7709 (tpp80) REVERT: C 3454 ARG cc_start: 0.8350 (ttp-110) cc_final: 0.8083 (ptm160) REVERT: C 3462 GLN cc_start: 0.8447 (mp10) cc_final: 0.8235 (mp10) REVERT: C 3466 ASN cc_start: 0.8363 (t0) cc_final: 0.7697 (t0) REVERT: C 3543 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8801 (mp) REVERT: C 3656 GLU cc_start: 0.8197 (tp30) cc_final: 0.7924 (tp30) REVERT: C 3861 MET cc_start: 0.2835 (OUTLIER) cc_final: 0.1028 (mmm) REVERT: C 4235 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: C 4691 GLU cc_start: 0.8152 (tp30) cc_final: 0.7601 (tm-30) REVERT: D 378 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8034 (ppp) REVERT: D 2875 MET cc_start: 0.7936 (tpp) cc_final: 0.6942 (mpp) REVERT: D 2945 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5823 (ptp) REVERT: D 3208 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8729 (pt0) REVERT: D 3240 MET cc_start: 0.7698 (tpp) cc_final: 0.7469 (mmt) REVERT: D 3356 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7658 (tpp80) REVERT: D 3454 ARG cc_start: 0.8391 (ptm160) cc_final: 0.8161 (ptm160) REVERT: D 3466 ASN cc_start: 0.8358 (t0) cc_final: 0.7684 (t0) REVERT: D 3543 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8804 (mp) REVERT: D 3656 GLU cc_start: 0.8207 (tp30) cc_final: 0.7931 (tp30) REVERT: D 3861 MET cc_start: 0.2825 (OUTLIER) cc_final: 0.1028 (mmm) REVERT: D 4235 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8267 (tt0) REVERT: D 4691 GLU cc_start: 0.8152 (tp30) cc_final: 0.7598 (tm-30) outliers start: 156 outliers final: 72 residues processed: 1008 average time/residue: 2.1839 time to fit residues: 3181.1568 Evaluate side-chains 990 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 888 time to evaluate : 12.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3543 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3861 MET Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4235 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3167 TYR Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3543 LEU Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3754 VAL Chi-restraints excluded: chain B residue 3861 MET Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1429 LEU Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3543 LEU Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3861 MET Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4235 GLU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 788 ILE Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1071 ASP Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3543 LEU Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3861 MET Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4235 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 581 optimal weight: 7.9990 chunk 1556 optimal weight: 4.9990 chunk 341 optimal weight: 6.9990 chunk 1014 optimal weight: 4.9990 chunk 426 optimal weight: 2.9990 chunk 1729 optimal weight: 10.0000 chunk 1436 optimal weight: 20.0000 chunk 800 optimal weight: 10.0000 chunk 143 optimal weight: 0.8980 chunk 572 optimal weight: 10.0000 chunk 908 optimal weight: 9.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 HIS A 905 HIS ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN B 839 HIS B 905 HIS ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN C 839 HIS C 905 HIS ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C3609 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4226 ASN D 839 HIS D 905 HIS ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D2621 GLN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 146480 Z= 0.409 Angle : 0.557 14.275 198376 Z= 0.281 Chirality : 0.041 0.195 21744 Planarity : 0.004 0.070 25732 Dihedral : 6.377 85.604 20100 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.02 % Favored : 97.96 % Rotamer: Outliers : 1.28 % Allowed : 8.73 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.92 (0.06), residues: 17800 helix: 2.28 (0.05), residues: 9372 sheet: 0.28 (0.13), residues: 1640 loop : 0.15 (0.08), residues: 6788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A3572 HIS 0.007 0.001 HIS B3700 PHE 0.030 0.002 PHE A2974 TYR 0.016 0.001 TYR B 894 ARG 0.017 0.000 ARG B1997 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 905 time to evaluate : 12.182 Fit side-chains REVERT: A 221 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8714 (pp) REVERT: A 378 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8014 (ppp) REVERT: A 2875 MET cc_start: 0.7941 (tpp) cc_final: 0.6895 (mpp) REVERT: A 2945 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.5637 (ptp) REVERT: A 3208 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8711 (pt0) REVERT: A 3454 ARG cc_start: 0.8368 (ttp-110) cc_final: 0.8100 (ptm160) REVERT: A 3466 ASN cc_start: 0.8414 (t0) cc_final: 0.7764 (t0) REVERT: A 3656 GLU cc_start: 0.8217 (tp30) cc_final: 0.7938 (tp30) REVERT: A 4235 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8262 (tt0) REVERT: E 7 THR cc_start: 0.9345 (OUTLIER) cc_final: 0.9138 (t) REVERT: E 58 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8332 (ttp80) REVERT: E 60 TRP cc_start: 0.9398 (OUTLIER) cc_final: 0.8663 (m100) REVERT: F 58 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8319 (ttp80) REVERT: G 58 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8308 (ttp80) REVERT: H 58 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: H 60 TRP cc_start: 0.9405 (OUTLIER) cc_final: 0.8659 (m100) REVERT: B 221 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 378 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8017 (ppp) REVERT: B 2875 MET cc_start: 0.7666 (mmm) cc_final: 0.6600 (mpp) REVERT: B 2945 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.5821 (ptp) REVERT: B 3167 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.8166 (m-80) REVERT: B 3208 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: B 3356 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7648 (tpp80) REVERT: B 3454 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.8151 (ptm160) REVERT: B 3466 ASN cc_start: 0.8336 (t0) cc_final: 0.7669 (t0) REVERT: B 4235 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8284 (tt0) REVERT: C 221 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8791 (pp) REVERT: C 378 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8014 (ppp) REVERT: C 2875 MET cc_start: 0.7989 (tpp) cc_final: 0.6994 (mpp) REVERT: C 2945 MET cc_start: 0.6484 (OUTLIER) cc_final: 0.5698 (ptp) REVERT: C 2971 SER cc_start: 0.9201 (m) cc_final: 0.8849 (p) REVERT: C 3167 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.8595 (m-80) REVERT: C 3208 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8753 (pt0) REVERT: C 3356 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7708 (tpp80) REVERT: C 3454 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8155 (ptm160) REVERT: C 3466 ASN cc_start: 0.8377 (t0) cc_final: 0.7720 (t0) REVERT: C 3656 GLU cc_start: 0.8197 (tp30) cc_final: 0.7917 (tp30) REVERT: C 4235 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: D 221 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8772 (pp) REVERT: D 378 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8034 (ppp) REVERT: D 2875 MET cc_start: 0.7915 (tpp) cc_final: 0.6923 (mpp) REVERT: D 2945 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5698 (ptp) REVERT: D 3208 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8704 (pt0) REVERT: D 3454 ARG cc_start: 0.8400 (ptm160) cc_final: 0.8191 (ptm160) REVERT: D 3466 ASN cc_start: 0.8342 (t0) cc_final: 0.7686 (t0) REVERT: D 3656 GLU cc_start: 0.8195 (tp30) cc_final: 0.7914 (tp30) REVERT: D 4235 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8260 (tt0) outliers start: 200 outliers final: 97 residues processed: 1043 average time/residue: 2.1128 time to fit residues: 3195.6853 Evaluate side-chains 1013 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 887 time to evaluate : 12.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1429 LEU Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1930 MET Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4235 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1113 ASP Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3167 TYR Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3754 VAL Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1113 ASP Chi-restraints excluded: chain C residue 1429 LEU Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3167 TYR Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4235 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 788 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1113 ASP Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4235 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1667 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 985 optimal weight: 4.9990 chunk 1263 optimal weight: 1.9990 chunk 978 optimal weight: 0.9990 chunk 1456 optimal weight: 4.9990 chunk 966 optimal weight: 5.9990 chunk 1723 optimal weight: 4.9990 chunk 1078 optimal weight: 3.9990 chunk 1050 optimal weight: 5.9990 chunk 795 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN B 905 HIS ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C2621 GLN C3609 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4226 ASN ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 146480 Z= 0.342 Angle : 0.541 13.848 198376 Z= 0.273 Chirality : 0.040 0.207 21744 Planarity : 0.004 0.074 25732 Dihedral : 6.303 84.282 20100 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.92 % Favored : 98.06 % Rotamer: Outliers : 1.10 % Allowed : 9.26 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.93 (0.06), residues: 17800 helix: 2.30 (0.05), residues: 9396 sheet: 0.26 (0.13), residues: 1640 loop : 0.15 (0.08), residues: 6764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 883 HIS 0.007 0.001 HIS D3774 PHE 0.030 0.001 PHE A2974 TYR 0.014 0.001 TYR A 894 ARG 0.017 0.000 ARG C1997 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 897 time to evaluate : 12.167 Fit side-chains REVERT: A 221 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8693 (pp) REVERT: A 378 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7999 (ppp) REVERT: A 2875 MET cc_start: 0.7939 (tpp) cc_final: 0.6931 (mpp) REVERT: A 2945 MET cc_start: 0.6464 (OUTLIER) cc_final: 0.5651 (ptp) REVERT: A 3208 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8682 (pt0) REVERT: A 3454 ARG cc_start: 0.8357 (ttp-110) cc_final: 0.8085 (ptm160) REVERT: A 3466 ASN cc_start: 0.8378 (t0) cc_final: 0.7741 (t0) REVERT: A 3543 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 3656 GLU cc_start: 0.8210 (tp30) cc_final: 0.7928 (tp30) REVERT: A 4235 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8250 (tt0) REVERT: E 7 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9152 (t) REVERT: E 58 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8355 (ttp80) REVERT: F 58 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8330 (ttp80) REVERT: G 58 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8333 (ttp80) REVERT: H 58 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8362 (ttp80) REVERT: B 221 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 378 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8008 (ppp) REVERT: B 1997 ARG cc_start: 0.8592 (ttp-110) cc_final: 0.8389 (ttm110) REVERT: B 2875 MET cc_start: 0.7682 (mmm) cc_final: 0.6744 (mpp) REVERT: B 2945 MET cc_start: 0.6502 (OUTLIER) cc_final: 0.5767 (ptp) REVERT: B 3208 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8746 (pt0) REVERT: B 3454 ARG cc_start: 0.8391 (ttp-110) cc_final: 0.8188 (ptm160) REVERT: B 3466 ASN cc_start: 0.8385 (t0) cc_final: 0.7716 (t0) REVERT: B 3543 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 3861 MET cc_start: 0.2475 (mpt) cc_final: 0.1148 (mmm) REVERT: B 4235 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: C 221 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8792 (pp) REVERT: C 378 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8005 (ppp) REVERT: C 2875 MET cc_start: 0.7929 (tpp) cc_final: 0.6921 (mpp) REVERT: C 2945 MET cc_start: 0.6450 (OUTLIER) cc_final: 0.5643 (ptp) REVERT: C 2971 SER cc_start: 0.9193 (m) cc_final: 0.8836 (p) REVERT: C 3208 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8744 (pt0) REVERT: C 3454 ARG cc_start: 0.8394 (ttp-110) cc_final: 0.8172 (ptm160) REVERT: C 3466 ASN cc_start: 0.8380 (t0) cc_final: 0.7724 (t0) REVERT: C 3543 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8792 (mp) REVERT: C 3656 GLU cc_start: 0.8193 (tp30) cc_final: 0.7917 (tp30) REVERT: C 3861 MET cc_start: 0.2499 (mpt) cc_final: 0.1148 (mmm) REVERT: C 4235 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: D 221 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8754 (pp) REVERT: D 378 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8022 (ppp) REVERT: D 2875 MET cc_start: 0.7914 (tpp) cc_final: 0.6921 (mpp) REVERT: D 2945 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5653 (ptp) REVERT: D 3208 GLU cc_start: 0.8945 (OUTLIER) cc_final: 0.8722 (pt0) REVERT: D 3466 ASN cc_start: 0.8348 (t0) cc_final: 0.7666 (t0) REVERT: D 3543 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8780 (mp) REVERT: D 3656 GLU cc_start: 0.8192 (tp30) cc_final: 0.7914 (tp30) REVERT: D 3861 MET cc_start: 0.2484 (mpt) cc_final: 0.1143 (mmm) REVERT: D 4235 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8248 (tt0) outliers start: 172 outliers final: 96 residues processed: 1018 average time/residue: 2.1115 time to fit residues: 3115.3784 Evaluate side-chains 1006 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 881 time to evaluate : 12.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2268 MET Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3543 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4235 GLU Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 60 TRP Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 60 TRP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3543 LEU Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3754 VAL Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1113 ASP Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2268 MET Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3543 LEU Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4235 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 788 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1113 ASP Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2268 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3543 LEU Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4235 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1066 optimal weight: 7.9990 chunk 688 optimal weight: 2.9990 chunk 1029 optimal weight: 9.9990 chunk 519 optimal weight: 5.9990 chunk 338 optimal weight: 9.9990 chunk 333 optimal weight: 7.9990 chunk 1095 optimal weight: 9.9990 chunk 1174 optimal weight: 50.0000 chunk 852 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 1354 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A2621 GLN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B2128 GLN B2621 GLN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C3212 ASN C3609 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4226 ASN ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 146480 Z= 0.538 Angle : 0.610 16.164 198376 Z= 0.306 Chirality : 0.043 0.208 21744 Planarity : 0.005 0.078 25732 Dihedral : 6.399 86.878 20100 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 1.14 % Allowed : 9.42 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.06), residues: 17800 helix: 2.20 (0.05), residues: 9360 sheet: 0.14 (0.12), residues: 1664 loop : 0.09 (0.08), residues: 6776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 883 HIS 0.010 0.001 HIS C 839 PHE 0.029 0.002 PHE A2974 TYR 0.017 0.002 TYR C2554 ARG 0.017 0.001 ARG B3226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 887 time to evaluate : 12.245 Fit side-chains REVERT: A 221 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8740 (pp) REVERT: A 1997 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8411 (ttm110) REVERT: A 2875 MET cc_start: 0.7933 (tpp) cc_final: 0.6931 (mpp) REVERT: A 2945 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5647 (ptp) REVERT: A 3208 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8721 (pt0) REVERT: A 3454 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.8117 (ptm160) REVERT: A 3466 ASN cc_start: 0.8400 (t0) cc_final: 0.7797 (t0) REVERT: A 3543 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8804 (mp) REVERT: A 3656 GLU cc_start: 0.8236 (tp30) cc_final: 0.7953 (tp30) REVERT: A 4235 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8282 (tt0) REVERT: E 58 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8345 (ttp80) REVERT: E 60 TRP cc_start: 0.9408 (OUTLIER) cc_final: 0.8660 (m100) REVERT: F 58 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8280 (ttp80) REVERT: G 58 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8335 (ttp80) REVERT: H 58 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8345 (ttp80) REVERT: H 60 TRP cc_start: 0.9411 (OUTLIER) cc_final: 0.8648 (m100) REVERT: B 221 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8783 (pp) REVERT: B 378 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8031 (ppp) REVERT: B 1997 ARG cc_start: 0.8594 (ttp-110) cc_final: 0.8390 (ttm110) REVERT: B 2875 MET cc_start: 0.7661 (mmm) cc_final: 0.6724 (mpp) REVERT: B 2945 MET cc_start: 0.6504 (OUTLIER) cc_final: 0.5750 (ptp) REVERT: B 2971 SER cc_start: 0.9223 (m) cc_final: 0.8893 (p) REVERT: B 3208 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8732 (pt0) REVERT: B 3454 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8207 (ptm160) REVERT: B 3466 ASN cc_start: 0.8371 (t0) cc_final: 0.7739 (t0) REVERT: B 3543 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8812 (mp) REVERT: B 4235 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8299 (tt0) REVERT: C 221 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8803 (pp) REVERT: C 378 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8027 (ppp) REVERT: C 1997 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8409 (ttm110) REVERT: C 2875 MET cc_start: 0.7950 (tpp) cc_final: 0.6919 (mpp) REVERT: C 2933 MET cc_start: 0.4098 (ppp) cc_final: 0.3708 (pmt) REVERT: C 2945 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.5699 (ptp) REVERT: C 2971 SER cc_start: 0.9215 (m) cc_final: 0.8877 (p) REVERT: C 3208 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.8752 (pt0) REVERT: C 3454 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8208 (ptm160) REVERT: C 3466 ASN cc_start: 0.8352 (t0) cc_final: 0.7735 (t0) REVERT: C 3543 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8827 (mp) REVERT: C 3656 GLU cc_start: 0.8221 (tp30) cc_final: 0.7938 (tp30) REVERT: C 4235 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: D 221 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8764 (pp) REVERT: D 378 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8043 (ppp) REVERT: D 1997 ARG cc_start: 0.8628 (ttp-110) cc_final: 0.8414 (ttm110) REVERT: D 2875 MET cc_start: 0.7875 (tpp) cc_final: 0.6876 (mpp) REVERT: D 2945 MET cc_start: 0.6470 (OUTLIER) cc_final: 0.5672 (ptp) REVERT: D 3208 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: D 3466 ASN cc_start: 0.8362 (t0) cc_final: 0.7705 (t0) REVERT: D 3543 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8812 (mp) REVERT: D 3656 GLU cc_start: 0.8237 (tp30) cc_final: 0.7951 (tp30) REVERT: D 4235 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8280 (tt0) outliers start: 177 outliers final: 106 residues processed: 1010 average time/residue: 2.1796 time to fit residues: 3178.4555 Evaluate side-chains 1010 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 875 time to evaluate : 12.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 804 LEU Chi-restraints excluded: chain A residue 855 CYS Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1502 VAL Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2268 MET Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3530 ASP Chi-restraints excluded: chain A residue 3543 LEU Chi-restraints excluded: chain A residue 3554 LEU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain A residue 4235 GLU Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain F residue 58 ARG Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 58 ARG Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 804 LEU Chi-restraints excluded: chain B residue 855 CYS Chi-restraints excluded: chain B residue 912 HIS Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1113 ASP Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 1502 VAL Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2268 MET Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3543 LEU Chi-restraints excluded: chain B residue 3554 LEU Chi-restraints excluded: chain B residue 3754 VAL Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain B residue 4235 GLU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 855 CYS Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1113 ASP Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1502 VAL Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1930 MET Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2268 MET Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3543 LEU Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain C residue 4235 GLU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 788 ILE Chi-restraints excluded: chain D residue 804 LEU Chi-restraints excluded: chain D residue 855 CYS Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1113 ASP Chi-restraints excluded: chain D residue 1429 LEU Chi-restraints excluded: chain D residue 1502 VAL Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2268 MET Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3530 ASP Chi-restraints excluded: chain D residue 3543 LEU Chi-restraints excluded: chain D residue 3554 LEU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Chi-restraints excluded: chain D residue 4235 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1567 optimal weight: 2.9990 chunk 1651 optimal weight: 4.9990 chunk 1506 optimal weight: 0.8980 chunk 1605 optimal weight: 6.9990 chunk 1650 optimal weight: 0.2980 chunk 966 optimal weight: 1.9990 chunk 699 optimal weight: 1.9990 chunk 1261 optimal weight: 0.9990 chunk 492 optimal weight: 3.9990 chunk 1451 optimal weight: 0.6980 chunk 1518 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1421 ASN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN F 71 GLN G 71 GLN B1421 ASN B2128 GLN B3215 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B3930 GLN B4226 ASN C1421 ASN C3609 GLN C4226 ASN D1421 ASN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D3930 GLN D4226 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 146480 Z= 0.160 Angle : 0.513 15.186 198376 Z= 0.257 Chirality : 0.038 0.210 21744 Planarity : 0.004 0.073 25732 Dihedral : 6.121 85.537 20100 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.84 % Favored : 98.14 % Rotamer: Outliers : 0.78 % Allowed : 9.83 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 1.99 (0.06), residues: 17800 helix: 2.38 (0.05), residues: 9392 sheet: 0.17 (0.12), residues: 1688 loop : 0.16 (0.08), residues: 6720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B3286 HIS 0.007 0.001 HIS D3774 PHE 0.032 0.001 PHE A2974 TYR 0.017 0.001 TYR C 894 ARG 0.019 0.000 ARG B3226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1047 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 926 time to evaluate : 10.943 Fit side-chains REVERT: A 221 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8662 (pp) REVERT: A 1997 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8342 (ttm110) REVERT: A 2875 MET cc_start: 0.7921 (tpp) cc_final: 0.6943 (mpp) REVERT: A 2933 MET cc_start: 0.4188 (ppp) cc_final: 0.3830 (pmt) REVERT: A 2945 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.5616 (ptp) REVERT: A 3208 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8707 (pt0) REVERT: A 3240 MET cc_start: 0.7349 (tpp) cc_final: 0.7139 (mmm) REVERT: A 3466 ASN cc_start: 0.8347 (t0) cc_final: 0.7758 (t0) REVERT: A 3656 GLU cc_start: 0.8171 (tp30) cc_final: 0.7895 (tp30) REVERT: A 3861 MET cc_start: 0.2918 (tpp) cc_final: 0.2536 (tpt) REVERT: B 221 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8742 (pp) REVERT: B 885 LEU cc_start: 0.9412 (tm) cc_final: 0.9168 (mp) REVERT: B 1997 ARG cc_start: 0.8556 (ttp-110) cc_final: 0.8322 (ttm110) REVERT: B 2875 MET cc_start: 0.7679 (mmm) cc_final: 0.6759 (mpp) REVERT: B 2945 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.5670 (ptp) REVERT: B 2971 SER cc_start: 0.9188 (m) cc_final: 0.8809 (p) REVERT: B 3208 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8728 (pt0) REVERT: B 3466 ASN cc_start: 0.8330 (t0) cc_final: 0.7708 (t0) REVERT: B 3861 MET cc_start: 0.3031 (tpp) cc_final: 0.2637 (tpt) REVERT: C 1929 GLN cc_start: 0.8223 (pt0) cc_final: 0.8018 (pm20) REVERT: C 1997 ARG cc_start: 0.8579 (ttp-110) cc_final: 0.8348 (ttm110) REVERT: C 2875 MET cc_start: 0.7955 (tpp) cc_final: 0.6941 (mpp) REVERT: C 2945 MET cc_start: 0.6483 (OUTLIER) cc_final: 0.5639 (ptp) REVERT: C 2971 SER cc_start: 0.9175 (m) cc_final: 0.8802 (p) REVERT: C 3208 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8719 (pt0) REVERT: C 3454 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.8143 (ptm160) REVERT: C 3466 ASN cc_start: 0.8350 (t0) cc_final: 0.7758 (t0) REVERT: C 3656 GLU cc_start: 0.8178 (tp30) cc_final: 0.7904 (tp30) REVERT: C 3861 MET cc_start: 0.3010 (tpp) cc_final: 0.2619 (tpt) REVERT: D 1997 ARG cc_start: 0.8574 (ttp-110) cc_final: 0.8345 (ttm110) REVERT: D 2875 MET cc_start: 0.7884 (tpp) cc_final: 0.6931 (mpp) REVERT: D 2945 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.5638 (ptp) REVERT: D 2971 SER cc_start: 0.9170 (m) cc_final: 0.8792 (p) REVERT: D 3208 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8723 (pt0) REVERT: D 3466 ASN cc_start: 0.8351 (t0) cc_final: 0.7740 (t0) REVERT: D 3656 GLU cc_start: 0.8167 (tp30) cc_final: 0.7889 (tp30) REVERT: D 3861 MET cc_start: 0.2999 (tpp) cc_final: 0.2608 (tpt) outliers start: 121 outliers final: 74 residues processed: 1014 average time/residue: 2.3371 time to fit residues: 3467.3323 Evaluate side-chains 960 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 876 time to evaluate : 11.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1113 ASP Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1113 ASP Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1930 MET Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1113 ASP Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2417 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 1600 optimal weight: 8.9990 chunk 1054 optimal weight: 4.9990 chunk 1698 optimal weight: 4.9990 chunk 1036 optimal weight: 0.0570 chunk 805 optimal weight: 0.8980 chunk 1180 optimal weight: 50.0000 chunk 1781 optimal weight: 2.9990 chunk 1639 optimal weight: 8.9990 chunk 1418 optimal weight: 7.9990 chunk 147 optimal weight: 0.0770 chunk 1095 optimal weight: 9.9990 overall best weight: 1.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3215 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C3609 GLN C4226 ASN ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 146480 Z= 0.217 Angle : 0.523 15.463 198376 Z= 0.260 Chirality : 0.038 0.206 21744 Planarity : 0.004 0.093 25732 Dihedral : 6.061 84.651 20100 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.93 % Favored : 98.06 % Rotamer: Outliers : 0.67 % Allowed : 10.06 % Favored : 89.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.06), residues: 17800 helix: 2.42 (0.05), residues: 9380 sheet: 0.21 (0.12), residues: 1696 loop : 0.16 (0.08), residues: 6724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 883 HIS 0.007 0.001 HIS D3774 PHE 0.031 0.001 PHE A2974 TYR 0.019 0.001 TYR D2257 ARG 0.018 0.000 ARG H 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 35600 Ramachandran restraints generated. 17800 Oldfield, 0 Emsley, 17800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 888 time to evaluate : 12.283 Fit side-chains REVERT: A 221 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8675 (pp) REVERT: A 885 LEU cc_start: 0.9408 (tm) cc_final: 0.9134 (mt) REVERT: A 1997 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8332 (ttm110) REVERT: A 2875 MET cc_start: 0.7906 (tpp) cc_final: 0.6931 (mpp) REVERT: A 2933 MET cc_start: 0.4224 (ppp) cc_final: 0.3850 (pmt) REVERT: A 2945 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5663 (ptt) REVERT: A 2968 MET cc_start: 0.9338 (mmp) cc_final: 0.9064 (mmp) REVERT: A 2971 SER cc_start: 0.9161 (m) cc_final: 0.8784 (p) REVERT: A 3208 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8736 (pt0) REVERT: A 3454 ARG cc_start: 0.8485 (ptm160) cc_final: 0.8164 (ptm160) REVERT: A 3466 ASN cc_start: 0.8373 (t0) cc_final: 0.7800 (t0) REVERT: A 3656 GLU cc_start: 0.8194 (tp30) cc_final: 0.7923 (tp30) REVERT: A 3861 MET cc_start: 0.3056 (tpp) cc_final: 0.2683 (tpt) REVERT: B 1997 ARG cc_start: 0.8568 (ttp-110) cc_final: 0.8321 (ttm110) REVERT: B 2875 MET cc_start: 0.7679 (mmm) cc_final: 0.6801 (mpp) REVERT: B 2945 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5584 (ptp) REVERT: B 2968 MET cc_start: 0.9382 (mmp) cc_final: 0.9044 (mmm) REVERT: B 2971 SER cc_start: 0.9191 (m) cc_final: 0.8776 (p) REVERT: B 3208 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (pt0) REVERT: B 3240 MET cc_start: 0.7255 (tpp) cc_final: 0.6970 (mmm) REVERT: B 3454 ARG cc_start: 0.8400 (ptm160) cc_final: 0.8075 (ptm160) REVERT: B 3466 ASN cc_start: 0.8364 (t0) cc_final: 0.7751 (t0) REVERT: B 3861 MET cc_start: 0.2931 (tpp) cc_final: 0.2536 (tpt) REVERT: C 1997 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.8336 (ttm110) REVERT: C 2875 MET cc_start: 0.7950 (tpp) cc_final: 0.6923 (mpp) REVERT: C 2933 MET cc_start: 0.4127 (ppp) cc_final: 0.3734 (pmt) REVERT: C 2945 MET cc_start: 0.6473 (OUTLIER) cc_final: 0.5695 (ptt) REVERT: C 2971 SER cc_start: 0.9173 (m) cc_final: 0.8806 (p) REVERT: C 3208 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8730 (pt0) REVERT: C 3454 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.8168 (ptm160) REVERT: C 3466 ASN cc_start: 0.8338 (t0) cc_final: 0.7733 (t0) REVERT: C 3656 GLU cc_start: 0.8175 (tp30) cc_final: 0.7922 (tp30) REVERT: C 3861 MET cc_start: 0.3026 (tpp) cc_final: 0.2617 (tpt) REVERT: D 1997 ARG cc_start: 0.8567 (ttp-110) cc_final: 0.8334 (ttm110) REVERT: D 2875 MET cc_start: 0.7870 (tpp) cc_final: 0.6933 (mpp) REVERT: D 2945 MET cc_start: 0.6451 (OUTLIER) cc_final: 0.5620 (ptp) REVERT: D 2971 SER cc_start: 0.9168 (m) cc_final: 0.8792 (p) REVERT: D 3208 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8732 (pt0) REVERT: D 3466 ASN cc_start: 0.8376 (t0) cc_final: 0.7797 (t0) REVERT: D 3656 GLU cc_start: 0.8173 (tp30) cc_final: 0.7906 (tp30) REVERT: D 3861 MET cc_start: 0.3013 (tpp) cc_final: 0.2611 (tpt) outliers start: 104 outliers final: 75 residues processed: 969 average time/residue: 2.1743 time to fit residues: 3043.5646 Evaluate side-chains 949 residues out of total 15608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 865 time to evaluate : 12.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1113 ASP Chi-restraints excluded: chain A residue 1737 VAL Chi-restraints excluded: chain A residue 1967 VAL Chi-restraints excluded: chain A residue 2541 THR Chi-restraints excluded: chain A residue 2945 MET Chi-restraints excluded: chain A residue 3171 CYS Chi-restraints excluded: chain A residue 3208 GLU Chi-restraints excluded: chain A residue 3754 VAL Chi-restraints excluded: chain A residue 3902 PHE Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 33 ASP Chi-restraints excluded: chain E residue 60 TRP Chi-restraints excluded: chain E residue 80 ASP Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 33 ASP Chi-restraints excluded: chain G residue 26 HIS Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 60 TRP Chi-restraints excluded: chain H residue 80 ASP Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 485 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 971 LEU Chi-restraints excluded: chain B residue 1041 CYS Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1113 ASP Chi-restraints excluded: chain B residue 1429 LEU Chi-restraints excluded: chain B residue 1737 VAL Chi-restraints excluded: chain B residue 1930 MET Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2541 THR Chi-restraints excluded: chain B residue 2573 THR Chi-restraints excluded: chain B residue 2945 MET Chi-restraints excluded: chain B residue 3171 CYS Chi-restraints excluded: chain B residue 3176 LEU Chi-restraints excluded: chain B residue 3208 GLU Chi-restraints excluded: chain B residue 3530 ASP Chi-restraints excluded: chain B residue 3902 PHE Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 485 LEU Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1041 CYS Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1113 ASP Chi-restraints excluded: chain C residue 1737 VAL Chi-restraints excluded: chain C residue 1930 MET Chi-restraints excluded: chain C residue 1967 VAL Chi-restraints excluded: chain C residue 2541 THR Chi-restraints excluded: chain C residue 2945 MET Chi-restraints excluded: chain C residue 3171 CYS Chi-restraints excluded: chain C residue 3208 GLU Chi-restraints excluded: chain C residue 3530 ASP Chi-restraints excluded: chain C residue 3554 LEU Chi-restraints excluded: chain C residue 3754 VAL Chi-restraints excluded: chain C residue 3902 PHE Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 971 LEU Chi-restraints excluded: chain D residue 1041 CYS Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1113 ASP Chi-restraints excluded: chain D residue 1737 VAL Chi-restraints excluded: chain D residue 1930 MET Chi-restraints excluded: chain D residue 1967 VAL Chi-restraints excluded: chain D residue 2541 THR Chi-restraints excluded: chain D residue 2573 THR Chi-restraints excluded: chain D residue 2945 MET Chi-restraints excluded: chain D residue 3171 CYS Chi-restraints excluded: chain D residue 3176 LEU Chi-restraints excluded: chain D residue 3208 GLU Chi-restraints excluded: chain D residue 3754 VAL Chi-restraints excluded: chain D residue 3902 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1788 random chunks: chunk 869 optimal weight: 9.9990 chunk 1126 optimal weight: 9.9990 chunk 1510 optimal weight: 7.9990 chunk 434 optimal weight: 5.9990 chunk 1307 optimal weight: 6.9990 chunk 209 optimal weight: 0.0870 chunk 394 optimal weight: 8.9990 chunk 1420 optimal weight: 6.9990 chunk 594 optimal weight: 8.9990 chunk 1458 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1421 ASN ** A3557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3609 GLN ** A3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4226 ASN F 71 GLN G 71 GLN ** B1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1421 ASN B3609 GLN ** B3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4226 ASN ** C1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1421 ASN C3212 ASN C3609 GLN ** C3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4226 ASN ** D1067 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 ASN ** D3557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3609 GLN ** D3774 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D4226 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.046198 restraints weight = 346787.095| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 2.61 r_work: 0.2455 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2302 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 146480 Z= 0.430 Angle : 0.585 15.094 198376 Z= 0.293 Chirality : 0.041 0.212 21744 Planarity : 0.005 0.105 25732 Dihedral : 6.201 83.990 20100 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.79 % Allowed : 10.10 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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 (0.06), residues: 17800 helix: 2.30 (0.05), residues: 9388 sheet: 0.18 (0.13), residues: 1664 loop : 0.11 (0.08), residues: 6748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.001 TRP B3286 HIS 0.008 0.001 HIS B 839 PHE 0.033 0.002 PHE B3553 TYR 0.022 0.002 TYR B2257 ARG 0.018 0.001 ARG D3571 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 47509.81 seconds wall clock time: 823 minutes 48.86 seconds (49428.86 seconds total)