Starting phenix.real_space_refine on Mon Mar 18 16:14:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uq4_42460/03_2024/8uq4_42460_updated.pdb" } resolution = 3.64 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= 0.010 sd= 0.024 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 24 5.49 5 S 936 5.16 5 C 88208 2.51 5 N 23596 2.21 5 O 25840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 680": "OD1" <-> "OD2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 997": "OD1" <-> "OD2" Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1083": "OE1" <-> "OE2" Residue "A ASP 1194": "OD1" <-> "OD2" Residue "A PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1199": "OD1" <-> "OD2" Residue "A PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1741": "OD1" <-> "OD2" Residue "A ASP 2300": "OD1" <-> "OD2" Residue "A PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2511": "OD1" <-> "OD2" Residue "A PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2581": "NH1" <-> "NH2" Residue "A PHE 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2730": "OD1" <-> "OD2" Residue "A TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 3192": "NH1" <-> "NH2" Residue "A GLU 3656": "OE1" <-> "OE2" Residue "A TYR 3688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 4852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 4896": "OD1" <-> "OD2" Residue "A ASP 4964": "OD1" <-> "OD2" Residue "B GLU 50": "OE1" <-> "OE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 680": "OD1" <-> "OD2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 997": "OD1" <-> "OD2" Residue "B TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1083": "OE1" <-> "OE2" Residue "B ASP 1194": "OD1" <-> "OD2" Residue "B PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1199": "OD1" <-> "OD2" Residue "B PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1741": "OD1" <-> "OD2" Residue "B ASP 2300": "OD1" <-> "OD2" Residue "B PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2511": "OD1" <-> "OD2" Residue "B PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2581": "NH1" <-> "NH2" Residue "B PHE 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2730": "OD1" <-> "OD2" Residue "B TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 3192": "NH1" <-> "NH2" Residue "B GLU 3656": "OE1" <-> "OE2" Residue "B TYR 3688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 4852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 4896": "OD1" <-> "OD2" Residue "B ASP 4964": "OD1" <-> "OD2" Residue "C GLU 50": "OE1" <-> "OE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 680": "OD1" <-> "OD2" Residue "C PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 997": "OD1" <-> "OD2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1194": "OD1" <-> "OD2" Residue "C PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1199": "OD1" <-> "OD2" Residue "C PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1741": "OD1" <-> "OD2" Residue "C ASP 2300": "OD1" <-> "OD2" Residue "C PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2511": "OD1" <-> "OD2" Residue "C PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2581": "NH1" <-> "NH2" Residue "C PHE 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2730": "OD1" <-> "OD2" Residue "C TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 3192": "NH1" <-> "NH2" Residue "C GLU 3656": "OE1" <-> "OE2" Residue "C TYR 3688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 4852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 4896": "OD1" <-> "OD2" Residue "C ASP 4964": "OD1" <-> "OD2" Residue "D GLU 50": "OE1" <-> "OE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 680": "OD1" <-> "OD2" Residue "D PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 985": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 997": "OD1" <-> "OD2" Residue "D TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1083": "OE1" <-> "OE2" Residue "D ASP 1194": "OD1" <-> "OD2" Residue "D PHE 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1199": "OD1" <-> "OD2" Residue "D PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1741": "OD1" <-> "OD2" Residue "D ASP 2300": "OD1" <-> "OD2" Residue "D PHE 2471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2511": "OD1" <-> "OD2" Residue "D PHE 2535": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 2581": "NH1" <-> "NH2" Residue "D PHE 2649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2720": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 2730": "OD1" <-> "OD2" Residue "D TYR 2901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 3109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 3192": "NH1" <-> "NH2" Residue "D GLU 3656": "OE1" <-> "OE2" Residue "D TYR 3688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4080": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 4725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4846": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 4852": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 4896": "OD1" <-> "OD2" Residue "D ASP 4964": "OD1" <-> "OD2" Time to flip residues: 0.41s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 138608 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "B" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "C" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "D" Number of atoms: 33771 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Conformer: "B" Number of residues, atoms: 4224, 33763 Classifications: {'peptide': 4224} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 156, 'TRANS': 4067} Chain breaks: 13 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 bond proxies already assigned to first conformer: 34485 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' ZN': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 33092 SG CYS A4888 178.509 177.753 86.312 1.00119.83 S ATOM 33117 SG CYS A4891 178.626 180.514 88.844 1.00116.90 S ATOM 70135 SG CYS B4888 204.140 178.491 86.280 1.00120.03 S ATOM 70160 SG CYS B4891 201.374 178.612 88.806 1.00116.82 S ATOM A030I SG CYS C4888 203.278 204.142 86.266 1.00120.62 S ATOM A0317 SG CYS C4891 203.158 201.377 88.793 1.00116.96 S ATOM A0T2L SG CYS D4888 177.635 203.276 86.267 1.00120.00 S ATOM A0T3A SG CYS D4891 180.401 203.157 88.794 1.00117.07 S Time building chain proxies: 94.97, per 1000 atoms: 0.69 Number of scatterers: 138608 At special positions: 0 Unit cell: (382.63, 382.63, 209.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 936 16.00 P 24 15.00 O 25840 8.00 N 23596 7.00 C 88208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A4806 " - pdb=" SG CYS A4812 " distance=2.03 Simple disulfide: pdb=" SG CYS B4806 " - pdb=" SG CYS B4812 " distance=2.03 Simple disulfide: pdb=" SG CYS C4806 " - pdb=" SG CYS C4812 " distance=2.03 Simple disulfide: pdb=" SG CYS D4806 " - pdb=" SG CYS D4812 " 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: 40.40 Conformation dependent library (CDL) restraints added in 34.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A5001 " pdb="ZN ZN A5001 " - pdb=" ND1 HIS A4913 " pdb="ZN ZN A5001 " - pdb=" NE2 HIS A4908 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4891 " pdb="ZN ZN A5001 " - pdb=" SG CYS A4888 " pdb=" ZN B5001 " pdb="ZN ZN B5001 " - pdb=" ND1 HIS B4913 " pdb="ZN ZN B5001 " - pdb=" NE2 HIS B4908 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4891 " pdb="ZN ZN B5001 " - pdb=" SG CYS B4888 " pdb=" ZN C5001 " pdb="ZN ZN C5001 " - pdb=" ND1 HIS C4913 " pdb="ZN ZN C5001 " - pdb=" NE2 HIS C4908 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4891 " pdb="ZN ZN C5001 " - pdb=" SG CYS C4888 " pdb=" ZN D5001 " pdb="ZN ZN D5001 " - pdb=" ND1 HIS D4913 " pdb="ZN ZN D5001 " - pdb=" NE2 HIS D4908 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4891 " pdb="ZN ZN D5001 " - pdb=" SG CYS D4888 " Number of angles added : 8 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 32464 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: 716 helices and 88 sheets defined 60.1% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 41.00 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 removed outlier: 3.983A pdb=" N CYS A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 84 Processing helix chain 'A' and resid 155 through 160 removed outlier: 4.535A pdb=" N TRP A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 155 through 160' Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.910A pdb=" N THR A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 271 removed outlier: 4.696A pdb=" N VAL A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 409 through 439 removed outlier: 3.598A pdb=" N LYS A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 446 removed outlier: 4.888A pdb=" N ASP A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 471 through 493 Processing helix chain 'A' and resid 494 through 509 removed outlier: 4.256A pdb=" N TYR A 508 " --> pdb=" O ARG A 504 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 518 Processing helix chain 'A' and resid 519 through 542 removed outlier: 4.809A pdb=" N LYS A 527 " --> pdb=" O GLY A 523 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.881A pdb=" N SER A 552 " --> pdb=" O CYS A 548 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.586A pdb=" N SER A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG A 561 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 Processing helix chain 'A' and resid 583 through 590 removed outlier: 5.737A pdb=" N LYS A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 604 removed outlier: 3.711A pdb=" N LEU A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.602A pdb=" N LEU A 611 " --> pdb=" O ASN A 607 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS A 620 " --> pdb=" O SER A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 640 Proline residue: A 638 - end of helix Processing helix chain 'A' and resid 821 through 826 removed outlier: 4.379A pdb=" N ALA A 825 " --> pdb=" O PRO A 821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 878 through 901 removed outlier: 6.426A pdb=" N LYS A 884 " --> pdb=" O ARG A 880 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU A 885 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 947 Processing helix chain 'A' and resid 954 through 961 removed outlier: 3.994A pdb=" N GLU A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A 961 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 972 removed outlier: 5.158A pdb=" N LEU A 972 " --> pdb=" O LYS A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 987 removed outlier: 3.829A pdb=" N ILE A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS A 987 " --> pdb=" O LEU A 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 982 through 987' Processing helix chain 'A' and resid 989 through 1015 removed outlier: 3.692A pdb=" N ASP A 997 " --> pdb=" O GLU A 993 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS A 998 " --> pdb=" O ALA A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1039 through 1061 removed outlier: 4.806A pdb=" N GLY A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.933A pdb=" N LEU A1224 " --> pdb=" O ASP A1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS A1225 " --> pdb=" O VAL A1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1220 through 1225' Processing helix chain 'A' and resid 1229 through 1235 removed outlier: 6.059A pdb=" N GLN A1233 " --> pdb=" O ILE A1229 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A1234 " --> pdb=" O CYS A1230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A1235 " --> pdb=" O GLY A1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1235' Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1437 through 1442 removed outlier: 4.054A pdb=" N VAL A1441 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP A1442 " --> pdb=" O PRO A1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1437 through 1442' Processing helix chain 'A' and resid 1489 through 1495 removed outlier: 3.525A pdb=" N SER A1493 " --> pdb=" O CYS A1489 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER A1495 " --> pdb=" O GLY A1491 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1571 removed outlier: 3.696A pdb=" N GLY A1569 " --> pdb=" O PRO A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1640 through 1648 removed outlier: 4.044A pdb=" N LEU A1644 " --> pdb=" O ASP A1640 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR A1645 " --> pdb=" O ILE A1641 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU A1646 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN A1647 " --> pdb=" O GLU A1643 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU A1648 " --> pdb=" O LEU A1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1640 through 1648' Processing helix chain 'A' and resid 1649 through 1666 removed outlier: 3.541A pdb=" N CYS A1665 " --> pdb=" O TYR A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1680 removed outlier: 3.931A pdb=" N SER A1678 " --> pdb=" O HIS A1674 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS A1679 " --> pdb=" O ALA A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 Processing helix chain 'A' and resid 1695 through 1710 Processing helix chain 'A' and resid 1711 through 1722 removed outlier: 5.282A pdb=" N ALA A1715 " --> pdb=" O LEU A1711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET A1721 " --> pdb=" O ALA A1717 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN A1722 " --> pdb=" O ARG A1718 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1736 removed outlier: 3.788A pdb=" N ILE A1736 " --> pdb=" O GLU A1732 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1805 removed outlier: 3.504A pdb=" N LYS A1800 " --> pdb=" O THR A1796 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N HIS A1805 " --> pdb=" O GLU A1801 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1832 Proline residue: A1820 - end of helix Processing helix chain 'A' and resid 1836 through 1847 Processing helix chain 'A' and resid 1892 through 1897 removed outlier: 3.784A pdb=" N MET A1896 " --> pdb=" O GLY A1892 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS A1897 " --> pdb=" O LEU A1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1892 through 1897' Processing helix chain 'A' and resid 1899 through 1948 removed outlier: 3.712A pdb=" N GLN A1905 " --> pdb=" O PRO A1901 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASP A1931 " --> pdb=" O ALA A1927 " (cutoff:3.500A) Processing helix chain 'A' and resid 1950 through 1955 removed outlier: 3.732A pdb=" N SER A1954 " --> pdb=" O ALA A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 1956 through 1967 removed outlier: 4.172A pdb=" N ARG A1960 " --> pdb=" O ALA A1956 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS A1963 " --> pdb=" O ALA A1959 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU A1964 " --> pdb=" O ARG A1960 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE A1965 " --> pdb=" O LYS A1961 " (cutoff:3.500A) Processing helix chain 'A' and resid 1968 through 1979 removed outlier: 5.292A pdb=" N PHE A1979 " --> pdb=" O MET A1975 " (cutoff:3.500A) Processing helix chain 'A' and resid 1989 through 2008 removed outlier: 3.512A pdb=" N LEU A1996 " --> pdb=" O ILE A1992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A2001 " --> pdb=" O LEU A1997 " (cutoff:3.500A) Processing helix chain 'A' and resid 2057 through 2073 removed outlier: 3.674A pdb=" N VAL A2067 " --> pdb=" O SER A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2094 Processing helix chain 'A' and resid 2095 through 2105 Proline residue: A2103 - end of helix Processing helix chain 'A' and resid 2109 through 2133 removed outlier: 3.925A pdb=" N VAL A2113 " --> pdb=" O ASN A2109 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU A2114 " --> pdb=" O GLY A2110 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP A2115 " --> pdb=" O VAL A2111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A2130 " --> pdb=" O ILE A2126 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER A2131 " --> pdb=" O ARG A2127 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL A2132 " --> pdb=" O SER A2128 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2135 through 2153 removed outlier: 5.518A pdb=" N LYS A2153 " --> pdb=" O ILE A2149 " (cutoff:3.500A) Processing helix chain 'A' and resid 2158 through 2166 Processing helix chain 'A' and resid 2167 through 2183 removed outlier: 4.769A pdb=" N GLY A2182 " --> pdb=" O VAL A2178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU A2183 " --> pdb=" O LEU A2179 " (cutoff:3.500A) Processing helix chain 'A' and resid 2189 through 2208 removed outlier: 3.975A pdb=" N SER A2207 " --> pdb=" O PHE A2203 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG A2208 " --> pdb=" O CYS A2204 " (cutoff:3.500A) Processing helix chain 'A' and resid 2209 through 2219 removed outlier: 4.087A pdb=" N HIS A2217 " --> pdb=" O ALA A2213 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A2218 " --> pdb=" O MET A2214 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER A2219 " --> pdb=" O PHE A2215 " (cutoff:3.500A) Processing helix chain 'A' and resid 2220 through 2225 Processing helix chain 'A' and resid 2238 through 2248 Processing helix chain 'A' and resid 2250 through 2257 Processing helix chain 'A' and resid 2258 through 2275 removed outlier: 3.681A pdb=" N LEU A2262 " --> pdb=" O ARG A2258 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2284 Processing helix chain 'A' and resid 2291 through 2307 removed outlier: 3.603A pdb=" N ARG A2297 " --> pdb=" O VAL A2293 " (cutoff:3.500A) Processing helix chain 'A' and resid 2313 through 2328 Proline residue: A2328 - end of helix Processing helix chain 'A' and resid 2342 through 2357 Proline residue: A2357 - end of helix Processing helix chain 'A' and resid 2383 through 2403 Processing helix chain 'A' and resid 2405 through 2412 Processing helix chain 'A' and resid 2413 through 2428 Proline residue: A2428 - end of helix Processing helix chain 'A' and resid 2429 through 2439 removed outlier: 5.667A pdb=" N ALA A2439 " --> pdb=" O VAL A2435 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2460 removed outlier: 3.739A pdb=" N GLY A2459 " --> pdb=" O ASP A2455 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE A2460 " --> pdb=" O MET A2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2455 through 2460' Processing helix chain 'A' and resid 2461 through 2475 removed outlier: 3.697A pdb=" N LYS A2465 " --> pdb=" O CYS A2461 " (cutoff:3.500A) Processing helix chain 'A' and resid 2480 through 2491 Processing helix chain 'A' and resid 2492 through 2504 removed outlier: 4.837A pdb=" N THR A2504 " --> pdb=" O ALA A2500 " (cutoff:3.500A) Processing helix chain 'A' and resid 2505 through 2511 removed outlier: 5.730A pdb=" N ASP A2511 " --> pdb=" O LEU A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2512 through 2532 removed outlier: 5.086A pdb=" N LEU A2525 " --> pdb=" O CYS A2521 " (cutoff:3.500A) Proline residue: A2526 - end of helix Processing helix chain 'A' and resid 2541 through 2559 removed outlier: 3.630A pdb=" N GLY A2558 " --> pdb=" O ARG A2554 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS A2559 " --> pdb=" O LEU A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2562 through 2580 removed outlier: 3.683A pdb=" N GLN A2579 " --> pdb=" O SER A2575 " (cutoff:3.500A) Processing helix chain 'A' and resid 2583 through 2593 removed outlier: 5.984A pdb=" N HIS A2587 " --> pdb=" O SER A2583 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU A2588 " --> pdb=" O MET A2584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A2591 " --> pdb=" O HIS A2587 " (cutoff:3.500A) Processing helix chain 'A' and resid 2600 through 2618 removed outlier: 3.854A pdb=" N LYS A2604 " --> pdb=" O ASN A2600 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N MET A2605 " --> pdb=" O GLU A2601 " (cutoff:3.500A) Proline residue: A2606 - end of helix Processing helix chain 'A' and resid 2634 through 2655 removed outlier: 6.023A pdb=" N LEU A2638 " --> pdb=" O SER A2634 " (cutoff:3.500A) Processing helix chain 'A' and resid 2659 through 2677 Proline residue: A2667 - end of helix Proline residue: A2677 - end of helix Processing helix chain 'A' and resid 2691 through 2696 Processing helix chain 'A' and resid 2714 through 2740 removed outlier: 4.622A pdb=" N LYS A2723 " --> pdb=" O TYR A2719 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A2724 " --> pdb=" O PHE A2720 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU A2726 " --> pdb=" O ASN A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2759 through 2764 removed outlier: 5.278A pdb=" N SER A2764 " --> pdb=" O TYR A2760 " (cutoff:3.500A) Processing helix chain 'A' and resid 2765 through 2785 removed outlier: 5.108A pdb=" N ILE A2770 " --> pdb=" O LYS A2766 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR A2771 " --> pdb=" O GLU A2767 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N TRP A2773 " --> pdb=" O GLU A2769 " (cutoff:3.500A) Proline residue: A2774 - end of helix removed outlier: 3.844A pdb=" N TRP A2785 " --> pdb=" O THR A2781 " (cutoff:3.500A) Processing helix chain 'A' and resid 2792 through 2802 removed outlier: 4.292A pdb=" N ASP A2796 " --> pdb=" O THR A2792 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A2799 " --> pdb=" O GLY A2795 " (cutoff:3.500A) Processing helix chain 'A' and resid 2834 through 2864 Processing helix chain 'A' and resid 2873 through 2878 removed outlier: 5.252A pdb=" N THR A2878 " --> pdb=" O TYR A2874 " (cutoff:3.500A) Processing helix chain 'A' and resid 2881 through 2900 removed outlier: 4.542A pdb=" N ASP A2885 " --> pdb=" O GLU A2881 " (cutoff:3.500A) Processing helix chain 'A' and resid 2920 through 2948 Processing helix chain 'A' and resid 2954 through 2979 removed outlier: 4.195A pdb=" N GLN A2958 " --> pdb=" O PHE A2954 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A2959 " --> pdb=" O PRO A2955 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU A2968 " --> pdb=" O ALA A2964 " (cutoff:3.500A) Proline residue: A2969 - end of helix Processing helix chain 'A' and resid 2980 through 2985 removed outlier: 4.782A pdb=" N ALA A2985 " --> pdb=" O TYR A2981 " (cutoff:3.500A) Processing helix chain 'A' and resid 2997 through 3016 Processing helix chain 'A' and resid 3018 through 3023 removed outlier: 4.434A pdb=" N GLY A3023 " --> pdb=" O ILE A3019 " (cutoff:3.500A) Processing helix chain 'A' and resid 3025 through 3040 removed outlier: 3.642A pdb=" N ILE A3029 " --> pdb=" O ASP A3025 " (cutoff:3.500A) Processing helix chain 'A' and resid 3041 through 3049 removed outlier: 3.990A pdb=" N VAL A3045 " --> pdb=" O ASP A3041 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3079 removed outlier: 3.613A pdb=" N LYS A3076 " --> pdb=" O MET A3072 " (cutoff:3.500A) Processing helix chain 'A' and resid 3088 through 3116 removed outlier: 5.148A pdb=" N LEU A3102 " --> pdb=" O THR A3098 " (cutoff:3.500A) Proline residue: A3103 - end of helix Processing helix chain 'A' and resid 3118 through 3123 removed outlier: 4.298A pdb=" N LEU A3123 " --> pdb=" O GLU A3119 " (cutoff:3.500A) Processing helix chain 'A' and resid 3124 through 3143 removed outlier: 6.655A pdb=" N VAL A3128 " --> pdb=" O GLU A3124 " (cutoff:3.500A) Processing helix chain 'A' and resid 3145 through 3152 Processing helix chain 'A' and resid 3153 through 3166 Processing helix chain 'A' and resid 3175 through 3180 removed outlier: 3.984A pdb=" N ASN A3179 " --> pdb=" O LEU A3175 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE A3180 " --> pdb=" O ASP A3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3175 through 3180' Processing helix chain 'A' and resid 3182 through 3187 Processing helix chain 'A' and resid 3189 through 3196 removed outlier: 4.609A pdb=" N SER A3196 " --> pdb=" O ARG A3192 " (cutoff:3.500A) Processing helix chain 'A' and resid 3200 through 3206 Proline residue: A3206 - end of helix Processing helix chain 'A' and resid 3210 through 3225 Processing helix chain 'A' and resid 3227 through 3232 removed outlier: 4.388A pdb=" N MET A3231 " --> pdb=" O ARG A3227 " (cutoff:3.500A) Proline residue: A3232 - end of helix No H-bonds generated for 'chain 'A' and resid 3227 through 3232' Processing helix chain 'A' and resid 3233 through 3250 removed outlier: 5.016A pdb=" N LEU A3239 " --> pdb=" O MET A3235 " (cutoff:3.500A) Proline residue: A3240 - end of helix Processing helix chain 'A' and resid 3253 through 3258 Proline residue: A3258 - end of helix Processing helix chain 'A' and resid 3269 through 3290 removed outlier: 4.099A pdb=" N MET A3273 " --> pdb=" O ASN A3269 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A3289 " --> pdb=" O TYR A3285 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE A3290 " --> pdb=" O ASN A3286 " (cutoff:3.500A) Processing helix chain 'A' and resid 3293 through 3311 removed outlier: 4.373A pdb=" N LYS A3297 " --> pdb=" O GLY A3293 " (cutoff:3.500A) Proline residue: A3305 - end of helix removed outlier: 5.860A pdb=" N LYS A3311 " --> pdb=" O ILE A3307 " (cutoff:3.500A) Processing helix chain 'A' and resid 3312 through 3329 removed outlier: 4.738A pdb=" N THR A3317 " --> pdb=" O GLN A3313 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU A3320 " --> pdb=" O LYS A3316 " (cutoff:3.500A) Proline residue: A3321 - end of helix removed outlier: 3.943A pdb=" N LYS A3329 " --> pdb=" O LYS A3325 " (cutoff:3.500A) Processing helix chain 'A' and resid 3599 through 3605 Processing helix chain 'A' and resid 3607 through 3612 Proline residue: A3612 - end of helix Processing helix chain 'A' and resid 3613 through 3632 removed outlier: 4.957A pdb=" N GLU A3630 " --> pdb=" O LYS A3626 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR A3631 " --> pdb=" O SER A3627 " (cutoff:3.500A) Processing helix chain 'A' and resid 3636 through 3647 removed outlier: 3.537A pdb=" N LYS A3646 " --> pdb=" O GLU A3642 " (cutoff:3.500A) Proline residue: A3647 - end of helix Processing helix chain 'A' and resid 3649 through 3654 removed outlier: 4.683A pdb=" N GLU A3654 " --> pdb=" O GLU A3650 " (cutoff:3.500A) Processing helix chain 'A' and resid 3662 through 3678 removed outlier: 5.731A pdb=" N GLU A3678 " --> pdb=" O THR A3674 " (cutoff:3.500A) Processing helix chain 'A' and resid 3685 through 3701 removed outlier: 3.650A pdb=" N ASP A3693 " --> pdb=" O MET A3689 " (cutoff:3.500A) Processing helix chain 'A' and resid 3713 through 3733 removed outlier: 3.956A pdb=" N LEU A3731 " --> pdb=" O GLN A3727 " (cutoff:3.500A) Processing helix chain 'A' and resid 3735 through 3748 removed outlier: 4.061A pdb=" N LYS A3748 " --> pdb=" O ILE A3744 " (cutoff:3.500A) Processing helix chain 'A' and resid 3752 through 3767 Processing helix chain 'A' and resid 3770 through 3785 Processing helix chain 'A' and resid 3786 through 3800 removed outlier: 4.992A pdb=" N PHE A3790 " --> pdb=" O ASP A3786 " (cutoff:3.500A) Processing helix chain 'A' and resid 3804 through 3818 Processing helix chain 'A' and resid 3832 through 3848 Processing helix chain 'A' and resid 3851 through 3860 Processing helix chain 'A' and resid 3869 through 3894 removed outlier: 4.824A pdb=" N GLY A3894 " --> pdb=" O TRP A3890 " (cutoff:3.500A) Processing helix chain 'A' and resid 3899 through 3925 Processing helix chain 'A' and resid 3928 through 3939 removed outlier: 4.995A pdb=" N ARG A3939 " --> pdb=" O LEU A3935 " (cutoff:3.500A) Processing helix chain 'A' and resid 3940 through 3962 removed outlier: 3.532A pdb=" N HIS A3949 " --> pdb=" O VAL A3945 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET A3956 " --> pdb=" O ALA A3952 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN A3960 " --> pdb=" O MET A3956 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A3961 " --> pdb=" O LYS A3957 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER A3962 " --> pdb=" O LEU A3958 " (cutoff:3.500A) Processing helix chain 'A' and resid 3964 through 3987 Processing helix chain 'A' and resid 3993 through 4007 Processing helix chain 'A' and resid 4008 through 4029 removed outlier: 3.512A pdb=" N LYS A4022 " --> pdb=" O ASP A4018 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A4023 " --> pdb=" O MET A4019 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS A4024 " --> pdb=" O PHE A4020 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASP A4025 " --> pdb=" O LEU A4021 " (cutoff:3.500A) Processing helix chain 'A' and resid 4030 through 4037 Proline residue: A4037 - end of helix Processing helix chain 'A' and resid 4044 through 4056 Processing helix chain 'A' and resid 4059 through 4071 removed outlier: 4.959A pdb=" N GLU A4071 " --> pdb=" O LEU A4067 " (cutoff:3.500A) Processing helix chain 'A' and resid 4079 through 4110 removed outlier: 4.702A pdb=" N GLU A4089 " --> pdb=" O LYS A4085 " (cutoff:3.500A) Proline residue: A4090 - end of helix removed outlier: 3.621A pdb=" N ASN A4097 " --> pdb=" O ASP A4093 " (cutoff:3.500A) Proline residue: A4110 - end of helix Processing helix chain 'A' and resid 4112 through 4123 Processing helix chain 'A' and resid 4124 through 4131 Proline residue: A4131 - end of helix Processing helix chain 'A' and resid 4153 through 4162 Processing helix chain 'A' and resid 4163 through 4179 Processing helix chain 'A' and resid 4184 through 4208 removed outlier: 3.627A pdb=" N VAL A4190 " --> pdb=" O MET A4186 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU A4208 " --> pdb=" O ALA A4204 " (cutoff:3.500A) Processing helix chain 'A' and resid 4237 through 4261 removed outlier: 3.767A pdb=" N MET A4258 " --> pdb=" O THR A4254 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A4259 " --> pdb=" O LEU A4255 " (cutoff:3.500A) Processing helix chain 'A' and resid 4263 through 4274 removed outlier: 4.390A pdb=" N LYS A4269 " --> pdb=" O LYS A4265 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS A4270 " --> pdb=" O LYS A4266 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A4271 " --> pdb=" O GLN A4267 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A4273 " --> pdb=" O LYS A4269 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET A4274 " --> pdb=" O LYS A4270 " (cutoff:3.500A) Processing helix chain 'A' and resid 4275 through 4310 Processing helix chain 'A' and resid 4480 through 4499 removed outlier: 4.202A pdb=" N ILE A4485 " --> pdb=" O TRP A4481 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A4486 " --> pdb=" O LYS A4482 " (cutoff:3.500A) Processing helix chain 'A' and resid 4500 through 4520 removed outlier: 3.688A pdb=" N ALA A4506 " --> pdb=" O MET A4502 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A4518 " --> pdb=" O ASN A4514 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE A4519 " --> pdb=" O PHE A4515 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR A4520 " --> pdb=" O ILE A4516 " (cutoff:3.500A) Processing helix chain 'A' and resid 4567 through 4612 removed outlier: 3.665A pdb=" N PHE A4584 " --> pdb=" O THR A4580 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A4595 " --> pdb=" O TYR A4591 " (cutoff:3.500A) Proline residue: A4596 - end of helix Processing helix chain 'A' and resid 4625 through 4638 removed outlier: 4.173A pdb=" N ARG A4632 " --> pdb=" O GLY A4628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU A4633 " --> pdb=" O GLN A4629 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A4634 " --> pdb=" O TRP A4630 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A4635 " --> pdb=" O ASP A4631 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN A4636 " --> pdb=" O ARG A4632 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A4637 " --> pdb=" O LEU A4633 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN A4638 " --> pdb=" O VAL A4634 " (cutoff:3.500A) Processing helix chain 'A' and resid 4648 through 4658 Processing helix chain 'A' and resid 4662 through 4671 Processing helix chain 'A' and resid 4674 through 4683 removed outlier: 3.947A pdb=" N ASP A4678 " --> pdb=" O LYS A4674 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A4679 " --> pdb=" O ALA A4675 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG A4683 " --> pdb=" O PHE A4679 " (cutoff:3.500A) Processing helix chain 'A' and resid 4693 through 4702 removed outlier: 5.968A pdb=" N ASP A4702 " --> pdb=" O LEU A4698 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4716 Processing helix chain 'A' and resid 4717 through 4735 removed outlier: 3.934A pdb=" N HIS A4733 " --> pdb=" O SER A4729 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A4734 " --> pdb=" O VAL A4730 " (cutoff:3.500A) Processing helix chain 'A' and resid 4736 through 4751 removed outlier: 4.805A pdb=" N ALA A4740 " --> pdb=" O ASN A4736 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA A4741 " --> pdb=" O PHE A4737 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N HIS A4742 " --> pdb=" O PHE A4738 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A4743 " --> pdb=" O PHE A4739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A4744 " --> pdb=" O ALA A4740 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ASP A4745 " --> pdb=" O ALA A4741 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE A4746 " --> pdb=" O HIS A4742 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA A4747 " --> pdb=" O LEU A4743 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N MET A4748 " --> pdb=" O LEU A4744 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LYS A4751 " --> pdb=" O ALA A4747 " (cutoff:3.500A) Processing helix chain 'A' and resid 4752 through 4762 removed outlier: 4.099A pdb=" N ILE A4756 " --> pdb=" O THR A4752 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A4760 " --> pdb=" O ILE A4756 " (cutoff:3.500A) Processing helix chain 'A' and resid 4763 through 4788 Processing helix chain 'A' and resid 4789 through 4794 removed outlier: 5.407A pdb=" N TYR A4793 " --> pdb=" O PHE A4789 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN A4794 " --> pdb=" O ARG A4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 4789 through 4794' Processing helix chain 'A' and resid 4808 through 4823 removed outlier: 4.716A pdb=" N VAL A4821 " --> pdb=" O MET A4817 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A4822 " --> pdb=" O TYR A4818 " (cutoff:3.500A) Processing helix chain 'A' and resid 4826 through 4831 removed outlier: 4.145A pdb=" N GLU A4830 " --> pdb=" O GLY A4826 " (cutoff:3.500A) Processing helix chain 'A' and resid 4839 through 4854 Processing helix chain 'A' and resid 4858 through 4887 Processing helix chain 'A' and resid 4894 through 4900 removed outlier: 4.015A pdb=" N PHE A4898 " --> pdb=" O GLY A4894 " (cutoff:3.500A) Processing helix chain 'A' and resid 4903 through 4911 Processing helix chain 'A' and resid 4914 through 4928 Processing helix chain 'A' and resid 4934 through 4947 Processing helix chain 'A' and resid 4957 through 4963 Processing helix chain 'A' and resid 857 through 862 removed outlier: 4.606A pdb=" N PHE A 862 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1772 through 1778 removed outlier: 4.926A pdb=" N CYS A1775 " --> pdb=" O SER A1772 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR A1778 " --> pdb=" O CYS A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 2594 through 2599 Proline residue: A2597 - end of helix No H-bonds generated for 'chain 'A' and resid 2594 through 2599' Processing helix chain 'A' and resid 4614 through 4619 Processing helix chain 'B' and resid 61 through 66 removed outlier: 3.982A pdb=" N CYS B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 84 Processing helix chain 'B' and resid 155 through 160 removed outlier: 4.534A pdb=" N TRP B 159 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP B 160 " --> pdb=" O GLU B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.910A pdb=" N THR B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 271 removed outlier: 4.696A pdb=" N VAL B 269 " --> pdb=" O GLY B 265 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 328 Processing helix chain 'B' and resid 409 through 439 removed outlier: 3.599A pdb=" N LYS B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 446 removed outlier: 4.888A pdb=" N ASP B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 464 Processing helix chain 'B' and resid 471 through 493 Processing helix chain 'B' and resid 494 through 509 removed outlier: 4.258A pdb=" N TYR B 508 " --> pdb=" O ARG B 504 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 518 Processing helix chain 'B' and resid 519 through 542 removed outlier: 4.810A pdb=" N LYS B 527 " --> pdb=" O GLY B 523 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER B 528 " --> pdb=" O GLU B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 553 removed outlier: 3.880A pdb=" N SER B 552 " --> pdb=" O CYS B 548 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 563 removed outlier: 3.586A pdb=" N SER B 560 " --> pdb=" O ASP B 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG B 561 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU B 562 " --> pdb=" O LEU B 558 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU B 563 " --> pdb=" O ILE B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 582 Processing helix chain 'B' and resid 583 through 590 removed outlier: 5.737A pdb=" N LYS B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 604 removed outlier: 3.711A pdb=" N LEU B 601 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.603A pdb=" N LEU B 611 " --> pdb=" O ASN B 607 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS B 620 " --> pdb=" O SER B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 640 Proline residue: B 638 - end of helix Processing helix chain 'B' and resid 821 through 826 removed outlier: 4.380A pdb=" N ALA B 825 " --> pdb=" O PRO B 821 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL B 826 " --> pdb=" O CYS B 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 821 through 826' Processing helix chain 'B' and resid 878 through 901 removed outlier: 6.425A pdb=" N LYS B 884 " --> pdb=" O ARG B 880 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU B 885 " --> pdb=" O ILE B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 947 Processing helix chain 'B' and resid 954 through 961 removed outlier: 3.994A pdb=" N GLU B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL B 961 " --> pdb=" O ALA B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 972 removed outlier: 5.159A pdb=" N LEU B 972 " --> pdb=" O LYS B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 987 removed outlier: 3.829A pdb=" N ILE B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS B 987 " --> pdb=" O LEU B 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 982 through 987' Processing helix chain 'B' and resid 989 through 1015 removed outlier: 3.693A pdb=" N ASP B 997 " --> pdb=" O GLU B 993 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS B 998 " --> pdb=" O ALA B 994 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1061 removed outlier: 4.806A pdb=" N GLY B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.932A pdb=" N LEU B1224 " --> pdb=" O ASP B1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS B1225 " --> pdb=" O VAL B1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1220 through 1225' Processing helix chain 'B' and resid 1229 through 1235 removed outlier: 6.059A pdb=" N GLN B1233 " --> pdb=" O ILE B1229 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU B1234 " --> pdb=" O CYS B1230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B1235 " --> pdb=" O GLY B1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1229 through 1235' Processing helix chain 'B' and resid 1416 through 1423 Processing helix chain 'B' and resid 1437 through 1442 removed outlier: 4.054A pdb=" N VAL B1441 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP B1442 " --> pdb=" O PRO B1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1437 through 1442' Processing helix chain 'B' and resid 1489 through 1495 removed outlier: 3.525A pdb=" N SER B1493 " --> pdb=" O CYS B1489 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER B1495 " --> pdb=" O GLY B1491 " (cutoff:3.500A) Processing helix chain 'B' and resid 1565 through 1571 removed outlier: 3.697A pdb=" N GLY B1569 " --> pdb=" O PRO B1565 " (cutoff:3.500A) Processing helix chain 'B' and resid 1640 through 1648 removed outlier: 4.044A pdb=" N LEU B1644 " --> pdb=" O ASP B1640 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR B1645 " --> pdb=" O ILE B1641 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU B1646 " --> pdb=" O LEU B1642 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN B1647 " --> pdb=" O GLU B1643 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU B1648 " --> pdb=" O LEU B1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1640 through 1648' Processing helix chain 'B' and resid 1649 through 1666 removed outlier: 3.540A pdb=" N CYS B1665 " --> pdb=" O TYR B1661 " (cutoff:3.500A) Processing helix chain 'B' and resid 1669 through 1680 removed outlier: 3.930A pdb=" N SER B1678 " --> pdb=" O HIS B1674 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N HIS B1679 " --> pdb=" O ALA B1675 " (cutoff:3.500A) Processing helix chain 'B' and resid 1681 through 1691 Processing helix chain 'B' and resid 1695 through 1710 Processing helix chain 'B' and resid 1711 through 1722 removed outlier: 5.283A pdb=" N ALA B1715 " --> pdb=" O LEU B1711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET B1721 " --> pdb=" O ALA B1717 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN B1722 " --> pdb=" O ARG B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1730 through 1736 removed outlier: 3.788A pdb=" N ILE B1736 " --> pdb=" O GLU B1732 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1805 removed outlier: 3.504A pdb=" N LYS B1800 " --> pdb=" O THR B1796 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B1805 " --> pdb=" O GLU B1801 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1832 Proline residue: B1820 - end of helix Processing helix chain 'B' and resid 1836 through 1847 Processing helix chain 'B' and resid 1892 through 1897 removed outlier: 3.784A pdb=" N MET B1896 " --> pdb=" O GLY B1892 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LYS B1897 " --> pdb=" O LEU B1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1892 through 1897' Processing helix chain 'B' and resid 1899 through 1948 removed outlier: 3.712A pdb=" N GLN B1905 " --> pdb=" O PRO B1901 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP B1931 " --> pdb=" O ALA B1927 " (cutoff:3.500A) Processing helix chain 'B' and resid 1950 through 1955 removed outlier: 3.732A pdb=" N SER B1954 " --> pdb=" O ALA B1950 " (cutoff:3.500A) Processing helix chain 'B' and resid 1956 through 1967 removed outlier: 4.172A pdb=" N ARG B1960 " --> pdb=" O ALA B1956 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS B1963 " --> pdb=" O ALA B1959 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N GLU B1964 " --> pdb=" O ARG B1960 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE B1965 " --> pdb=" O LYS B1961 " (cutoff:3.500A) Processing helix chain 'B' and resid 1968 through 1979 removed outlier: 5.292A pdb=" N PHE B1979 " --> pdb=" O MET B1975 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 2008 removed outlier: 3.512A pdb=" N LEU B1996 " --> pdb=" O ILE B1992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B2001 " --> pdb=" O LEU B1997 " (cutoff:3.500A) Processing helix chain 'B' and resid 2057 through 2073 removed outlier: 3.674A pdb=" N VAL B2067 " --> pdb=" O SER B2063 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2094 Processing helix chain 'B' and resid 2095 through 2105 Proline residue: B2103 - end of helix Processing helix chain 'B' and resid 2109 through 2133 removed outlier: 3.925A pdb=" N VAL B2113 " --> pdb=" O ASN B2109 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU B2114 " --> pdb=" O GLY B2110 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP B2115 " --> pdb=" O VAL B2111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B2130 " --> pdb=" O ILE B2126 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER B2131 " --> pdb=" O ARG B2127 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL B2132 " --> pdb=" O SER B2128 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ARG B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2135 through 2153 removed outlier: 3.501A pdb=" N LYS B2140 " --> pdb=" O LYS B2136 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS B2153 " --> pdb=" O ILE B2149 " (cutoff:3.500A) Processing helix chain 'B' and resid 2158 through 2166 Processing helix chain 'B' and resid 2167 through 2183 removed outlier: 4.769A pdb=" N GLY B2182 " --> pdb=" O VAL B2178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B2183 " --> pdb=" O LEU B2179 " (cutoff:3.500A) Processing helix chain 'B' and resid 2189 through 2208 removed outlier: 3.976A pdb=" N SER B2207 " --> pdb=" O PHE B2203 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG B2208 " --> pdb=" O CYS B2204 " (cutoff:3.500A) Processing helix chain 'B' and resid 2209 through 2219 removed outlier: 4.086A pdb=" N HIS B2217 " --> pdb=" O ALA B2213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B2218 " --> pdb=" O MET B2214 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N SER B2219 " --> pdb=" O PHE B2215 " (cutoff:3.500A) Processing helix chain 'B' and resid 2220 through 2225 Processing helix chain 'B' and resid 2238 through 2248 Processing helix chain 'B' and resid 2250 through 2257 Processing helix chain 'B' and resid 2258 through 2275 removed outlier: 3.682A pdb=" N LEU B2262 " --> pdb=" O ARG B2258 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2284 Processing helix chain 'B' and resid 2291 through 2307 removed outlier: 3.602A pdb=" N ARG B2297 " --> pdb=" O VAL B2293 " (cutoff:3.500A) Processing helix chain 'B' and resid 2313 through 2328 Proline residue: B2328 - end of helix Processing helix chain 'B' and resid 2342 through 2357 Proline residue: B2357 - end of helix Processing helix chain 'B' and resid 2383 through 2403 Processing helix chain 'B' and resid 2405 through 2412 Processing helix chain 'B' and resid 2413 through 2428 Proline residue: B2428 - end of helix Processing helix chain 'B' and resid 2429 through 2439 removed outlier: 5.668A pdb=" N ALA B2439 " --> pdb=" O VAL B2435 " (cutoff:3.500A) Processing helix chain 'B' and resid 2455 through 2460 removed outlier: 3.740A pdb=" N GLY B2459 " --> pdb=" O ASP B2455 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B2460 " --> pdb=" O MET B2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2455 through 2460' Processing helix chain 'B' and resid 2461 through 2475 removed outlier: 3.696A pdb=" N LYS B2465 " --> pdb=" O CYS B2461 " (cutoff:3.500A) Processing helix chain 'B' and resid 2480 through 2491 Processing helix chain 'B' and resid 2492 through 2504 removed outlier: 4.837A pdb=" N THR B2504 " --> pdb=" O ALA B2500 " (cutoff:3.500A) Processing helix chain 'B' and resid 2505 through 2511 removed outlier: 5.730A pdb=" N ASP B2511 " --> pdb=" O LEU B2507 " (cutoff:3.500A) Processing helix chain 'B' and resid 2512 through 2532 removed outlier: 5.086A pdb=" N LEU B2525 " --> pdb=" O CYS B2521 " (cutoff:3.500A) Proline residue: B2526 - end of helix Processing helix chain 'B' and resid 2541 through 2559 removed outlier: 3.631A pdb=" N GLY B2558 " --> pdb=" O ARG B2554 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N CYS B2559 " --> pdb=" O LEU B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2562 through 2580 removed outlier: 3.683A pdb=" N GLN B2579 " --> pdb=" O SER B2575 " (cutoff:3.500A) Processing helix chain 'B' and resid 2583 through 2593 removed outlier: 5.984A pdb=" N HIS B2587 " --> pdb=" O SER B2583 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B2588 " --> pdb=" O MET B2584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG B2591 " --> pdb=" O HIS B2587 " (cutoff:3.500A) Processing helix chain 'B' and resid 2600 through 2618 removed outlier: 3.854A pdb=" N LYS B2604 " --> pdb=" O ASN B2600 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N MET B2605 " --> pdb=" O GLU B2601 " (cutoff:3.500A) Proline residue: B2606 - end of helix Processing helix chain 'B' and resid 2634 through 2655 removed outlier: 6.024A pdb=" N LEU B2638 " --> pdb=" O SER B2634 " (cutoff:3.500A) Processing helix chain 'B' and resid 2659 through 2677 Proline residue: B2667 - end of helix Proline residue: B2677 - end of helix Processing helix chain 'B' and resid 2691 through 2696 Processing helix chain 'B' and resid 2714 through 2740 removed outlier: 4.623A pdb=" N LYS B2723 " --> pdb=" O TYR B2719 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B2724 " --> pdb=" O PHE B2720 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU B2726 " --> pdb=" O ASN B2722 " (cutoff:3.500A) Processing helix chain 'B' and resid 2759 through 2764 removed outlier: 5.278A pdb=" N SER B2764 " --> pdb=" O TYR B2760 " (cutoff:3.500A) Processing helix chain 'B' and resid 2765 through 2785 removed outlier: 5.109A pdb=" N ILE B2770 " --> pdb=" O LYS B2766 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR B2771 " --> pdb=" O GLU B2767 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP B2773 " --> pdb=" O GLU B2769 " (cutoff:3.500A) Proline residue: B2774 - end of helix removed outlier: 3.843A pdb=" N TRP B2785 " --> pdb=" O THR B2781 " (cutoff:3.500A) Processing helix chain 'B' and resid 2792 through 2802 removed outlier: 4.292A pdb=" N ASP B2796 " --> pdb=" O THR B2792 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B2799 " --> pdb=" O GLY B2795 " (cutoff:3.500A) Processing helix chain 'B' and resid 2834 through 2864 Processing helix chain 'B' and resid 2873 through 2878 removed outlier: 5.253A pdb=" N THR B2878 " --> pdb=" O TYR B2874 " (cutoff:3.500A) Processing helix chain 'B' and resid 2881 through 2900 removed outlier: 4.543A pdb=" N ASP B2885 " --> pdb=" O GLU B2881 " (cutoff:3.500A) Processing helix chain 'B' and resid 2920 through 2948 Processing helix chain 'B' and resid 2954 through 2979 removed outlier: 4.196A pdb=" N GLN B2958 " --> pdb=" O PHE B2954 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU B2959 " --> pdb=" O PRO B2955 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU B2968 " --> pdb=" O ALA B2964 " (cutoff:3.500A) Proline residue: B2969 - end of helix Processing helix chain 'B' and resid 2980 through 2985 removed outlier: 4.783A pdb=" N ALA B2985 " --> pdb=" O TYR B2981 " (cutoff:3.500A) Processing helix chain 'B' and resid 2997 through 3016 Processing helix chain 'B' and resid 3018 through 3023 removed outlier: 4.433A pdb=" N GLY B3023 " --> pdb=" O ILE B3019 " (cutoff:3.500A) Processing helix chain 'B' and resid 3025 through 3040 removed outlier: 3.642A pdb=" N ILE B3029 " --> pdb=" O ASP B3025 " (cutoff:3.500A) Processing helix chain 'B' and resid 3041 through 3049 removed outlier: 3.991A pdb=" N VAL B3045 " --> pdb=" O ASP B3041 " (cutoff:3.500A) Processing helix chain 'B' and resid 3050 through 3079 removed outlier: 3.614A pdb=" N LYS B3076 " --> pdb=" O MET B3072 " (cutoff:3.500A) Processing helix chain 'B' and resid 3088 through 3116 removed outlier: 5.148A pdb=" N LEU B3102 " --> pdb=" O THR B3098 " (cutoff:3.500A) Proline residue: B3103 - end of helix Processing helix chain 'B' and resid 3118 through 3123 removed outlier: 4.298A pdb=" N LEU B3123 " --> pdb=" O GLU B3119 " (cutoff:3.500A) Processing helix chain 'B' and resid 3124 through 3143 removed outlier: 6.655A pdb=" N VAL B3128 " --> pdb=" O GLU B3124 " (cutoff:3.500A) Processing helix chain 'B' and resid 3145 through 3152 Processing helix chain 'B' and resid 3153 through 3166 Processing helix chain 'B' and resid 3175 through 3180 removed outlier: 3.984A pdb=" N ASN B3179 " --> pdb=" O LEU B3175 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE B3180 " --> pdb=" O ASP B3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 3175 through 3180' Processing helix chain 'B' and resid 3182 through 3187 Processing helix chain 'B' and resid 3189 through 3196 removed outlier: 4.609A pdb=" N SER B3196 " --> pdb=" O ARG B3192 " (cutoff:3.500A) Processing helix chain 'B' and resid 3200 through 3206 Proline residue: B3206 - end of helix Processing helix chain 'B' and resid 3210 through 3225 Processing helix chain 'B' and resid 3227 through 3232 removed outlier: 4.388A pdb=" N MET B3231 " --> pdb=" O ARG B3227 " (cutoff:3.500A) Proline residue: B3232 - end of helix No H-bonds generated for 'chain 'B' and resid 3227 through 3232' Processing helix chain 'B' and resid 3233 through 3250 removed outlier: 5.017A pdb=" N LEU B3239 " --> pdb=" O MET B3235 " (cutoff:3.500A) Proline residue: B3240 - end of helix Processing helix chain 'B' and resid 3253 through 3258 Proline residue: B3258 - end of helix Processing helix chain 'B' and resid 3269 through 3290 removed outlier: 4.098A pdb=" N MET B3273 " --> pdb=" O ASN B3269 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B3289 " --> pdb=" O TYR B3285 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B3290 " --> pdb=" O ASN B3286 " (cutoff:3.500A) Processing helix chain 'B' and resid 3293 through 3311 removed outlier: 4.374A pdb=" N LYS B3297 " --> pdb=" O GLY B3293 " (cutoff:3.500A) Proline residue: B3305 - end of helix removed outlier: 5.859A pdb=" N LYS B3311 " --> pdb=" O ILE B3307 " (cutoff:3.500A) Processing helix chain 'B' and resid 3312 through 3329 removed outlier: 4.738A pdb=" N THR B3317 " --> pdb=" O GLN B3313 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU B3320 " --> pdb=" O LYS B3316 " (cutoff:3.500A) Proline residue: B3321 - end of helix removed outlier: 3.944A pdb=" N LYS B3329 " --> pdb=" O LYS B3325 " (cutoff:3.500A) Processing helix chain 'B' and resid 3599 through 3605 Processing helix chain 'B' and resid 3607 through 3612 Proline residue: B3612 - end of helix Processing helix chain 'B' and resid 3613 through 3632 removed outlier: 4.956A pdb=" N GLU B3630 " --> pdb=" O LYS B3626 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR B3631 " --> pdb=" O SER B3627 " (cutoff:3.500A) Processing helix chain 'B' and resid 3636 through 3647 removed outlier: 3.537A pdb=" N LYS B3646 " --> pdb=" O GLU B3642 " (cutoff:3.500A) Proline residue: B3647 - end of helix Processing helix chain 'B' and resid 3649 through 3654 removed outlier: 4.682A pdb=" N GLU B3654 " --> pdb=" O GLU B3650 " (cutoff:3.500A) Processing helix chain 'B' and resid 3662 through 3678 removed outlier: 5.732A pdb=" N GLU B3678 " --> pdb=" O THR B3674 " (cutoff:3.500A) Processing helix chain 'B' and resid 3685 through 3701 removed outlier: 3.651A pdb=" N ASP B3693 " --> pdb=" O MET B3689 " (cutoff:3.500A) Processing helix chain 'B' and resid 3713 through 3733 removed outlier: 3.955A pdb=" N LEU B3731 " --> pdb=" O GLN B3727 " (cutoff:3.500A) Processing helix chain 'B' and resid 3735 through 3748 removed outlier: 4.062A pdb=" N LYS B3748 " --> pdb=" O ILE B3744 " (cutoff:3.500A) Processing helix chain 'B' and resid 3752 through 3767 Processing helix chain 'B' and resid 3770 through 3785 Processing helix chain 'B' and resid 3786 through 3800 removed outlier: 4.991A pdb=" N PHE B3790 " --> pdb=" O ASP B3786 " (cutoff:3.500A) Processing helix chain 'B' and resid 3804 through 3818 Processing helix chain 'B' and resid 3832 through 3848 Processing helix chain 'B' and resid 3851 through 3860 Processing helix chain 'B' and resid 3869 through 3894 removed outlier: 4.824A pdb=" N GLY B3894 " --> pdb=" O TRP B3890 " (cutoff:3.500A) Processing helix chain 'B' and resid 3899 through 3925 Processing helix chain 'B' and resid 3928 through 3939 removed outlier: 4.995A pdb=" N ARG B3939 " --> pdb=" O LEU B3935 " (cutoff:3.500A) Processing helix chain 'B' and resid 3940 through 3962 removed outlier: 3.532A pdb=" N HIS B3949 " --> pdb=" O VAL B3945 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET B3956 " --> pdb=" O ALA B3952 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN B3960 " --> pdb=" O MET B3956 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B3961 " --> pdb=" O LYS B3957 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER B3962 " --> pdb=" O LEU B3958 " (cutoff:3.500A) Processing helix chain 'B' and resid 3964 through 3987 Processing helix chain 'B' and resid 3993 through 4007 Processing helix chain 'B' and resid 4008 through 4029 removed outlier: 3.510A pdb=" N LYS B4022 " --> pdb=" O ASP B4018 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU B4023 " --> pdb=" O MET B4019 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS B4024 " --> pdb=" O PHE B4020 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP B4025 " --> pdb=" O LEU B4021 " (cutoff:3.500A) Processing helix chain 'B' and resid 4030 through 4037 Proline residue: B4037 - end of helix Processing helix chain 'B' and resid 4044 through 4056 Processing helix chain 'B' and resid 4059 through 4071 removed outlier: 4.960A pdb=" N GLU B4071 " --> pdb=" O LEU B4067 " (cutoff:3.500A) Processing helix chain 'B' and resid 4079 through 4110 removed outlier: 4.701A pdb=" N GLU B4089 " --> pdb=" O LYS B4085 " (cutoff:3.500A) Proline residue: B4090 - end of helix removed outlier: 3.621A pdb=" N ASN B4097 " --> pdb=" O ASP B4093 " (cutoff:3.500A) Proline residue: B4110 - end of helix Processing helix chain 'B' and resid 4112 through 4123 Processing helix chain 'B' and resid 4124 through 4131 Proline residue: B4131 - end of helix Processing helix chain 'B' and resid 4153 through 4162 Processing helix chain 'B' and resid 4163 through 4179 Processing helix chain 'B' and resid 4184 through 4208 removed outlier: 3.627A pdb=" N VAL B4190 " --> pdb=" O MET B4186 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU B4208 " --> pdb=" O ALA B4204 " (cutoff:3.500A) Processing helix chain 'B' and resid 4237 through 4261 removed outlier: 3.766A pdb=" N MET B4258 " --> pdb=" O THR B4254 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B4259 " --> pdb=" O LEU B4255 " (cutoff:3.500A) Processing helix chain 'B' and resid 4263 through 4274 removed outlier: 4.391A pdb=" N LYS B4269 " --> pdb=" O LYS B4265 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYS B4270 " --> pdb=" O LYS B4266 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL B4271 " --> pdb=" O GLN B4267 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS B4273 " --> pdb=" O LYS B4269 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET B4274 " --> pdb=" O LYS B4270 " (cutoff:3.500A) Processing helix chain 'B' and resid 4275 through 4310 Processing helix chain 'B' and resid 4480 through 4499 removed outlier: 4.201A pdb=" N ILE B4485 " --> pdb=" O TRP B4481 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B4486 " --> pdb=" O LYS B4482 " (cutoff:3.500A) Processing helix chain 'B' and resid 4500 through 4520 removed outlier: 3.688A pdb=" N ALA B4506 " --> pdb=" O MET B4502 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B4518 " --> pdb=" O ASN B4514 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE B4519 " --> pdb=" O PHE B4515 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR B4520 " --> pdb=" O ILE B4516 " (cutoff:3.500A) Processing helix chain 'B' and resid 4567 through 4612 removed outlier: 3.666A pdb=" N PHE B4584 " --> pdb=" O THR B4580 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL B4595 " --> pdb=" O TYR B4591 " (cutoff:3.500A) Proline residue: B4596 - end of helix Processing helix chain 'B' and resid 4625 through 4638 removed outlier: 4.173A pdb=" N ARG B4632 " --> pdb=" O GLY B4628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU B4633 " --> pdb=" O GLN B4629 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL B4634 " --> pdb=" O TRP B4630 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE B4635 " --> pdb=" O ASP B4631 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN B4636 " --> pdb=" O ARG B4632 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B4637 " --> pdb=" O LEU B4633 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN B4638 " --> pdb=" O VAL B4634 " (cutoff:3.500A) Processing helix chain 'B' and resid 4648 through 4658 Processing helix chain 'B' and resid 4662 through 4671 Processing helix chain 'B' and resid 4674 through 4683 removed outlier: 3.947A pdb=" N ASP B4678 " --> pdb=" O LYS B4674 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE B4679 " --> pdb=" O ALA B4675 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG B4683 " --> pdb=" O PHE B4679 " (cutoff:3.500A) Processing helix chain 'B' and resid 4693 through 4702 removed outlier: 5.968A pdb=" N ASP B4702 " --> pdb=" O LEU B4698 " (cutoff:3.500A) Processing helix chain 'B' and resid 4703 through 4716 Processing helix chain 'B' and resid 4717 through 4735 removed outlier: 3.934A pdb=" N HIS B4733 " --> pdb=" O SER B4729 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR B4734 " --> pdb=" O VAL B4730 " (cutoff:3.500A) Processing helix chain 'B' and resid 4736 through 4751 removed outlier: 4.805A pdb=" N ALA B4740 " --> pdb=" O ASN B4736 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA B4741 " --> pdb=" O PHE B4737 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS B4742 " --> pdb=" O PHE B4738 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU B4743 " --> pdb=" O PHE B4739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B4744 " --> pdb=" O ALA B4740 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP B4745 " --> pdb=" O ALA B4741 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE B4746 " --> pdb=" O HIS B4742 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA B4747 " --> pdb=" O LEU B4743 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N MET B4748 " --> pdb=" O LEU B4744 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS B4751 " --> pdb=" O ALA B4747 " (cutoff:3.500A) Processing helix chain 'B' and resid 4752 through 4762 removed outlier: 4.100A pdb=" N ILE B4756 " --> pdb=" O THR B4752 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL B4760 " --> pdb=" O ILE B4756 " (cutoff:3.500A) Processing helix chain 'B' and resid 4763 through 4788 Processing helix chain 'B' and resid 4789 through 4794 removed outlier: 5.406A pdb=" N TYR B4793 " --> pdb=" O PHE B4789 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N ASN B4794 " --> pdb=" O ARG B4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 4789 through 4794' Processing helix chain 'B' and resid 4808 through 4823 removed outlier: 4.715A pdb=" N VAL B4821 " --> pdb=" O MET B4817 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG B4822 " --> pdb=" O TYR B4818 " (cutoff:3.500A) Processing helix chain 'B' and resid 4826 through 4831 removed outlier: 4.144A pdb=" N GLU B4830 " --> pdb=" O GLY B4826 " (cutoff:3.500A) Processing helix chain 'B' and resid 4839 through 4854 Processing helix chain 'B' and resid 4858 through 4887 Processing helix chain 'B' and resid 4894 through 4900 removed outlier: 4.015A pdb=" N PHE B4898 " --> pdb=" O GLY B4894 " (cutoff:3.500A) Processing helix chain 'B' and resid 4903 through 4911 Processing helix chain 'B' and resid 4914 through 4928 Processing helix chain 'B' and resid 4934 through 4947 Processing helix chain 'B' and resid 4957 through 4963 Processing helix chain 'B' and resid 857 through 862 removed outlier: 4.607A pdb=" N PHE B 862 " --> pdb=" O GLN B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 1772 through 1778 removed outlier: 4.925A pdb=" N CYS B1775 " --> pdb=" O SER B1772 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR B1778 " --> pdb=" O CYS B1775 " (cutoff:3.500A) Processing helix chain 'B' and resid 2594 through 2599 Proline residue: B2597 - end of helix No H-bonds generated for 'chain 'B' and resid 2594 through 2599' Processing helix chain 'B' and resid 4614 through 4619 Processing helix chain 'C' and resid 61 through 66 removed outlier: 3.983A pdb=" N CYS C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.534A pdb=" N TRP C 159 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP C 160 " --> pdb=" O GLU C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 253 through 259 removed outlier: 3.911A pdb=" N THR C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 271 removed outlier: 4.697A pdb=" N VAL C 269 " --> pdb=" O GLY C 265 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 409 through 439 removed outlier: 3.599A pdb=" N LYS C 439 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 446 removed outlier: 4.888A pdb=" N ASP C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 464 Processing helix chain 'C' and resid 471 through 493 Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.257A pdb=" N TYR C 508 " --> pdb=" O ARG C 504 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER C 509 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 518 Processing helix chain 'C' and resid 519 through 542 removed outlier: 4.810A pdb=" N LYS C 527 " --> pdb=" O GLY C 523 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER C 528 " --> pdb=" O GLU C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 553 removed outlier: 3.881A pdb=" N SER C 552 " --> pdb=" O CYS C 548 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 563 removed outlier: 3.585A pdb=" N SER C 560 " --> pdb=" O ASP C 556 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ARG C 561 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU C 563 " --> pdb=" O ILE C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 582 Processing helix chain 'C' and resid 583 through 590 removed outlier: 5.737A pdb=" N LYS C 590 " --> pdb=" O LEU C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 604 removed outlier: 3.711A pdb=" N LEU C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 removed outlier: 3.603A pdb=" N LEU C 611 " --> pdb=" O ASN C 607 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS C 620 " --> pdb=" O SER C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 640 Proline residue: C 638 - end of helix Processing helix chain 'C' and resid 821 through 826 removed outlier: 4.380A pdb=" N ALA C 825 " --> pdb=" O PRO C 821 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL C 826 " --> pdb=" O CYS C 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 821 through 826' Processing helix chain 'C' and resid 878 through 901 removed outlier: 6.425A pdb=" N LYS C 884 " --> pdb=" O ARG C 880 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU C 885 " --> pdb=" O ILE C 881 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 947 Processing helix chain 'C' and resid 954 through 961 removed outlier: 3.994A pdb=" N GLU C 958 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 961 " --> pdb=" O ALA C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 972 removed outlier: 5.158A pdb=" N LEU C 972 " --> pdb=" O LYS C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 987 removed outlier: 3.829A pdb=" N ILE C 986 " --> pdb=" O ASP C 982 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS C 987 " --> pdb=" O LEU C 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 982 through 987' Processing helix chain 'C' and resid 989 through 1015 removed outlier: 3.692A pdb=" N ASP C 997 " --> pdb=" O GLU C 993 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS C 998 " --> pdb=" O ALA C 994 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1061 removed outlier: 4.805A pdb=" N GLY C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1225 removed outlier: 3.933A pdb=" N LEU C1224 " --> pdb=" O ASP C1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS C1225 " --> pdb=" O VAL C1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1220 through 1225' Processing helix chain 'C' and resid 1229 through 1235 removed outlier: 6.060A pdb=" N GLN C1233 " --> pdb=" O ILE C1229 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C1234 " --> pdb=" O CYS C1230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C1235 " --> pdb=" O GLY C1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1229 through 1235' Processing helix chain 'C' and resid 1416 through 1423 Processing helix chain 'C' and resid 1437 through 1442 removed outlier: 4.054A pdb=" N VAL C1441 " --> pdb=" O GLU C1437 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP C1442 " --> pdb=" O PRO C1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1437 through 1442' Processing helix chain 'C' and resid 1489 through 1495 removed outlier: 3.526A pdb=" N SER C1493 " --> pdb=" O CYS C1489 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER C1495 " --> pdb=" O GLY C1491 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1571 removed outlier: 3.697A pdb=" N GLY C1569 " --> pdb=" O PRO C1565 " (cutoff:3.500A) Processing helix chain 'C' and resid 1640 through 1648 removed outlier: 4.044A pdb=" N LEU C1644 " --> pdb=" O ASP C1640 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N THR C1645 " --> pdb=" O ILE C1641 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C1646 " --> pdb=" O LEU C1642 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN C1647 " --> pdb=" O GLU C1643 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU C1648 " --> pdb=" O LEU C1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1640 through 1648' Processing helix chain 'C' and resid 1649 through 1666 removed outlier: 3.540A pdb=" N CYS C1665 " --> pdb=" O TYR C1661 " (cutoff:3.500A) Processing helix chain 'C' and resid 1669 through 1680 removed outlier: 3.930A pdb=" N SER C1678 " --> pdb=" O HIS C1674 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS C1679 " --> pdb=" O ALA C1675 " (cutoff:3.500A) Processing helix chain 'C' and resid 1681 through 1691 Processing helix chain 'C' and resid 1695 through 1710 Processing helix chain 'C' and resid 1711 through 1722 removed outlier: 5.282A pdb=" N ALA C1715 " --> pdb=" O LEU C1711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET C1721 " --> pdb=" O ALA C1717 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN C1722 " --> pdb=" O ARG C1718 " (cutoff:3.500A) Processing helix chain 'C' and resid 1730 through 1736 removed outlier: 3.789A pdb=" N ILE C1736 " --> pdb=" O GLU C1732 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1805 removed outlier: 3.504A pdb=" N LYS C1800 " --> pdb=" O THR C1796 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS C1805 " --> pdb=" O GLU C1801 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1832 Proline residue: C1820 - end of helix Processing helix chain 'C' and resid 1836 through 1847 Processing helix chain 'C' and resid 1892 through 1897 removed outlier: 3.784A pdb=" N MET C1896 " --> pdb=" O GLY C1892 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS C1897 " --> pdb=" O LEU C1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1892 through 1897' Processing helix chain 'C' and resid 1899 through 1948 removed outlier: 3.712A pdb=" N GLN C1905 " --> pdb=" O PRO C1901 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP C1931 " --> pdb=" O ALA C1927 " (cutoff:3.500A) Processing helix chain 'C' and resid 1950 through 1955 removed outlier: 3.732A pdb=" N SER C1954 " --> pdb=" O ALA C1950 " (cutoff:3.500A) Processing helix chain 'C' and resid 1956 through 1967 removed outlier: 4.172A pdb=" N ARG C1960 " --> pdb=" O ALA C1956 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS C1963 " --> pdb=" O ALA C1959 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU C1964 " --> pdb=" O ARG C1960 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N PHE C1965 " --> pdb=" O LYS C1961 " (cutoff:3.500A) Processing helix chain 'C' and resid 1968 through 1979 removed outlier: 5.291A pdb=" N PHE C1979 " --> pdb=" O MET C1975 " (cutoff:3.500A) Processing helix chain 'C' and resid 1989 through 2008 removed outlier: 3.512A pdb=" N LEU C1996 " --> pdb=" O ILE C1992 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU C2001 " --> pdb=" O LEU C1997 " (cutoff:3.500A) Processing helix chain 'C' and resid 2057 through 2073 removed outlier: 3.673A pdb=" N VAL C2067 " --> pdb=" O SER C2063 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2094 Processing helix chain 'C' and resid 2095 through 2105 Proline residue: C2103 - end of helix Processing helix chain 'C' and resid 2109 through 2133 removed outlier: 3.925A pdb=" N VAL C2113 " --> pdb=" O ASN C2109 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLU C2114 " --> pdb=" O GLY C2110 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP C2115 " --> pdb=" O VAL C2111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C2130 " --> pdb=" O ILE C2126 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER C2131 " --> pdb=" O ARG C2127 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL C2132 " --> pdb=" O SER C2128 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG C2133 " --> pdb=" O LEU C2129 " (cutoff:3.500A) Processing helix chain 'C' and resid 2135 through 2153 removed outlier: 5.517A pdb=" N LYS C2153 " --> pdb=" O ILE C2149 " (cutoff:3.500A) Processing helix chain 'C' and resid 2158 through 2166 Processing helix chain 'C' and resid 2167 through 2183 removed outlier: 4.769A pdb=" N GLY C2182 " --> pdb=" O VAL C2178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C2183 " --> pdb=" O LEU C2179 " (cutoff:3.500A) Processing helix chain 'C' and resid 2189 through 2208 removed outlier: 3.975A pdb=" N SER C2207 " --> pdb=" O PHE C2203 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG C2208 " --> pdb=" O CYS C2204 " (cutoff:3.500A) Processing helix chain 'C' and resid 2209 through 2219 removed outlier: 4.087A pdb=" N HIS C2217 " --> pdb=" O ALA C2213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU C2218 " --> pdb=" O MET C2214 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N SER C2219 " --> pdb=" O PHE C2215 " (cutoff:3.500A) Processing helix chain 'C' and resid 2220 through 2225 Processing helix chain 'C' and resid 2238 through 2248 Processing helix chain 'C' and resid 2250 through 2257 Processing helix chain 'C' and resid 2258 through 2275 removed outlier: 3.682A pdb=" N LEU C2262 " --> pdb=" O ARG C2258 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2284 Processing helix chain 'C' and resid 2291 through 2307 removed outlier: 3.602A pdb=" N ARG C2297 " --> pdb=" O VAL C2293 " (cutoff:3.500A) Processing helix chain 'C' and resid 2313 through 2328 Proline residue: C2328 - end of helix Processing helix chain 'C' and resid 2342 through 2357 Proline residue: C2357 - end of helix Processing helix chain 'C' and resid 2383 through 2403 Processing helix chain 'C' and resid 2405 through 2412 Processing helix chain 'C' and resid 2413 through 2428 Proline residue: C2428 - end of helix Processing helix chain 'C' and resid 2429 through 2439 removed outlier: 5.668A pdb=" N ALA C2439 " --> pdb=" O VAL C2435 " (cutoff:3.500A) Processing helix chain 'C' and resid 2455 through 2460 removed outlier: 3.739A pdb=" N GLY C2459 " --> pdb=" O ASP C2455 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE C2460 " --> pdb=" O MET C2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2455 through 2460' Processing helix chain 'C' and resid 2461 through 2475 removed outlier: 3.696A pdb=" N LYS C2465 " --> pdb=" O CYS C2461 " (cutoff:3.500A) Processing helix chain 'C' and resid 2480 through 2491 Processing helix chain 'C' and resid 2492 through 2504 removed outlier: 4.837A pdb=" N THR C2504 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing helix chain 'C' and resid 2505 through 2511 removed outlier: 5.730A pdb=" N ASP C2511 " --> pdb=" O LEU C2507 " (cutoff:3.500A) Processing helix chain 'C' and resid 2512 through 2532 removed outlier: 5.086A pdb=" N LEU C2525 " --> pdb=" O CYS C2521 " (cutoff:3.500A) Proline residue: C2526 - end of helix Processing helix chain 'C' and resid 2541 through 2559 removed outlier: 3.630A pdb=" N GLY C2558 " --> pdb=" O ARG C2554 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N CYS C2559 " --> pdb=" O LEU C2555 " (cutoff:3.500A) Processing helix chain 'C' and resid 2562 through 2580 removed outlier: 3.683A pdb=" N GLN C2579 " --> pdb=" O SER C2575 " (cutoff:3.500A) Processing helix chain 'C' and resid 2583 through 2593 removed outlier: 5.984A pdb=" N HIS C2587 " --> pdb=" O SER C2583 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LEU C2588 " --> pdb=" O MET C2584 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG C2591 " --> pdb=" O HIS C2587 " (cutoff:3.500A) Processing helix chain 'C' and resid 2600 through 2618 removed outlier: 3.853A pdb=" N LYS C2604 " --> pdb=" O ASN C2600 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N MET C2605 " --> pdb=" O GLU C2601 " (cutoff:3.500A) Proline residue: C2606 - end of helix Processing helix chain 'C' and resid 2634 through 2655 removed outlier: 6.023A pdb=" N LEU C2638 " --> pdb=" O SER C2634 " (cutoff:3.500A) Processing helix chain 'C' and resid 2659 through 2677 Proline residue: C2667 - end of helix Proline residue: C2677 - end of helix Processing helix chain 'C' and resid 2691 through 2696 Processing helix chain 'C' and resid 2714 through 2740 removed outlier: 4.622A pdb=" N LYS C2723 " --> pdb=" O TYR C2719 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C2724 " --> pdb=" O PHE C2720 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU C2726 " --> pdb=" O ASN C2722 " (cutoff:3.500A) Processing helix chain 'C' and resid 2759 through 2764 removed outlier: 5.278A pdb=" N SER C2764 " --> pdb=" O TYR C2760 " (cutoff:3.500A) Processing helix chain 'C' and resid 2765 through 2785 removed outlier: 5.109A pdb=" N ILE C2770 " --> pdb=" O LYS C2766 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR C2771 " --> pdb=" O GLU C2767 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP C2773 " --> pdb=" O GLU C2769 " (cutoff:3.500A) Proline residue: C2774 - end of helix removed outlier: 3.843A pdb=" N TRP C2785 " --> pdb=" O THR C2781 " (cutoff:3.500A) Processing helix chain 'C' and resid 2792 through 2802 removed outlier: 4.292A pdb=" N ASP C2796 " --> pdb=" O THR C2792 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C2799 " --> pdb=" O GLY C2795 " (cutoff:3.500A) Processing helix chain 'C' and resid 2834 through 2864 Processing helix chain 'C' and resid 2873 through 2878 removed outlier: 5.253A pdb=" N THR C2878 " --> pdb=" O TYR C2874 " (cutoff:3.500A) Processing helix chain 'C' and resid 2881 through 2900 removed outlier: 4.544A pdb=" N ASP C2885 " --> pdb=" O GLU C2881 " (cutoff:3.500A) Processing helix chain 'C' and resid 2920 through 2948 Processing helix chain 'C' and resid 2954 through 2979 removed outlier: 4.195A pdb=" N GLN C2958 " --> pdb=" O PHE C2954 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU C2959 " --> pdb=" O PRO C2955 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU C2968 " --> pdb=" O ALA C2964 " (cutoff:3.500A) Proline residue: C2969 - end of helix Processing helix chain 'C' and resid 2980 through 2985 removed outlier: 4.782A pdb=" N ALA C2985 " --> pdb=" O TYR C2981 " (cutoff:3.500A) Processing helix chain 'C' and resid 2997 through 3016 Processing helix chain 'C' and resid 3018 through 3023 removed outlier: 4.434A pdb=" N GLY C3023 " --> pdb=" O ILE C3019 " (cutoff:3.500A) Processing helix chain 'C' and resid 3025 through 3040 removed outlier: 3.642A pdb=" N ILE C3029 " --> pdb=" O ASP C3025 " (cutoff:3.500A) Processing helix chain 'C' and resid 3041 through 3049 removed outlier: 3.990A pdb=" N VAL C3045 " --> pdb=" O ASP C3041 " (cutoff:3.500A) Processing helix chain 'C' and resid 3050 through 3079 removed outlier: 3.614A pdb=" N LYS C3076 " --> pdb=" O MET C3072 " (cutoff:3.500A) Processing helix chain 'C' and resid 3088 through 3116 removed outlier: 5.148A pdb=" N LEU C3102 " --> pdb=" O THR C3098 " (cutoff:3.500A) Proline residue: C3103 - end of helix Processing helix chain 'C' and resid 3118 through 3123 removed outlier: 4.297A pdb=" N LEU C3123 " --> pdb=" O GLU C3119 " (cutoff:3.500A) Processing helix chain 'C' and resid 3124 through 3143 removed outlier: 6.654A pdb=" N VAL C3128 " --> pdb=" O GLU C3124 " (cutoff:3.500A) Processing helix chain 'C' and resid 3145 through 3152 Processing helix chain 'C' and resid 3153 through 3166 Processing helix chain 'C' and resid 3175 through 3180 removed outlier: 3.984A pdb=" N ASN C3179 " --> pdb=" O LEU C3175 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE C3180 " --> pdb=" O ASP C3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 3175 through 3180' Processing helix chain 'C' and resid 3182 through 3187 Processing helix chain 'C' and resid 3189 through 3196 removed outlier: 4.608A pdb=" N SER C3196 " --> pdb=" O ARG C3192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3200 through 3206 Proline residue: C3206 - end of helix Processing helix chain 'C' and resid 3210 through 3225 Processing helix chain 'C' and resid 3227 through 3232 removed outlier: 4.388A pdb=" N MET C3231 " --> pdb=" O ARG C3227 " (cutoff:3.500A) Proline residue: C3232 - end of helix No H-bonds generated for 'chain 'C' and resid 3227 through 3232' Processing helix chain 'C' and resid 3233 through 3250 removed outlier: 5.016A pdb=" N LEU C3239 " --> pdb=" O MET C3235 " (cutoff:3.500A) Proline residue: C3240 - end of helix Processing helix chain 'C' and resid 3253 through 3258 Proline residue: C3258 - end of helix Processing helix chain 'C' and resid 3269 through 3290 removed outlier: 4.098A pdb=" N MET C3273 " --> pdb=" O ASN C3269 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY C3289 " --> pdb=" O TYR C3285 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE C3290 " --> pdb=" O ASN C3286 " (cutoff:3.500A) Processing helix chain 'C' and resid 3293 through 3311 removed outlier: 4.374A pdb=" N LYS C3297 " --> pdb=" O GLY C3293 " (cutoff:3.500A) Proline residue: C3305 - end of helix removed outlier: 5.861A pdb=" N LYS C3311 " --> pdb=" O ILE C3307 " (cutoff:3.500A) Processing helix chain 'C' and resid 3312 through 3329 removed outlier: 4.737A pdb=" N THR C3317 " --> pdb=" O GLN C3313 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU C3320 " --> pdb=" O LYS C3316 " (cutoff:3.500A) Proline residue: C3321 - end of helix removed outlier: 3.944A pdb=" N LYS C3329 " --> pdb=" O LYS C3325 " (cutoff:3.500A) Processing helix chain 'C' and resid 3599 through 3605 Processing helix chain 'C' and resid 3607 through 3612 Proline residue: C3612 - end of helix Processing helix chain 'C' and resid 3613 through 3632 removed outlier: 4.956A pdb=" N GLU C3630 " --> pdb=" O LYS C3626 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C3631 " --> pdb=" O SER C3627 " (cutoff:3.500A) Processing helix chain 'C' and resid 3636 through 3647 removed outlier: 3.537A pdb=" N LYS C3646 " --> pdb=" O GLU C3642 " (cutoff:3.500A) Proline residue: C3647 - end of helix Processing helix chain 'C' and resid 3649 through 3654 removed outlier: 4.683A pdb=" N GLU C3654 " --> pdb=" O GLU C3650 " (cutoff:3.500A) Processing helix chain 'C' and resid 3662 through 3678 removed outlier: 5.731A pdb=" N GLU C3678 " --> pdb=" O THR C3674 " (cutoff:3.500A) Processing helix chain 'C' and resid 3685 through 3701 removed outlier: 3.651A pdb=" N ASP C3693 " --> pdb=" O MET C3689 " (cutoff:3.500A) Processing helix chain 'C' and resid 3713 through 3733 removed outlier: 3.956A pdb=" N LEU C3731 " --> pdb=" O GLN C3727 " (cutoff:3.500A) Processing helix chain 'C' and resid 3735 through 3748 removed outlier: 4.062A pdb=" N LYS C3748 " --> pdb=" O ILE C3744 " (cutoff:3.500A) Processing helix chain 'C' and resid 3752 through 3767 Processing helix chain 'C' and resid 3770 through 3785 Processing helix chain 'C' and resid 3786 through 3800 removed outlier: 4.992A pdb=" N PHE C3790 " --> pdb=" O ASP C3786 " (cutoff:3.500A) Processing helix chain 'C' and resid 3804 through 3818 Processing helix chain 'C' and resid 3832 through 3848 Processing helix chain 'C' and resid 3851 through 3860 Processing helix chain 'C' and resid 3869 through 3894 removed outlier: 4.823A pdb=" N GLY C3894 " --> pdb=" O TRP C3890 " (cutoff:3.500A) Processing helix chain 'C' and resid 3899 through 3925 Processing helix chain 'C' and resid 3928 through 3939 removed outlier: 4.995A pdb=" N ARG C3939 " --> pdb=" O LEU C3935 " (cutoff:3.500A) Processing helix chain 'C' and resid 3940 through 3962 removed outlier: 3.532A pdb=" N HIS C3949 " --> pdb=" O VAL C3945 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET C3956 " --> pdb=" O ALA C3952 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLN C3960 " --> pdb=" O MET C3956 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP C3961 " --> pdb=" O LYS C3957 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER C3962 " --> pdb=" O LEU C3958 " (cutoff:3.500A) Processing helix chain 'C' and resid 3964 through 3987 Processing helix chain 'C' and resid 3993 through 4007 Processing helix chain 'C' and resid 4008 through 4029 removed outlier: 3.511A pdb=" N LYS C4022 " --> pdb=" O ASP C4018 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C4023 " --> pdb=" O MET C4019 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS C4024 " --> pdb=" O PHE C4020 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP C4025 " --> pdb=" O LEU C4021 " (cutoff:3.500A) Processing helix chain 'C' and resid 4030 through 4037 Proline residue: C4037 - end of helix Processing helix chain 'C' and resid 4044 through 4056 Processing helix chain 'C' and resid 4059 through 4071 removed outlier: 4.959A pdb=" N GLU C4071 " --> pdb=" O LEU C4067 " (cutoff:3.500A) Processing helix chain 'C' and resid 4079 through 4110 removed outlier: 4.702A pdb=" N GLU C4089 " --> pdb=" O LYS C4085 " (cutoff:3.500A) Proline residue: C4090 - end of helix removed outlier: 3.621A pdb=" N ASN C4097 " --> pdb=" O ASP C4093 " (cutoff:3.500A) Proline residue: C4110 - end of helix Processing helix chain 'C' and resid 4112 through 4123 Processing helix chain 'C' and resid 4124 through 4131 Proline residue: C4131 - end of helix Processing helix chain 'C' and resid 4153 through 4162 Processing helix chain 'C' and resid 4163 through 4179 Processing helix chain 'C' and resid 4184 through 4208 removed outlier: 3.626A pdb=" N VAL C4190 " --> pdb=" O MET C4186 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLU C4208 " --> pdb=" O ALA C4204 " (cutoff:3.500A) Processing helix chain 'C' and resid 4237 through 4261 removed outlier: 3.767A pdb=" N MET C4258 " --> pdb=" O THR C4254 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C4259 " --> pdb=" O LEU C4255 " (cutoff:3.500A) Processing helix chain 'C' and resid 4263 through 4274 removed outlier: 4.391A pdb=" N LYS C4269 " --> pdb=" O LYS C4265 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYS C4270 " --> pdb=" O LYS C4266 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL C4271 " --> pdb=" O GLN C4267 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS C4273 " --> pdb=" O LYS C4269 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET C4274 " --> pdb=" O LYS C4270 " (cutoff:3.500A) Processing helix chain 'C' and resid 4275 through 4310 Processing helix chain 'C' and resid 4480 through 4499 removed outlier: 4.202A pdb=" N ILE C4485 " --> pdb=" O TRP C4481 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA C4486 " --> pdb=" O LYS C4482 " (cutoff:3.500A) Processing helix chain 'C' and resid 4500 through 4520 removed outlier: 3.688A pdb=" N ALA C4506 " --> pdb=" O MET C4502 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C4518 " --> pdb=" O ASN C4514 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE C4519 " --> pdb=" O PHE C4515 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR C4520 " --> pdb=" O ILE C4516 " (cutoff:3.500A) Processing helix chain 'C' and resid 4567 through 4612 removed outlier: 3.664A pdb=" N PHE C4584 " --> pdb=" O THR C4580 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL C4595 " --> pdb=" O TYR C4591 " (cutoff:3.500A) Proline residue: C4596 - end of helix Processing helix chain 'C' and resid 4625 through 4638 removed outlier: 4.173A pdb=" N ARG C4632 " --> pdb=" O GLY C4628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU C4633 " --> pdb=" O GLN C4629 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N VAL C4634 " --> pdb=" O TRP C4630 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE C4635 " --> pdb=" O ASP C4631 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN C4636 " --> pdb=" O ARG C4632 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR C4637 " --> pdb=" O LEU C4633 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN C4638 " --> pdb=" O VAL C4634 " (cutoff:3.500A) Processing helix chain 'C' and resid 4648 through 4658 Processing helix chain 'C' and resid 4662 through 4671 Processing helix chain 'C' and resid 4674 through 4683 removed outlier: 3.947A pdb=" N ASP C4678 " --> pdb=" O LYS C4674 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE C4679 " --> pdb=" O ALA C4675 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C4683 " --> pdb=" O PHE C4679 " (cutoff:3.500A) Processing helix chain 'C' and resid 4693 through 4702 removed outlier: 5.968A pdb=" N ASP C4702 " --> pdb=" O LEU C4698 " (cutoff:3.500A) Processing helix chain 'C' and resid 4703 through 4716 Processing helix chain 'C' and resid 4717 through 4735 removed outlier: 3.933A pdb=" N HIS C4733 " --> pdb=" O SER C4729 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR C4734 " --> pdb=" O VAL C4730 " (cutoff:3.500A) Processing helix chain 'C' and resid 4736 through 4751 removed outlier: 4.806A pdb=" N ALA C4740 " --> pdb=" O ASN C4736 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA C4741 " --> pdb=" O PHE C4737 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N HIS C4742 " --> pdb=" O PHE C4738 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU C4743 " --> pdb=" O PHE C4739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU C4744 " --> pdb=" O ALA C4740 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP C4745 " --> pdb=" O ALA C4741 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE C4746 " --> pdb=" O HIS C4742 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA C4747 " --> pdb=" O LEU C4743 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N MET C4748 " --> pdb=" O LEU C4744 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS C4751 " --> pdb=" O ALA C4747 " (cutoff:3.500A) Processing helix chain 'C' and resid 4752 through 4762 removed outlier: 4.100A pdb=" N ILE C4756 " --> pdb=" O THR C4752 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL C4760 " --> pdb=" O ILE C4756 " (cutoff:3.500A) Processing helix chain 'C' and resid 4763 through 4788 Processing helix chain 'C' and resid 4789 through 4794 removed outlier: 5.405A pdb=" N TYR C4793 " --> pdb=" O PHE C4789 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN C4794 " --> pdb=" O ARG C4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 4789 through 4794' Processing helix chain 'C' and resid 4808 through 4823 removed outlier: 4.716A pdb=" N VAL C4821 " --> pdb=" O MET C4817 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C4822 " --> pdb=" O TYR C4818 " (cutoff:3.500A) Processing helix chain 'C' and resid 4826 through 4831 removed outlier: 4.144A pdb=" N GLU C4830 " --> pdb=" O GLY C4826 " (cutoff:3.500A) Processing helix chain 'C' and resid 4839 through 4854 Processing helix chain 'C' and resid 4858 through 4887 Processing helix chain 'C' and resid 4894 through 4900 removed outlier: 4.014A pdb=" N PHE C4898 " --> pdb=" O GLY C4894 " (cutoff:3.500A) Processing helix chain 'C' and resid 4903 through 4911 Processing helix chain 'C' and resid 4914 through 4928 Processing helix chain 'C' and resid 4934 through 4947 Processing helix chain 'C' and resid 4957 through 4963 Processing helix chain 'C' and resid 857 through 862 removed outlier: 4.607A pdb=" N PHE C 862 " --> pdb=" O GLN C 859 " (cutoff:3.500A) Processing helix chain 'C' and resid 1772 through 1778 removed outlier: 4.925A pdb=" N CYS C1775 " --> pdb=" O SER C1772 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR C1778 " --> pdb=" O CYS C1775 " (cutoff:3.500A) Processing helix chain 'C' and resid 2594 through 2599 Proline residue: C2597 - end of helix No H-bonds generated for 'chain 'C' and resid 2594 through 2599' Processing helix chain 'C' and resid 4614 through 4619 Processing helix chain 'D' and resid 61 through 66 removed outlier: 3.982A pdb=" N CYS D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 84 Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.536A pdb=" N TRP D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N TRP D 160 " --> pdb=" O GLU D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 253 through 259 removed outlier: 3.910A pdb=" N THR D 259 " --> pdb=" O GLU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 271 removed outlier: 4.696A pdb=" N VAL D 269 " --> pdb=" O GLY D 265 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA D 271 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 328 Processing helix chain 'D' and resid 409 through 439 removed outlier: 3.598A pdb=" N LYS D 439 " --> pdb=" O ALA D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 446 removed outlier: 4.887A pdb=" N ASP D 446 " --> pdb=" O ALA D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 464 Processing helix chain 'D' and resid 471 through 493 Processing helix chain 'D' and resid 494 through 509 removed outlier: 4.257A pdb=" N TYR D 508 " --> pdb=" O ARG D 504 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N SER D 509 " --> pdb=" O LEU D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 518 Processing helix chain 'D' and resid 519 through 542 removed outlier: 4.808A pdb=" N LYS D 527 " --> pdb=" O GLY D 523 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N SER D 528 " --> pdb=" O GLU D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 553 removed outlier: 3.881A pdb=" N SER D 552 " --> pdb=" O CYS D 548 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 563 removed outlier: 3.586A pdb=" N SER D 560 " --> pdb=" O ASP D 556 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG D 561 " --> pdb=" O TRP D 557 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU D 562 " --> pdb=" O LEU D 558 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU D 563 " --> pdb=" O ILE D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 582 Processing helix chain 'D' and resid 583 through 590 removed outlier: 5.738A pdb=" N LYS D 590 " --> pdb=" O LEU D 586 " (cutoff:3.500A) Processing helix chain 'D' and resid 591 through 604 removed outlier: 3.710A pdb=" N LEU D 601 " --> pdb=" O ILE D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.602A pdb=" N LEU D 611 " --> pdb=" O ASN D 607 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N CYS D 620 " --> pdb=" O SER D 616 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 640 Proline residue: D 638 - end of helix Processing helix chain 'D' and resid 821 through 826 removed outlier: 4.380A pdb=" N ALA D 825 " --> pdb=" O PRO D 821 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL D 826 " --> pdb=" O CYS D 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 821 through 826' Processing helix chain 'D' and resid 878 through 901 removed outlier: 6.424A pdb=" N LYS D 884 " --> pdb=" O ARG D 880 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LEU D 885 " --> pdb=" O ILE D 881 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 947 Processing helix chain 'D' and resid 954 through 961 removed outlier: 3.995A pdb=" N GLU D 958 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL D 961 " --> pdb=" O ALA D 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 972 removed outlier: 5.158A pdb=" N LEU D 972 " --> pdb=" O LYS D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 982 through 987 removed outlier: 3.829A pdb=" N ILE D 986 " --> pdb=" O ASP D 982 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS D 987 " --> pdb=" O LEU D 983 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 982 through 987' Processing helix chain 'D' and resid 989 through 1015 removed outlier: 3.692A pdb=" N ASP D 997 " --> pdb=" O GLU D 993 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS D 998 " --> pdb=" O ALA D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1039 through 1061 removed outlier: 4.805A pdb=" N GLY D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1225 removed outlier: 3.932A pdb=" N LEU D1224 " --> pdb=" O ASP D1220 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N LYS D1225 " --> pdb=" O VAL D1221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1220 through 1225' Processing helix chain 'D' and resid 1229 through 1235 removed outlier: 6.059A pdb=" N GLN D1233 " --> pdb=" O ILE D1229 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLU D1234 " --> pdb=" O CYS D1230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D1235 " --> pdb=" O GLY D1231 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1229 through 1235' Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1437 through 1442 removed outlier: 4.053A pdb=" N VAL D1441 " --> pdb=" O GLU D1437 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TRP D1442 " --> pdb=" O PRO D1438 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1437 through 1442' Processing helix chain 'D' and resid 1489 through 1495 removed outlier: 3.526A pdb=" N SER D1493 " --> pdb=" O CYS D1489 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER D1495 " --> pdb=" O GLY D1491 " (cutoff:3.500A) Processing helix chain 'D' and resid 1565 through 1571 removed outlier: 3.696A pdb=" N GLY D1569 " --> pdb=" O PRO D1565 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1648 removed outlier: 4.043A pdb=" N LEU D1644 " --> pdb=" O ASP D1640 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N THR D1645 " --> pdb=" O ILE D1641 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU D1646 " --> pdb=" O LEU D1642 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN D1647 " --> pdb=" O GLU D1643 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N GLU D1648 " --> pdb=" O LEU D1644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1640 through 1648' Processing helix chain 'D' and resid 1649 through 1666 removed outlier: 3.540A pdb=" N CYS D1665 " --> pdb=" O TYR D1661 " (cutoff:3.500A) Processing helix chain 'D' and resid 1669 through 1680 removed outlier: 3.930A pdb=" N SER D1678 " --> pdb=" O HIS D1674 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N HIS D1679 " --> pdb=" O ALA D1675 " (cutoff:3.500A) Processing helix chain 'D' and resid 1681 through 1691 Processing helix chain 'D' and resid 1695 through 1710 Processing helix chain 'D' and resid 1711 through 1722 removed outlier: 5.283A pdb=" N ALA D1715 " --> pdb=" O LEU D1711 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D1721 " --> pdb=" O ALA D1717 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN D1722 " --> pdb=" O ARG D1718 " (cutoff:3.500A) Processing helix chain 'D' and resid 1730 through 1736 removed outlier: 3.789A pdb=" N ILE D1736 " --> pdb=" O GLU D1732 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1805 removed outlier: 3.504A pdb=" N LYS D1800 " --> pdb=" O THR D1796 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS D1805 " --> pdb=" O GLU D1801 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1832 Proline residue: D1820 - end of helix Processing helix chain 'D' and resid 1836 through 1847 Processing helix chain 'D' and resid 1892 through 1897 removed outlier: 3.784A pdb=" N MET D1896 " --> pdb=" O GLY D1892 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS D1897 " --> pdb=" O LEU D1893 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1892 through 1897' Processing helix chain 'D' and resid 1899 through 1948 removed outlier: 3.712A pdb=" N GLN D1905 " --> pdb=" O PRO D1901 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP D1931 " --> pdb=" O ALA D1927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1950 through 1955 removed outlier: 3.732A pdb=" N SER D1954 " --> pdb=" O ALA D1950 " (cutoff:3.500A) Processing helix chain 'D' and resid 1956 through 1967 removed outlier: 4.172A pdb=" N ARG D1960 " --> pdb=" O ALA D1956 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS D1963 " --> pdb=" O ALA D1959 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N GLU D1964 " --> pdb=" O ARG D1960 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N PHE D1965 " --> pdb=" O LYS D1961 " (cutoff:3.500A) Processing helix chain 'D' and resid 1968 through 1979 removed outlier: 5.291A pdb=" N PHE D1979 " --> pdb=" O MET D1975 " (cutoff:3.500A) Processing helix chain 'D' and resid 1989 through 2008 removed outlier: 3.513A pdb=" N LEU D1996 " --> pdb=" O ILE D1992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D2001 " --> pdb=" O LEU D1997 " (cutoff:3.500A) Processing helix chain 'D' and resid 2057 through 2073 removed outlier: 3.673A pdb=" N VAL D2067 " --> pdb=" O SER D2063 " (cutoff:3.500A) Processing helix chain 'D' and resid 2077 through 2094 Processing helix chain 'D' and resid 2095 through 2105 Proline residue: D2103 - end of helix Processing helix chain 'D' and resid 2109 through 2133 removed outlier: 3.925A pdb=" N VAL D2113 " --> pdb=" O ASN D2109 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU D2114 " --> pdb=" O GLY D2110 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ASP D2115 " --> pdb=" O VAL D2111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D2130 " --> pdb=" O ILE D2126 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER D2131 " --> pdb=" O ARG D2127 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N VAL D2132 " --> pdb=" O SER D2128 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG D2133 " --> pdb=" O LEU D2129 " (cutoff:3.500A) Processing helix chain 'D' and resid 2135 through 2153 removed outlier: 5.518A pdb=" N LYS D2153 " --> pdb=" O ILE D2149 " (cutoff:3.500A) Processing helix chain 'D' and resid 2158 through 2166 Processing helix chain 'D' and resid 2167 through 2183 removed outlier: 4.769A pdb=" N GLY D2182 " --> pdb=" O VAL D2178 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU D2183 " --> pdb=" O LEU D2179 " (cutoff:3.500A) Processing helix chain 'D' and resid 2189 through 2208 removed outlier: 3.975A pdb=" N SER D2207 " --> pdb=" O PHE D2203 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ARG D2208 " --> pdb=" O CYS D2204 " (cutoff:3.500A) Processing helix chain 'D' and resid 2209 through 2219 removed outlier: 4.087A pdb=" N HIS D2217 " --> pdb=" O ALA D2213 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU D2218 " --> pdb=" O MET D2214 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N SER D2219 " --> pdb=" O PHE D2215 " (cutoff:3.500A) Processing helix chain 'D' and resid 2220 through 2225 Processing helix chain 'D' and resid 2238 through 2248 Processing helix chain 'D' and resid 2250 through 2257 Processing helix chain 'D' and resid 2258 through 2275 removed outlier: 3.682A pdb=" N LEU D2262 " --> pdb=" O ARG D2258 " (cutoff:3.500A) Processing helix chain 'D' and resid 2277 through 2284 Processing helix chain 'D' and resid 2291 through 2307 removed outlier: 3.603A pdb=" N ARG D2297 " --> pdb=" O VAL D2293 " (cutoff:3.500A) Processing helix chain 'D' and resid 2313 through 2328 Proline residue: D2328 - end of helix Processing helix chain 'D' and resid 2342 through 2357 Proline residue: D2357 - end of helix Processing helix chain 'D' and resid 2383 through 2403 Processing helix chain 'D' and resid 2405 through 2412 Processing helix chain 'D' and resid 2413 through 2428 Proline residue: D2428 - end of helix Processing helix chain 'D' and resid 2429 through 2439 removed outlier: 5.669A pdb=" N ALA D2439 " --> pdb=" O VAL D2435 " (cutoff:3.500A) Processing helix chain 'D' and resid 2455 through 2460 removed outlier: 3.739A pdb=" N GLY D2459 " --> pdb=" O ASP D2455 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N PHE D2460 " --> pdb=" O MET D2456 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2455 through 2460' Processing helix chain 'D' and resid 2461 through 2475 removed outlier: 3.696A pdb=" N LYS D2465 " --> pdb=" O CYS D2461 " (cutoff:3.500A) Processing helix chain 'D' and resid 2480 through 2491 Processing helix chain 'D' and resid 2492 through 2504 removed outlier: 4.837A pdb=" N THR D2504 " --> pdb=" O ALA D2500 " (cutoff:3.500A) Processing helix chain 'D' and resid 2505 through 2511 removed outlier: 5.731A pdb=" N ASP D2511 " --> pdb=" O LEU D2507 " (cutoff:3.500A) Processing helix chain 'D' and resid 2512 through 2532 removed outlier: 5.086A pdb=" N LEU D2525 " --> pdb=" O CYS D2521 " (cutoff:3.500A) Proline residue: D2526 - end of helix Processing helix chain 'D' and resid 2541 through 2559 removed outlier: 3.631A pdb=" N GLY D2558 " --> pdb=" O ARG D2554 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N CYS D2559 " --> pdb=" O LEU D2555 " (cutoff:3.500A) Processing helix chain 'D' and resid 2562 through 2580 removed outlier: 3.683A pdb=" N GLN D2579 " --> pdb=" O SER D2575 " (cutoff:3.500A) Processing helix chain 'D' and resid 2583 through 2593 removed outlier: 5.983A pdb=" N HIS D2587 " --> pdb=" O SER D2583 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D2588 " --> pdb=" O MET D2584 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG D2591 " --> pdb=" O HIS D2587 " (cutoff:3.500A) Processing helix chain 'D' and resid 2600 through 2618 removed outlier: 3.854A pdb=" N LYS D2604 " --> pdb=" O ASN D2600 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N MET D2605 " --> pdb=" O GLU D2601 " (cutoff:3.500A) Proline residue: D2606 - end of helix Processing helix chain 'D' and resid 2634 through 2655 removed outlier: 6.023A pdb=" N LEU D2638 " --> pdb=" O SER D2634 " (cutoff:3.500A) Processing helix chain 'D' and resid 2659 through 2677 Proline residue: D2667 - end of helix Proline residue: D2677 - end of helix Processing helix chain 'D' and resid 2691 through 2696 Processing helix chain 'D' and resid 2714 through 2740 removed outlier: 4.622A pdb=" N LYS D2723 " --> pdb=" O TYR D2719 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR D2724 " --> pdb=" O PHE D2720 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N GLU D2726 " --> pdb=" O ASN D2722 " (cutoff:3.500A) Processing helix chain 'D' and resid 2759 through 2764 removed outlier: 5.277A pdb=" N SER D2764 " --> pdb=" O TYR D2760 " (cutoff:3.500A) Processing helix chain 'D' and resid 2765 through 2785 removed outlier: 5.109A pdb=" N ILE D2770 " --> pdb=" O LYS D2766 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR D2771 " --> pdb=" O GLU D2767 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP D2773 " --> pdb=" O GLU D2769 " (cutoff:3.500A) Proline residue: D2774 - end of helix removed outlier: 3.843A pdb=" N TRP D2785 " --> pdb=" O THR D2781 " (cutoff:3.500A) Processing helix chain 'D' and resid 2792 through 2802 removed outlier: 4.292A pdb=" N ASP D2796 " --> pdb=" O THR D2792 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D2799 " --> pdb=" O GLY D2795 " (cutoff:3.500A) Processing helix chain 'D' and resid 2834 through 2864 Processing helix chain 'D' and resid 2873 through 2878 removed outlier: 5.252A pdb=" N THR D2878 " --> pdb=" O TYR D2874 " (cutoff:3.500A) Processing helix chain 'D' and resid 2881 through 2900 removed outlier: 4.543A pdb=" N ASP D2885 " --> pdb=" O GLU D2881 " (cutoff:3.500A) Processing helix chain 'D' and resid 2920 through 2948 Processing helix chain 'D' and resid 2954 through 2979 removed outlier: 4.195A pdb=" N GLN D2958 " --> pdb=" O PHE D2954 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU D2959 " --> pdb=" O PRO D2955 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU D2968 " --> pdb=" O ALA D2964 " (cutoff:3.500A) Proline residue: D2969 - end of helix Processing helix chain 'D' and resid 2980 through 2985 removed outlier: 4.783A pdb=" N ALA D2985 " --> pdb=" O TYR D2981 " (cutoff:3.500A) Processing helix chain 'D' and resid 2997 through 3016 Processing helix chain 'D' and resid 3018 through 3023 removed outlier: 4.434A pdb=" N GLY D3023 " --> pdb=" O ILE D3019 " (cutoff:3.500A) Processing helix chain 'D' and resid 3025 through 3040 removed outlier: 3.641A pdb=" N ILE D3029 " --> pdb=" O ASP D3025 " (cutoff:3.500A) Processing helix chain 'D' and resid 3041 through 3049 removed outlier: 3.990A pdb=" N VAL D3045 " --> pdb=" O ASP D3041 " (cutoff:3.500A) Processing helix chain 'D' and resid 3050 through 3079 removed outlier: 3.614A pdb=" N LYS D3076 " --> pdb=" O MET D3072 " (cutoff:3.500A) Processing helix chain 'D' and resid 3088 through 3116 removed outlier: 5.148A pdb=" N LEU D3102 " --> pdb=" O THR D3098 " (cutoff:3.500A) Proline residue: D3103 - end of helix Processing helix chain 'D' and resid 3118 through 3123 removed outlier: 4.298A pdb=" N LEU D3123 " --> pdb=" O GLU D3119 " (cutoff:3.500A) Processing helix chain 'D' and resid 3124 through 3143 removed outlier: 6.655A pdb=" N VAL D3128 " --> pdb=" O GLU D3124 " (cutoff:3.500A) Processing helix chain 'D' and resid 3145 through 3152 Processing helix chain 'D' and resid 3153 through 3166 Processing helix chain 'D' and resid 3175 through 3180 removed outlier: 3.983A pdb=" N ASN D3179 " --> pdb=" O LEU D3175 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ILE D3180 " --> pdb=" O ASP D3176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 3175 through 3180' Processing helix chain 'D' and resid 3182 through 3187 Processing helix chain 'D' and resid 3189 through 3196 removed outlier: 4.609A pdb=" N SER D3196 " --> pdb=" O ARG D3192 " (cutoff:3.500A) Processing helix chain 'D' and resid 3200 through 3206 Proline residue: D3206 - end of helix Processing helix chain 'D' and resid 3210 through 3225 Processing helix chain 'D' and resid 3227 through 3232 removed outlier: 4.388A pdb=" N MET D3231 " --> pdb=" O ARG D3227 " (cutoff:3.500A) Proline residue: D3232 - end of helix No H-bonds generated for 'chain 'D' and resid 3227 through 3232' Processing helix chain 'D' and resid 3233 through 3250 removed outlier: 5.017A pdb=" N LEU D3239 " --> pdb=" O MET D3235 " (cutoff:3.500A) Proline residue: D3240 - end of helix Processing helix chain 'D' and resid 3253 through 3258 Proline residue: D3258 - end of helix Processing helix chain 'D' and resid 3269 through 3290 removed outlier: 4.099A pdb=" N MET D3273 " --> pdb=" O ASN D3269 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY D3289 " --> pdb=" O TYR D3285 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ILE D3290 " --> pdb=" O ASN D3286 " (cutoff:3.500A) Processing helix chain 'D' and resid 3293 through 3311 removed outlier: 4.374A pdb=" N LYS D3297 " --> pdb=" O GLY D3293 " (cutoff:3.500A) Proline residue: D3305 - end of helix removed outlier: 5.860A pdb=" N LYS D3311 " --> pdb=" O ILE D3307 " (cutoff:3.500A) Processing helix chain 'D' and resid 3312 through 3329 removed outlier: 4.738A pdb=" N THR D3317 " --> pdb=" O GLN D3313 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU D3320 " --> pdb=" O LYS D3316 " (cutoff:3.500A) Proline residue: D3321 - end of helix removed outlier: 3.944A pdb=" N LYS D3329 " --> pdb=" O LYS D3325 " (cutoff:3.500A) Processing helix chain 'D' and resid 3599 through 3605 Processing helix chain 'D' and resid 3607 through 3612 Proline residue: D3612 - end of helix Processing helix chain 'D' and resid 3613 through 3632 removed outlier: 4.957A pdb=" N GLU D3630 " --> pdb=" O LYS D3626 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR D3631 " --> pdb=" O SER D3627 " (cutoff:3.500A) Processing helix chain 'D' and resid 3636 through 3647 removed outlier: 3.537A pdb=" N LYS D3646 " --> pdb=" O GLU D3642 " (cutoff:3.500A) Proline residue: D3647 - end of helix Processing helix chain 'D' and resid 3649 through 3654 removed outlier: 4.683A pdb=" N GLU D3654 " --> pdb=" O GLU D3650 " (cutoff:3.500A) Processing helix chain 'D' and resid 3662 through 3678 removed outlier: 5.731A pdb=" N GLU D3678 " --> pdb=" O THR D3674 " (cutoff:3.500A) Processing helix chain 'D' and resid 3685 through 3701 removed outlier: 3.651A pdb=" N ASP D3693 " --> pdb=" O MET D3689 " (cutoff:3.500A) Processing helix chain 'D' and resid 3713 through 3733 removed outlier: 3.955A pdb=" N LEU D3731 " --> pdb=" O GLN D3727 " (cutoff:3.500A) Processing helix chain 'D' and resid 3735 through 3748 removed outlier: 4.062A pdb=" N LYS D3748 " --> pdb=" O ILE D3744 " (cutoff:3.500A) Processing helix chain 'D' and resid 3752 through 3767 Processing helix chain 'D' and resid 3770 through 3785 Processing helix chain 'D' and resid 3786 through 3800 removed outlier: 4.991A pdb=" N PHE D3790 " --> pdb=" O ASP D3786 " (cutoff:3.500A) Processing helix chain 'D' and resid 3804 through 3818 Processing helix chain 'D' and resid 3832 through 3848 Processing helix chain 'D' and resid 3851 through 3860 Processing helix chain 'D' and resid 3869 through 3894 removed outlier: 4.824A pdb=" N GLY D3894 " --> pdb=" O TRP D3890 " (cutoff:3.500A) Processing helix chain 'D' and resid 3899 through 3925 Processing helix chain 'D' and resid 3928 through 3939 removed outlier: 4.994A pdb=" N ARG D3939 " --> pdb=" O LEU D3935 " (cutoff:3.500A) Processing helix chain 'D' and resid 3940 through 3962 removed outlier: 3.532A pdb=" N HIS D3949 " --> pdb=" O VAL D3945 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET D3956 " --> pdb=" O ALA D3952 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLN D3960 " --> pdb=" O MET D3956 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ASP D3961 " --> pdb=" O LYS D3957 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D3962 " --> pdb=" O LEU D3958 " (cutoff:3.500A) Processing helix chain 'D' and resid 3964 through 3987 Processing helix chain 'D' and resid 3993 through 4007 Processing helix chain 'D' and resid 4008 through 4029 removed outlier: 3.511A pdb=" N LYS D4022 " --> pdb=" O ASP D4018 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU D4023 " --> pdb=" O MET D4019 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS D4024 " --> pdb=" O PHE D4020 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP D4025 " --> pdb=" O LEU D4021 " (cutoff:3.500A) Processing helix chain 'D' and resid 4030 through 4037 Proline residue: D4037 - end of helix Processing helix chain 'D' and resid 4044 through 4056 Processing helix chain 'D' and resid 4059 through 4071 removed outlier: 4.958A pdb=" N GLU D4071 " --> pdb=" O LEU D4067 " (cutoff:3.500A) Processing helix chain 'D' and resid 4079 through 4110 removed outlier: 4.701A pdb=" N GLU D4089 " --> pdb=" O LYS D4085 " (cutoff:3.500A) Proline residue: D4090 - end of helix removed outlier: 3.622A pdb=" N ASN D4097 " --> pdb=" O ASP D4093 " (cutoff:3.500A) Proline residue: D4110 - end of helix Processing helix chain 'D' and resid 4112 through 4123 Processing helix chain 'D' and resid 4124 through 4131 Proline residue: D4131 - end of helix Processing helix chain 'D' and resid 4153 through 4162 Processing helix chain 'D' and resid 4163 through 4179 Processing helix chain 'D' and resid 4184 through 4208 removed outlier: 3.626A pdb=" N VAL D4190 " --> pdb=" O MET D4186 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N GLU D4208 " --> pdb=" O ALA D4204 " (cutoff:3.500A) Processing helix chain 'D' and resid 4237 through 4261 removed outlier: 3.766A pdb=" N MET D4258 " --> pdb=" O THR D4254 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU D4259 " --> pdb=" O LEU D4255 " (cutoff:3.500A) Processing helix chain 'D' and resid 4263 through 4274 removed outlier: 4.390A pdb=" N LYS D4269 " --> pdb=" O LYS D4265 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LYS D4270 " --> pdb=" O LYS D4266 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL D4271 " --> pdb=" O GLN D4267 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D4273 " --> pdb=" O LYS D4269 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N MET D4274 " --> pdb=" O LYS D4270 " (cutoff:3.500A) Processing helix chain 'D' and resid 4275 through 4310 Processing helix chain 'D' and resid 4480 through 4499 removed outlier: 4.203A pdb=" N ILE D4485 " --> pdb=" O TRP D4481 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA D4486 " --> pdb=" O LYS D4482 " (cutoff:3.500A) Processing helix chain 'D' and resid 4500 through 4520 removed outlier: 3.688A pdb=" N ALA D4506 " --> pdb=" O MET D4502 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D4518 " --> pdb=" O ASN D4514 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N PHE D4519 " --> pdb=" O PHE D4515 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYR D4520 " --> pdb=" O ILE D4516 " (cutoff:3.500A) Processing helix chain 'D' and resid 4567 through 4612 removed outlier: 3.665A pdb=" N PHE D4584 " --> pdb=" O THR D4580 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL D4595 " --> pdb=" O TYR D4591 " (cutoff:3.500A) Proline residue: D4596 - end of helix Processing helix chain 'D' and resid 4625 through 4638 removed outlier: 4.172A pdb=" N ARG D4632 " --> pdb=" O GLY D4628 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU D4633 " --> pdb=" O GLN D4629 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL D4634 " --> pdb=" O TRP D4630 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D4635 " --> pdb=" O ASP D4631 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASN D4636 " --> pdb=" O ARG D4632 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D4637 " --> pdb=" O LEU D4633 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLN D4638 " --> pdb=" O VAL D4634 " (cutoff:3.500A) Processing helix chain 'D' and resid 4648 through 4658 Processing helix chain 'D' and resid 4662 through 4671 Processing helix chain 'D' and resid 4674 through 4683 removed outlier: 3.947A pdb=" N ASP D4678 " --> pdb=" O LYS D4674 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N PHE D4679 " --> pdb=" O ALA D4675 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D4683 " --> pdb=" O PHE D4679 " (cutoff:3.500A) Processing helix chain 'D' and resid 4693 through 4702 removed outlier: 5.968A pdb=" N ASP D4702 " --> pdb=" O LEU D4698 " (cutoff:3.500A) Processing helix chain 'D' and resid 4703 through 4716 Processing helix chain 'D' and resid 4717 through 4735 removed outlier: 3.933A pdb=" N HIS D4733 " --> pdb=" O SER D4729 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N TYR D4734 " --> pdb=" O VAL D4730 " (cutoff:3.500A) Processing helix chain 'D' and resid 4736 through 4751 removed outlier: 4.806A pdb=" N ALA D4740 " --> pdb=" O ASN D4736 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ALA D4741 " --> pdb=" O PHE D4737 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS D4742 " --> pdb=" O PHE D4738 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LEU D4743 " --> pdb=" O PHE D4739 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU D4744 " --> pdb=" O ALA D4740 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ASP D4745 " --> pdb=" O ALA D4741 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE D4746 " --> pdb=" O HIS D4742 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA D4747 " --> pdb=" O LEU D4743 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N MET D4748 " --> pdb=" O LEU D4744 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LYS D4751 " --> pdb=" O ALA D4747 " (cutoff:3.500A) Processing helix chain 'D' and resid 4752 through 4762 removed outlier: 4.100A pdb=" N ILE D4756 " --> pdb=" O THR D4752 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL D4760 " --> pdb=" O ILE D4756 " (cutoff:3.500A) Processing helix chain 'D' and resid 4763 through 4788 Processing helix chain 'D' and resid 4789 through 4794 removed outlier: 5.407A pdb=" N TYR D4793 " --> pdb=" O PHE D4789 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN D4794 " --> pdb=" O ARG D4790 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 4789 through 4794' Processing helix chain 'D' and resid 4808 through 4823 removed outlier: 4.716A pdb=" N VAL D4821 " --> pdb=" O MET D4817 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG D4822 " --> pdb=" O TYR D4818 " (cutoff:3.500A) Processing helix chain 'D' and resid 4826 through 4831 removed outlier: 4.145A pdb=" N GLU D4830 " --> pdb=" O GLY D4826 " (cutoff:3.500A) Processing helix chain 'D' and resid 4839 through 4854 Processing helix chain 'D' and resid 4858 through 4887 Processing helix chain 'D' and resid 4894 through 4900 removed outlier: 4.014A pdb=" N PHE D4898 " --> pdb=" O GLY D4894 " (cutoff:3.500A) Processing helix chain 'D' and resid 4903 through 4911 Processing helix chain 'D' and resid 4914 through 4928 Processing helix chain 'D' and resid 4934 through 4947 Processing helix chain 'D' and resid 4957 through 4963 Processing helix chain 'D' and resid 857 through 862 removed outlier: 4.607A pdb=" N PHE D 862 " --> pdb=" O GLN D 859 " (cutoff:3.500A) Processing helix chain 'D' and resid 1772 through 1778 removed outlier: 4.925A pdb=" N CYS D1775 " --> pdb=" O SER D1772 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR D1778 " --> pdb=" O CYS D1775 " (cutoff:3.500A) Processing helix chain 'D' and resid 2594 through 2599 Proline residue: D2597 - end of helix No H-bonds generated for 'chain 'D' and resid 2594 through 2599' Processing helix chain 'D' and resid 4614 through 4619 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 57 through 68 removed outlier: 5.010A pdb=" N SER E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.940A pdb=" N TYR E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 68 removed outlier: 5.010A pdb=" N SER F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.939A pdb=" N TYR F 83 " --> pdb=" O PRO F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 44 Processing helix chain 'G' and resid 57 through 68 removed outlier: 5.010A pdb=" N SER G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 83 removed outlier: 3.939A pdb=" N TYR G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 44 Processing helix chain 'H' and resid 57 through 68 removed outlier: 5.010A pdb=" N SER H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 83 removed outlier: 3.939A pdb=" N TYR H 83 " --> pdb=" O PRO H 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.667A pdb=" N ILE A 28 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU A 22 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ALA A 39 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N VAL A 20 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 67 through 70 removed outlier: 6.801A pdb=" N LEU A 120 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A 121 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET A 128 " --> pdb=" O HIS A 123 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 161 through 164 Processing sheet with id= 4, first strand: chain 'A' and resid 193 through 196 Processing sheet with id= 5, first strand: chain 'A' and resid 233 through 238 removed outlier: 5.866A pdb=" N VAL A 233 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 243 through 246 Processing sheet with id= 7, first strand: chain 'A' and resid 297 through 300 removed outlier: 5.316A pdb=" N LEU A 297 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 304 " --> pdb=" O HIS A 299 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'A' and resid 329 through 332 removed outlier: 3.606A pdb=" N TYR A 362 " --> pdb=" O ARG A 332 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'A' and resid 370 through 374 Processing sheet with id= 10, first strand: chain 'A' and resid 737 through 741 removed outlier: 5.746A pdb=" N LEU A 730 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS A 731 " --> pdb=" O ASP A 728 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS A 692 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A1637 " --> pdb=" O ILE A1632 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'A' and resid 764 through 770 removed outlier: 3.907A pdb=" N ASP A 753 " --> pdb=" O VAL A 679 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS A 671 " --> pdb=" O LEU A 761 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS A 799 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 777 through 780 Processing sheet with id= 13, first strand: chain 'A' and resid 849 through 852 removed outlier: 5.223A pdb=" N GLN A1211 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A1212 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY A1099 " --> pdb=" O MET A1168 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A1160 " --> pdb=" O THR A1107 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 6.574A pdb=" N GLN A1022 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A1029 " --> pdb=" O GLN A1022 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL A1024 " --> pdb=" O ARG A1027 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'A' and resid 1147 through 1150 removed outlier: 6.841A pdb=" N ARG A1133 " --> pdb=" O ARG A1119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A1115 " --> pdb=" O PHE A1137 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A1139 " --> pdb=" O MET A1113 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET A1113 " --> pdb=" O GLY A1139 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP A1112 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE A1087 " --> pdb=" O SER A1252 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A1595 " --> pdb=" O LYS A1253 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'A' and resid 1280 through 1286 removed outlier: 3.724A pdb=" N PHE A1553 " --> pdb=" O VAL A1285 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY A1558 " --> pdb=" O TYR A1427 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR A1427 " --> pdb=" O GLY A1558 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A1505 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A1517 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N GLY A1516 " --> pdb=" O VAL A1533 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'A' and resid 1307 through 1310 removed outlier: 4.549A pdb=" N THR A1537 " --> pdb=" O CYS A1310 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE A1301 " --> pdb=" O LEU A1591 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS A1587 " --> pdb=" O SER A1305 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'A' and resid 2443 through 2446 removed outlier: 4.545A pdb=" N ASN A2450 " --> pdb=" O ALA A2446 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'A' and resid 2745 through 2748 removed outlier: 6.691A pdb=" N ILE A2746 " --> pdb=" O GLN A2754 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A2754 " --> pdb=" O ILE A2746 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A2748 " --> pdb=" O LYS A2752 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'A' and resid 2787 through 2791 removed outlier: 3.764A pdb=" N ARG A2788 " --> pdb=" O SER A2904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER A2904 " --> pdb=" O ARG A2788 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'A' and resid 4132 through 4139 removed outlier: 4.522A pdb=" N PHE A4132 " --> pdb=" O ILE A4152 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.667A pdb=" N ILE B 28 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU B 22 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N ALA B 39 " --> pdb=" O VAL B 20 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N VAL B 20 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'B' and resid 67 through 70 removed outlier: 6.800A pdb=" N LEU B 120 " --> pdb=" O GLU B 70 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU B 121 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET B 128 " --> pdb=" O HIS B 123 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'B' and resid 161 through 164 Processing sheet with id= 25, first strand: chain 'B' and resid 193 through 196 Processing sheet with id= 26, first strand: chain 'B' and resid 233 through 238 removed outlier: 5.866A pdb=" N VAL B 233 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'B' and resid 243 through 246 Processing sheet with id= 28, first strand: chain 'B' and resid 297 through 300 removed outlier: 5.316A pdb=" N LEU B 297 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS B 304 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'B' and resid 329 through 332 removed outlier: 3.607A pdb=" N TYR B 362 " --> pdb=" O ARG B 332 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'B' and resid 370 through 374 Processing sheet with id= 31, first strand: chain 'B' and resid 737 through 741 removed outlier: 5.745A pdb=" N LEU B 730 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HIS B 731 " --> pdb=" O ASP B 728 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS B 692 " --> pdb=" O SER B 795 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B1637 " --> pdb=" O ILE B1632 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'B' and resid 764 through 770 removed outlier: 3.907A pdb=" N ASP B 753 " --> pdb=" O VAL B 679 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS B 671 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS B 799 " --> pdb=" O ASP B 680 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'B' and resid 777 through 780 Processing sheet with id= 34, first strand: chain 'B' and resid 849 through 852 removed outlier: 5.222A pdb=" N GLN B1211 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B1212 " --> pdb=" O VAL B1108 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY B1099 " --> pdb=" O MET B1168 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP B1160 " --> pdb=" O THR B1107 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'B' and resid 1021 through 1024 removed outlier: 6.574A pdb=" N GLN B1022 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN B1029 " --> pdb=" O GLN B1022 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL B1024 " --> pdb=" O ARG B1027 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'B' and resid 1147 through 1150 removed outlier: 6.840A pdb=" N ARG B1133 " --> pdb=" O ARG B1119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL B1115 " --> pdb=" O PHE B1137 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY B1139 " --> pdb=" O MET B1113 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET B1113 " --> pdb=" O GLY B1139 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP B1112 " --> pdb=" O GLY B1208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE B1087 " --> pdb=" O SER B1252 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B1595 " --> pdb=" O LYS B1253 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'B' and resid 1280 through 1286 removed outlier: 3.724A pdb=" N PHE B1553 " --> pdb=" O VAL B1285 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY B1558 " --> pdb=" O TYR B1427 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR B1427 " --> pdb=" O GLY B1558 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B1505 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1517 " --> pdb=" O ASP B1512 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLY B1516 " --> pdb=" O VAL B1533 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'B' and resid 1307 through 1310 removed outlier: 4.549A pdb=" N THR B1537 " --> pdb=" O CYS B1310 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B1301 " --> pdb=" O LEU B1591 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS B1587 " --> pdb=" O SER B1305 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'B' and resid 2443 through 2446 removed outlier: 4.545A pdb=" N ASN B2450 " --> pdb=" O ALA B2446 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'B' and resid 2745 through 2748 removed outlier: 6.691A pdb=" N ILE B2746 " --> pdb=" O GLN B2754 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B2754 " --> pdb=" O ILE B2746 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER B2748 " --> pdb=" O LYS B2752 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'B' and resid 2787 through 2791 removed outlier: 3.764A pdb=" N ARG B2788 " --> pdb=" O SER B2904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B2904 " --> pdb=" O ARG B2788 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'B' and resid 4132 through 4139 removed outlier: 4.522A pdb=" N PHE B4132 " --> pdb=" O ILE B4152 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.666A pdb=" N ILE C 28 " --> pdb=" O GLU C 31 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU C 22 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N ALA C 39 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N VAL C 20 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'C' and resid 67 through 70 removed outlier: 6.801A pdb=" N LEU C 120 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU C 121 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N MET C 128 " --> pdb=" O HIS C 123 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'C' and resid 161 through 164 Processing sheet with id= 46, first strand: chain 'C' and resid 193 through 196 Processing sheet with id= 47, first strand: chain 'C' and resid 233 through 238 removed outlier: 5.866A pdb=" N VAL C 233 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'C' and resid 243 through 246 Processing sheet with id= 49, first strand: chain 'C' and resid 297 through 300 removed outlier: 5.316A pdb=" N LEU C 297 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS C 304 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.607A pdb=" N TYR C 362 " --> pdb=" O ARG C 332 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'C' and resid 370 through 374 Processing sheet with id= 52, first strand: chain 'C' and resid 737 through 741 removed outlier: 5.745A pdb=" N LEU C 730 " --> pdb=" O VAL C 741 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N HIS C 731 " --> pdb=" O ASP C 728 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS C 692 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C1637 " --> pdb=" O ILE C1632 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'C' and resid 764 through 770 removed outlier: 3.907A pdb=" N ASP C 753 " --> pdb=" O VAL C 679 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N LYS C 671 " --> pdb=" O LEU C 761 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS C 799 " --> pdb=" O ASP C 680 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'C' and resid 777 through 780 Processing sheet with id= 55, first strand: chain 'C' and resid 849 through 852 removed outlier: 5.222A pdb=" N GLN C1211 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL C1212 " --> pdb=" O VAL C1108 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N GLY C1099 " --> pdb=" O MET C1168 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP C1160 " --> pdb=" O THR C1107 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'C' and resid 1021 through 1024 removed outlier: 6.574A pdb=" N GLN C1022 " --> pdb=" O ASN C1029 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN C1029 " --> pdb=" O GLN C1022 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL C1024 " --> pdb=" O ARG C1027 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'C' and resid 1147 through 1150 removed outlier: 6.840A pdb=" N ARG C1133 " --> pdb=" O ARG C1119 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C1115 " --> pdb=" O PHE C1137 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY C1139 " --> pdb=" O MET C1113 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N MET C1113 " --> pdb=" O GLY C1139 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ASP C1112 " --> pdb=" O GLY C1208 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE C1087 " --> pdb=" O SER C1252 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU C1595 " --> pdb=" O LYS C1253 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'C' and resid 1280 through 1286 removed outlier: 3.724A pdb=" N PHE C1553 " --> pdb=" O VAL C1285 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N GLY C1558 " --> pdb=" O TYR C1427 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N TYR C1427 " --> pdb=" O GLY C1558 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C1505 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU C1517 " --> pdb=" O ASP C1512 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N GLY C1516 " --> pdb=" O VAL C1533 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'C' and resid 1307 through 1310 removed outlier: 4.549A pdb=" N THR C1537 " --> pdb=" O CYS C1310 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE C1301 " --> pdb=" O LEU C1591 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N HIS C1587 " --> pdb=" O SER C1305 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'C' and resid 2443 through 2446 removed outlier: 4.545A pdb=" N ASN C2450 " --> pdb=" O ALA C2446 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'C' and resid 2745 through 2748 removed outlier: 6.692A pdb=" N ILE C2746 " --> pdb=" O GLN C2754 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN C2754 " --> pdb=" O ILE C2746 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N SER C2748 " --> pdb=" O LYS C2752 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'C' and resid 2787 through 2791 removed outlier: 3.763A pdb=" N ARG C2788 " --> pdb=" O SER C2904 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C2904 " --> pdb=" O ARG C2788 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'C' and resid 4132 through 4139 removed outlier: 4.523A pdb=" N PHE C4132 " --> pdb=" O ILE C4152 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.667A pdb=" N ILE D 28 " --> pdb=" O GLU D 31 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LEU D 22 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N ALA D 39 " --> pdb=" O VAL D 20 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N VAL D 20 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'D' and resid 67 through 70 removed outlier: 6.801A pdb=" N LEU D 120 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU D 121 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET D 128 " --> pdb=" O HIS D 123 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'D' and resid 161 through 164 Processing sheet with id= 67, first strand: chain 'D' and resid 193 through 196 Processing sheet with id= 68, first strand: chain 'D' and resid 233 through 238 removed outlier: 5.866A pdb=" N VAL D 233 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'D' and resid 243 through 246 Processing sheet with id= 70, first strand: chain 'D' and resid 297 through 300 removed outlier: 5.315A pdb=" N LEU D 297 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS D 304 " --> pdb=" O HIS D 299 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.607A pdb=" N TYR D 362 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'D' and resid 370 through 374 Processing sheet with id= 73, first strand: chain 'D' and resid 737 through 741 removed outlier: 5.745A pdb=" N LEU D 730 " --> pdb=" O VAL D 741 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N HIS D 731 " --> pdb=" O ASP D 728 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N HIS D 692 " --> pdb=" O SER D 795 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D1637 " --> pdb=" O ILE D1632 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'D' and resid 764 through 770 removed outlier: 3.907A pdb=" N ASP D 753 " --> pdb=" O VAL D 679 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LYS D 671 " --> pdb=" O LEU D 761 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS D 799 " --> pdb=" O ASP D 680 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'D' and resid 777 through 780 Processing sheet with id= 76, first strand: chain 'D' and resid 849 through 852 removed outlier: 5.222A pdb=" N GLN D1211 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D1212 " --> pdb=" O VAL D1108 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N GLY D1099 " --> pdb=" O MET D1168 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP D1160 " --> pdb=" O THR D1107 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'D' and resid 1021 through 1024 removed outlier: 6.574A pdb=" N GLN D1022 " --> pdb=" O ASN D1029 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN D1029 " --> pdb=" O GLN D1022 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VAL D1024 " --> pdb=" O ARG D1027 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'D' and resid 1147 through 1150 removed outlier: 6.840A pdb=" N ARG D1133 " --> pdb=" O ARG D1119 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D1115 " --> pdb=" O PHE D1137 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY D1139 " --> pdb=" O MET D1113 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N MET D1113 " --> pdb=" O GLY D1139 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ASP D1112 " --> pdb=" O GLY D1208 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ILE D1087 " --> pdb=" O SER D1252 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU D1595 " --> pdb=" O LYS D1253 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'D' and resid 1280 through 1286 removed outlier: 3.724A pdb=" N PHE D1553 " --> pdb=" O VAL D1285 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY D1558 " --> pdb=" O TYR D1427 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR D1427 " --> pdb=" O GLY D1558 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D1505 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU D1517 " --> pdb=" O ASP D1512 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N GLY D1516 " --> pdb=" O VAL D1533 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'D' and resid 1307 through 1310 removed outlier: 4.550A pdb=" N THR D1537 " --> pdb=" O CYS D1310 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE D1301 " --> pdb=" O LEU D1591 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N HIS D1587 " --> pdb=" O SER D1305 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'D' and resid 2443 through 2446 removed outlier: 4.545A pdb=" N ASN D2450 " --> pdb=" O ALA D2446 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'D' and resid 2745 through 2748 removed outlier: 6.692A pdb=" N ILE D2746 " --> pdb=" O GLN D2754 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN D2754 " --> pdb=" O ILE D2746 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER D2748 " --> pdb=" O LYS D2752 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'D' and resid 2787 through 2791 removed outlier: 3.764A pdb=" N ARG D2788 " --> pdb=" O SER D2904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D2904 " --> pdb=" O ARG D2788 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'D' and resid 4132 through 4139 removed outlier: 4.521A pdb=" N PHE D4132 " --> pdb=" O ILE D4152 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain 'E' and resid 3 through 8 removed outlier: 3.522A pdb=" N GLU E 4 " --> pdb=" O THR E 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR E 76 " --> pdb=" O GLU E 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG E 72 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN E 71 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL E 24 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'F' and resid 3 through 8 removed outlier: 3.522A pdb=" N GLU F 4 " --> pdb=" O THR F 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR F 76 " --> pdb=" O GLU F 4 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ARG F 72 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN F 71 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N VAL F 24 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'G' and resid 3 through 8 removed outlier: 3.523A pdb=" N GLU G 4 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR G 76 " --> pdb=" O GLU G 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG G 72 " --> pdb=" O ILE G 8 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN G 71 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N VAL G 24 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 88, first strand: chain 'H' and resid 3 through 8 removed outlier: 3.523A pdb=" N GLU H 4 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR H 76 " --> pdb=" O GLU H 4 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG H 72 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLN H 71 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL H 24 " --> pdb=" O LEU H 105 " (cutoff:3.500A) 7379 hydrogen bonds defined for protein. 21961 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: 102.36 Time building geometry restraints manager: 44.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 41433 1.33 - 1.46: 32292 1.46 - 1.58: 66359 1.58 - 1.71: 32 1.71 - 1.83: 1512 Bond restraints: 141628 Sorted by residual: bond pdb=" CG MET B3689 " pdb=" SD MET B3689 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.29e+00 bond pdb=" CG MET C3689 " pdb=" SD MET C3689 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.29e+00 bond pdb=" CG MET A3689 " pdb=" SD MET A3689 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.28e+00 bond pdb=" CG MET D3689 " pdb=" SD MET D3689 " ideal model delta sigma weight residual 1.803 1.758 0.045 2.50e-02 1.60e+03 3.27e+00 bond pdb=" CB TRP C 902 " pdb=" CG TRP C 902 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.12e+00 ... (remaining 141623 not shown) Histogram of bond angle deviations from ideal: 94.55 - 103.63: 1947 103.63 - 112.71: 75322 112.71 - 121.79: 85494 121.79 - 130.87: 27829 130.87 - 139.95: 764 Bond angle restraints: 191356 Sorted by residual: angle pdb=" CB MET B4292 " pdb=" CG MET B4292 " pdb=" SD MET B4292 " ideal model delta sigma weight residual 112.70 135.13 -22.43 3.00e+00 1.11e-01 5.59e+01 angle pdb=" CB MET C4292 " pdb=" CG MET C4292 " pdb=" SD MET C4292 " ideal model delta sigma weight residual 112.70 135.12 -22.42 3.00e+00 1.11e-01 5.58e+01 angle pdb=" CB MET D4292 " pdb=" CG MET D4292 " pdb=" SD MET D4292 " ideal model delta sigma weight residual 112.70 135.10 -22.40 3.00e+00 1.11e-01 5.57e+01 angle pdb=" CB MET A4292 " pdb=" CG MET A4292 " pdb=" SD MET A4292 " ideal model delta sigma weight residual 112.70 135.05 -22.35 3.00e+00 1.11e-01 5.55e+01 angle pdb=" CB MET D2512 " pdb=" CG MET D2512 " pdb=" SD MET D2512 " ideal model delta sigma weight residual 112.70 129.15 -16.45 3.00e+00 1.11e-01 3.01e+01 ... (remaining 191351 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 77484 17.62 - 35.24: 6399 35.24 - 52.86: 1063 52.86 - 70.48: 314 70.48 - 88.10: 152 Dihedral angle restraints: 85412 sinusoidal: 35052 harmonic: 50360 Sorted by residual: dihedral pdb=" CA PHE D4640 " pdb=" C PHE D4640 " pdb=" N PRO D4641 " pdb=" CA PRO D4641 " ideal model delta harmonic sigma weight residual 180.00 -136.99 -43.01 0 5.00e+00 4.00e-02 7.40e+01 dihedral pdb=" CA PHE C4640 " pdb=" C PHE C4640 " pdb=" N PRO C4641 " pdb=" CA PRO C4641 " ideal model delta harmonic sigma weight residual -180.00 -137.01 -42.99 0 5.00e+00 4.00e-02 7.39e+01 dihedral pdb=" CA PHE B4640 " pdb=" C PHE B4640 " pdb=" N PRO B4641 " pdb=" CA PRO B4641 " ideal model delta harmonic sigma weight residual 180.00 -137.04 -42.96 0 5.00e+00 4.00e-02 7.38e+01 ... (remaining 85409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 19285 0.075 - 0.150: 1633 0.150 - 0.226: 57 0.226 - 0.301: 5 0.301 - 0.376: 8 Chirality restraints: 20988 Sorted by residual: chirality pdb=" CB ILE C2478 " pdb=" CA ILE C2478 " pdb=" CG1 ILE C2478 " pdb=" CG2 ILE C2478 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE B2478 " pdb=" CA ILE B2478 " pdb=" CG1 ILE B2478 " pdb=" CG2 ILE B2478 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB ILE D2478 " pdb=" CA ILE D2478 " pdb=" CG1 ILE D2478 " pdb=" CG2 ILE D2478 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.47e+00 ... (remaining 20985 not shown) Planarity restraints: 24588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A4640 " 0.100 5.00e-02 4.00e+02 1.54e-01 3.82e+01 pdb=" N PRO A4641 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO A4641 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO A4641 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B4640 " 0.100 5.00e-02 4.00e+02 1.54e-01 3.82e+01 pdb=" N PRO B4641 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO B4641 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO B4641 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C4640 " 0.100 5.00e-02 4.00e+02 1.54e-01 3.81e+01 pdb=" N PRO C4641 " -0.267 5.00e-02 4.00e+02 pdb=" CA PRO C4641 " 0.088 5.00e-02 4.00e+02 pdb=" CD PRO C4641 " 0.078 5.00e-02 4.00e+02 ... (remaining 24585 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 2535 2.66 - 3.22: 142515 3.22 - 3.78: 233895 3.78 - 4.34: 315407 4.34 - 4.90: 495636 Nonbonded interactions: 1189988 Sorted by model distance: nonbonded pdb=" OG SER D2764 " pdb=" OE1 GLU D2767 " model vdw 2.104 2.440 nonbonded pdb=" OG SER B2764 " pdb=" OE1 GLU B2767 " model vdw 2.104 2.440 nonbonded pdb=" OG SER C2764 " pdb=" OE1 GLU C2767 " model vdw 2.104 2.440 nonbonded pdb=" OG SER A2764 " pdb=" OE1 GLU A2767 " model vdw 2.104 2.440 nonbonded pdb=" NH2 ARG D 290 " pdb=" O THR D 351 " model vdw 2.120 2.520 ... (remaining 1189983 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 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'B' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'C' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) selection = (chain 'D' and (resid 10 through 2577 or resid 2579 through 2837 or resid 2839 t \ hrough 4967 or resid 5001 through 5003)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 8.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 31.240 Check model and map are aligned: 1.540 Set scattering table: 0.970 Process input model: 441.080 Find NCS groups from input model: 7.690 Set up NCS constraints: 0.980 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:2.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 494.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 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 0.050 141628 Z= 0.228 Angle : 0.752 22.431 191356 Z= 0.423 Chirality : 0.043 0.376 20988 Planarity : 0.005 0.154 24588 Dihedral : 13.895 88.102 52936 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.33 % Favored : 96.58 % Rotamer: Outliers : 0.24 % Allowed : 0.43 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 0.41 (0.06), residues: 17212 helix: 1.10 (0.06), residues: 8960 sheet: -0.15 (0.13), residues: 1468 loop : -0.67 (0.08), residues: 6784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP A2785 HIS 0.012 0.001 HIS B3732 PHE 0.028 0.002 PHE B3162 TYR 0.030 0.002 TYR D1703 ARG 0.017 0.001 ARG B2886 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 887 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 850 time to evaluate : 12.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8748 (tpt) cc_final: 0.8475 (tpt) REVERT: A 240 HIS cc_start: 0.7809 (m-70) cc_final: 0.7603 (m-70) REVERT: A 902 TRP cc_start: 0.4070 (t-100) cc_final: 0.3470 (t-100) REVERT: A 995 MET cc_start: 0.8761 (ttt) cc_final: 0.8559 (ttt) REVERT: A 1168 MET cc_start: 0.8593 (mmm) cc_final: 0.7949 (mmm) REVERT: A 1306 MET cc_start: 0.8711 (mtp) cc_final: 0.8495 (mtm) REVERT: A 1975 MET cc_start: 0.8844 (tmm) cc_final: 0.8588 (tmm) REVERT: A 2234 MET cc_start: 0.8585 (tpp) cc_final: 0.8372 (tpt) REVERT: A 2279 MET cc_start: 0.8310 (tmm) cc_final: 0.7977 (tmm) REVERT: A 2384 MET cc_start: 0.8935 (mmm) cc_final: 0.8578 (mmp) REVERT: A 2512 MET cc_start: 0.9126 (ttp) cc_final: 0.8842 (tpp) REVERT: A 2541 HIS cc_start: 0.9070 (m90) cc_final: 0.8732 (m-70) REVERT: A 2584 MET cc_start: 0.8782 (mpp) cc_final: 0.8413 (mpp) REVERT: A 2585 MET cc_start: 0.8074 (mpp) cc_final: 0.7873 (mmt) REVERT: A 2605 MET cc_start: 0.8626 (tmm) cc_final: 0.8335 (tmm) REVERT: A 2688 MET cc_start: 0.8094 (mmp) cc_final: 0.7874 (tpp) REVERT: A 2689 MET cc_start: 0.6053 (ttt) cc_final: 0.5767 (ttt) REVERT: A 2719 TYR cc_start: 0.8681 (t80) cc_final: 0.7907 (t80) REVERT: A 2779 LEU cc_start: 0.9486 (OUTLIER) cc_final: 0.9242 (tp) REVERT: A 2782 MET cc_start: 0.8835 (tpt) cc_final: 0.8358 (mmm) REVERT: A 2848 TYR cc_start: 0.9108 (t80) cc_final: 0.8743 (t80) REVERT: A 2849 HIS cc_start: 0.9230 (t70) cc_final: 0.8567 (t-170) REVERT: A 2874 TYR cc_start: 0.7811 (t80) cc_final: 0.7506 (t80) REVERT: A 2886 ARG cc_start: 0.9238 (mpt180) cc_final: 0.8895 (mmt90) REVERT: A 2975 PHE cc_start: 0.8869 (m-80) cc_final: 0.8568 (m-80) REVERT: A 2982 PHE cc_start: 0.8852 (m-80) cc_final: 0.8261 (m-80) REVERT: A 3131 TYR cc_start: 0.9143 (m-80) cc_final: 0.8583 (m-80) REVERT: A 3245 TYR cc_start: 0.9078 (t80) cc_final: 0.8455 (t80) REVERT: A 3689 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7557 (mpp) REVERT: A 3719 MET cc_start: 0.8549 (mmp) cc_final: 0.8147 (tmm) REVERT: A 3954 MET cc_start: 0.8470 (mmm) cc_final: 0.8237 (mmt) REVERT: A 4186 MET cc_start: 0.8636 (mmm) cc_final: 0.8045 (mmm) REVERT: A 4256 MET cc_start: 0.8247 (mmt) cc_final: 0.7997 (mmm) REVERT: A 4274 MET cc_start: 0.6255 (OUTLIER) cc_final: 0.5848 (mpp) REVERT: A 4279 MET cc_start: 0.6958 (mtt) cc_final: 0.6744 (mtt) REVERT: E 58 LYS cc_start: 0.8581 (pttm) cc_final: 0.8102 (pttm) REVERT: E 62 GLU cc_start: 0.8308 (mp0) cc_final: 0.7671 (mp0) REVERT: E 101 ASP cc_start: 0.7977 (t70) cc_final: 0.7649 (t0) REVERT: F 4 GLU cc_start: 0.7770 (mp0) cc_final: 0.7415 (mp0) REVERT: F 101 ASP cc_start: 0.8096 (t70) cc_final: 0.7825 (t0) REVERT: G 4 GLU cc_start: 0.7683 (mp0) cc_final: 0.7329 (mp0) REVERT: G 101 ASP cc_start: 0.8050 (t70) cc_final: 0.7772 (t0) REVERT: H 101 ASP cc_start: 0.7993 (t70) cc_final: 0.7652 (t0) REVERT: B 81 MET cc_start: 0.8798 (tpt) cc_final: 0.8534 (tpt) REVERT: B 240 HIS cc_start: 0.7754 (m-70) cc_final: 0.7541 (m-70) REVERT: B 895 MET cc_start: 0.8896 (mtm) cc_final: 0.8166 (tpt) REVERT: B 902 TRP cc_start: 0.3861 (t-100) cc_final: 0.3557 (t-100) REVERT: B 1306 MET cc_start: 0.8749 (mtp) cc_final: 0.8516 (mtm) REVERT: B 1729 MET cc_start: 0.7926 (ptt) cc_final: 0.7705 (ptp) REVERT: B 1975 MET cc_start: 0.8899 (tmm) cc_final: 0.8497 (tmm) REVERT: B 2150 MET cc_start: 0.8410 (mtp) cc_final: 0.8179 (mtt) REVERT: B 2167 MET cc_start: 0.8524 (ptm) cc_final: 0.8224 (ptm) REVERT: B 2234 MET cc_start: 0.8702 (tpp) cc_final: 0.8451 (tpp) REVERT: B 2279 MET cc_start: 0.8298 (tmm) cc_final: 0.7941 (tmm) REVERT: B 2384 MET cc_start: 0.8888 (mmm) cc_final: 0.8472 (mmp) REVERT: B 2512 MET cc_start: 0.9247 (ttp) cc_final: 0.8877 (tpp) REVERT: B 2541 HIS cc_start: 0.9012 (m90) cc_final: 0.8639 (m170) REVERT: B 2584 MET cc_start: 0.8691 (mpp) cc_final: 0.8304 (mpp) REVERT: B 2605 MET cc_start: 0.8538 (tmm) cc_final: 0.8214 (tmm) REVERT: B 2719 TYR cc_start: 0.8730 (t80) cc_final: 0.7671 (t80) REVERT: B 2732 TRP cc_start: 0.8984 (t60) cc_final: 0.8769 (t60) REVERT: B 2782 MET cc_start: 0.8849 (tpt) cc_final: 0.8433 (mmm) REVERT: B 2849 HIS cc_start: 0.9296 (t70) cc_final: 0.8676 (t-170) REVERT: B 2874 TYR cc_start: 0.7820 (t80) cc_final: 0.7431 (t80) REVERT: B 2939 TYR cc_start: 0.8830 (m-80) cc_final: 0.8169 (m-10) REVERT: B 2975 PHE cc_start: 0.8877 (m-80) cc_final: 0.8551 (m-80) REVERT: B 2982 PHE cc_start: 0.8797 (m-80) cc_final: 0.8219 (m-80) REVERT: B 3131 TYR cc_start: 0.9163 (m-80) cc_final: 0.8378 (m-80) REVERT: B 3181 TYR cc_start: 0.8135 (t80) cc_final: 0.7745 (t80) REVERT: B 3245 TYR cc_start: 0.9077 (t80) cc_final: 0.8528 (t80) REVERT: B 3304 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8826 (tp-100) REVERT: B 3689 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7508 (mpp) REVERT: B 4274 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5914 (mpp) REVERT: B 4279 MET cc_start: 0.7049 (mtt) cc_final: 0.6845 (mtt) REVERT: B 4568 MET cc_start: 0.7637 (mmm) cc_final: 0.7324 (tpp) REVERT: B 4672 MET cc_start: 0.7967 (mtm) cc_final: 0.7686 (mtp) REVERT: B 4728 MET cc_start: 0.8445 (mmm) cc_final: 0.8196 (mmt) REVERT: C 81 MET cc_start: 0.8822 (tpt) cc_final: 0.8534 (tpt) REVERT: C 902 TRP cc_start: 0.3734 (t-100) cc_final: 0.3451 (t-100) REVERT: C 995 MET cc_start: 0.8762 (ttt) cc_final: 0.8558 (ttt) REVERT: C 1306 MET cc_start: 0.8739 (mtp) cc_final: 0.8510 (mtm) REVERT: C 1628 MET cc_start: 0.8722 (ttm) cc_final: 0.8430 (ttm) REVERT: C 1729 MET cc_start: 0.7874 (ptt) cc_final: 0.7663 (ptp) REVERT: C 1975 MET cc_start: 0.8882 (tmm) cc_final: 0.8485 (tmm) REVERT: C 2234 MET cc_start: 0.8705 (tpp) cc_final: 0.8459 (tpp) REVERT: C 2279 MET cc_start: 0.8353 (tmm) cc_final: 0.8027 (tmm) REVERT: C 2384 MET cc_start: 0.8884 (mmm) cc_final: 0.8605 (mmm) REVERT: C 2512 MET cc_start: 0.9225 (ttp) cc_final: 0.8805 (tpp) REVERT: C 2541 HIS cc_start: 0.9033 (m90) cc_final: 0.8655 (m170) REVERT: C 2584 MET cc_start: 0.8683 (mpp) cc_final: 0.8329 (mpp) REVERT: C 2688 MET cc_start: 0.8031 (mmp) cc_final: 0.7784 (mmm) REVERT: C 2719 TYR cc_start: 0.8699 (t80) cc_final: 0.7857 (t80) REVERT: C 2782 MET cc_start: 0.8833 (tpt) cc_final: 0.8412 (mmm) REVERT: C 2849 HIS cc_start: 0.9294 (t70) cc_final: 0.8673 (t-170) REVERT: C 2874 TYR cc_start: 0.7787 (t80) cc_final: 0.7226 (t80) REVERT: C 2886 ARG cc_start: 0.9286 (mpt180) cc_final: 0.8974 (mmt90) REVERT: C 2939 TYR cc_start: 0.8858 (m-80) cc_final: 0.8216 (m-10) REVERT: C 2975 PHE cc_start: 0.8880 (m-80) cc_final: 0.8547 (m-80) REVERT: C 2982 PHE cc_start: 0.8799 (m-80) cc_final: 0.8247 (m-80) REVERT: C 3131 TYR cc_start: 0.9149 (m-80) cc_final: 0.8328 (m-80) REVERT: C 3181 TYR cc_start: 0.8143 (t80) cc_final: 0.7837 (t80) REVERT: C 3245 TYR cc_start: 0.9067 (t80) cc_final: 0.8528 (t80) REVERT: C 3304 GLN cc_start: 0.9268 (tp-100) cc_final: 0.8869 (tp-100) REVERT: C 3689 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7560 (mpp) REVERT: C 4186 MET cc_start: 0.8435 (mmm) cc_final: 0.7986 (mmm) REVERT: C 4274 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.5885 (mpp) REVERT: C 4279 MET cc_start: 0.6954 (mtt) cc_final: 0.6747 (mtt) REVERT: C 4672 MET cc_start: 0.8021 (mtm) cc_final: 0.7756 (mtp) REVERT: D 81 MET cc_start: 0.8811 (tpt) cc_final: 0.8509 (tpt) REVERT: D 902 TRP cc_start: 0.3801 (t-100) cc_final: 0.3174 (t-100) REVERT: D 1168 MET cc_start: 0.8615 (mmm) cc_final: 0.7931 (mmm) REVERT: D 1306 MET cc_start: 0.8753 (mtp) cc_final: 0.8527 (mtm) REVERT: D 1975 MET cc_start: 0.8860 (tmm) cc_final: 0.8442 (tmm) REVERT: D 2234 MET cc_start: 0.8674 (tpp) cc_final: 0.8462 (tpt) REVERT: D 2279 MET cc_start: 0.8312 (tmm) cc_final: 0.7989 (tmm) REVERT: D 2384 MET cc_start: 0.8921 (mmm) cc_final: 0.8581 (mmp) REVERT: D 2512 MET cc_start: 0.9210 (ttp) cc_final: 0.8827 (tpp) REVERT: D 2541 HIS cc_start: 0.9040 (m90) cc_final: 0.8660 (m170) REVERT: D 2584 MET cc_start: 0.8698 (mpp) cc_final: 0.8362 (mpp) REVERT: D 2605 MET cc_start: 0.8550 (tmm) cc_final: 0.8249 (tmm) REVERT: D 2688 MET cc_start: 0.8000 (mmp) cc_final: 0.7791 (mmm) REVERT: D 2719 TYR cc_start: 0.8718 (t80) cc_final: 0.7684 (t80) REVERT: D 2782 MET cc_start: 0.8849 (tpt) cc_final: 0.8430 (mmm) REVERT: D 2848 TYR cc_start: 0.9109 (t80) cc_final: 0.8730 (t80) REVERT: D 2849 HIS cc_start: 0.9261 (t70) cc_final: 0.8704 (t-170) REVERT: D 2874 TYR cc_start: 0.7902 (t80) cc_final: 0.7589 (t80) REVERT: D 2939 TYR cc_start: 0.8897 (m-80) cc_final: 0.8275 (m-10) REVERT: D 2975 PHE cc_start: 0.8878 (m-80) cc_final: 0.8519 (m-80) REVERT: D 2982 PHE cc_start: 0.8821 (m-80) cc_final: 0.8234 (m-80) REVERT: D 3131 TYR cc_start: 0.9139 (m-80) cc_final: 0.8608 (m-80) REVERT: D 3181 TYR cc_start: 0.8150 (t80) cc_final: 0.7859 (t80) REVERT: D 3245 TYR cc_start: 0.9083 (t80) cc_final: 0.8481 (t80) REVERT: D 3689 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7599 (mpp) REVERT: D 4274 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5928 (mpp) REVERT: D 4672 MET cc_start: 0.8124 (mtm) cc_final: 0.7690 (mtp) REVERT: D 4728 MET cc_start: 0.8463 (mmm) cc_final: 0.8207 (mmp) outliers start: 37 outliers final: 4 residues processed: 858 average time/residue: 1.2059 time to fit residues: 1813.8575 Evaluate side-chains 751 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 738 time to evaluate : 12.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 2779 LEU Chi-restraints excluded: chain A residue 3689 MET Chi-restraints excluded: chain A residue 4274 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 3689 MET Chi-restraints excluded: chain B residue 4274 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 3689 MET Chi-restraints excluded: chain C residue 4274 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 3689 MET Chi-restraints excluded: chain D residue 4274 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1459 optimal weight: 9.9990 chunk 1309 optimal weight: 20.0000 chunk 726 optimal weight: 30.0000 chunk 447 optimal weight: 4.9990 chunk 883 optimal weight: 2.9990 chunk 699 optimal weight: 9.9990 chunk 1354 optimal weight: 10.0000 chunk 524 optimal weight: 8.9990 chunk 823 optimal weight: 9.9990 chunk 1008 optimal weight: 20.0000 chunk 1569 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3865 ASN ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 HIS ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3865 ASN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3308 ASN ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C3865 ASN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1005 ASN ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3308 ASN ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D3865 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 141628 Z= 0.390 Angle : 0.688 13.465 191356 Z= 0.355 Chirality : 0.043 0.270 20988 Planarity : 0.005 0.139 24588 Dihedral : 6.741 86.114 19066 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.40 % Rotamer: Outliers : 0.35 % Allowed : 3.42 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.06), residues: 17212 helix: 1.28 (0.05), residues: 9000 sheet: -0.19 (0.13), residues: 1536 loop : -0.68 (0.08), residues: 6676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 893 HIS 0.024 0.001 HIS A3034 PHE 0.024 0.002 PHE D2921 TYR 0.032 0.002 TYR D1703 ARG 0.009 0.001 ARG B2886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 790 time to evaluate : 12.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8805 (tpt) cc_final: 0.8575 (tpt) REVERT: A 240 HIS cc_start: 0.7852 (m-70) cc_final: 0.7540 (m-70) REVERT: A 902 TRP cc_start: 0.4612 (t-100) cc_final: 0.3761 (t-100) REVERT: A 995 MET cc_start: 0.8842 (ttt) cc_final: 0.8620 (ttt) REVERT: A 1306 MET cc_start: 0.8799 (mtp) cc_final: 0.8561 (mtm) REVERT: A 1975 MET cc_start: 0.8836 (tmm) cc_final: 0.8413 (tmm) REVERT: A 2172 MET cc_start: 0.8846 (tpp) cc_final: 0.8492 (tpp) REVERT: A 2214 MET cc_start: 0.9347 (mmm) cc_final: 0.9076 (tpp) REVERT: A 2279 MET cc_start: 0.8249 (tmm) cc_final: 0.8016 (tmm) REVERT: A 2541 HIS cc_start: 0.9137 (m90) cc_final: 0.8803 (m-70) REVERT: A 2584 MET cc_start: 0.8717 (mpp) cc_final: 0.8377 (mpp) REVERT: A 2585 MET cc_start: 0.8336 (mpp) cc_final: 0.8025 (mmt) REVERT: A 2605 MET cc_start: 0.8678 (tmm) cc_final: 0.8352 (tmm) REVERT: A 2689 MET cc_start: 0.6421 (ttt) cc_final: 0.6144 (ttt) REVERT: A 2719 TYR cc_start: 0.8744 (t80) cc_final: 0.7916 (t80) REVERT: A 2782 MET cc_start: 0.9028 (tpt) cc_final: 0.8500 (mmm) REVERT: A 2843 MET cc_start: 0.9066 (ppp) cc_final: 0.8578 (ppp) REVERT: A 2849 HIS cc_start: 0.9319 (t70) cc_final: 0.8677 (t-170) REVERT: A 2874 TYR cc_start: 0.7965 (t80) cc_final: 0.7702 (t80) REVERT: A 2975 PHE cc_start: 0.8933 (m-80) cc_final: 0.8586 (m-80) REVERT: A 2982 PHE cc_start: 0.8807 (m-80) cc_final: 0.8221 (m-80) REVERT: A 3131 TYR cc_start: 0.9176 (m-80) cc_final: 0.8515 (m-80) REVERT: A 3246 MET cc_start: 0.8942 (mmt) cc_final: 0.8738 (mmt) REVERT: A 3304 GLN cc_start: 0.9311 (tp-100) cc_final: 0.8955 (tp-100) REVERT: A 4143 LYS cc_start: 0.9005 (tppt) cc_final: 0.8684 (tppt) REVERT: A 4728 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: E 101 ASP cc_start: 0.8171 (t70) cc_final: 0.7870 (t0) REVERT: F 4 GLU cc_start: 0.7797 (mp0) cc_final: 0.7302 (mp0) REVERT: F 67 MET cc_start: 0.8575 (mtp) cc_final: 0.8322 (mtp) REVERT: F 101 ASP cc_start: 0.8224 (t70) cc_final: 0.7961 (t0) REVERT: G 4 GLU cc_start: 0.7739 (mp0) cc_final: 0.7266 (mp0) REVERT: G 101 ASP cc_start: 0.8220 (t70) cc_final: 0.7967 (t0) REVERT: H 67 MET cc_start: 0.8580 (mtp) cc_final: 0.8283 (mtp) REVERT: H 101 ASP cc_start: 0.8153 (t70) cc_final: 0.7885 (t0) REVERT: B 81 MET cc_start: 0.8842 (tpt) cc_final: 0.8618 (tpt) REVERT: B 240 HIS cc_start: 0.7809 (m-70) cc_final: 0.7522 (m-70) REVERT: B 902 TRP cc_start: 0.4244 (t-100) cc_final: 0.3657 (t-100) REVERT: B 935 MET cc_start: 0.8848 (ppp) cc_final: 0.8509 (ppp) REVERT: B 1306 MET cc_start: 0.8822 (mtp) cc_final: 0.8586 (mtm) REVERT: B 1729 MET cc_start: 0.7943 (ptt) cc_final: 0.7720 (ptp) REVERT: B 1975 MET cc_start: 0.8874 (tmm) cc_final: 0.8430 (tmm) REVERT: B 2162 MET cc_start: 0.8751 (mmp) cc_final: 0.8391 (mmp) REVERT: B 2167 MET cc_start: 0.8817 (ptm) cc_final: 0.8389 (ptm) REVERT: B 2172 MET cc_start: 0.8843 (tpp) cc_final: 0.8555 (tpp) REVERT: B 2214 MET cc_start: 0.9282 (mmm) cc_final: 0.8735 (mmm) REVERT: B 2279 MET cc_start: 0.8261 (tmm) cc_final: 0.7993 (tmm) REVERT: B 2541 HIS cc_start: 0.9110 (m90) cc_final: 0.8779 (m-70) REVERT: B 2584 MET cc_start: 0.8624 (mpp) cc_final: 0.8247 (mpp) REVERT: B 2585 MET cc_start: 0.9045 (mmt) cc_final: 0.8486 (mmt) REVERT: B 2605 MET cc_start: 0.8574 (tmm) cc_final: 0.8236 (tmm) REVERT: B 2688 MET cc_start: 0.8372 (mmm) cc_final: 0.8171 (tpp) REVERT: B 2689 MET cc_start: 0.5799 (ttt) cc_final: 0.5396 (ttt) REVERT: B 2719 TYR cc_start: 0.8715 (t80) cc_final: 0.8078 (t80) REVERT: B 2732 TRP cc_start: 0.9020 (t60) cc_final: 0.8782 (t60) REVERT: B 2782 MET cc_start: 0.9052 (tpt) cc_final: 0.8657 (mmm) REVERT: B 2798 MET cc_start: 0.8877 (ppp) cc_final: 0.8629 (ppp) REVERT: B 2828 MET cc_start: 0.7632 (mtt) cc_final: 0.7263 (mtp) REVERT: B 2843 MET cc_start: 0.9063 (ppp) cc_final: 0.8679 (ppp) REVERT: B 2849 HIS cc_start: 0.9352 (t70) cc_final: 0.8839 (t-170) REVERT: B 2874 TYR cc_start: 0.8042 (t80) cc_final: 0.7637 (t80) REVERT: B 2939 TYR cc_start: 0.8948 (m-80) cc_final: 0.8266 (m-10) REVERT: B 2975 PHE cc_start: 0.8877 (m-80) cc_final: 0.8560 (m-80) REVERT: B 2982 PHE cc_start: 0.8767 (m-80) cc_final: 0.8176 (m-80) REVERT: B 3046 MET cc_start: 0.8949 (tpp) cc_final: 0.8638 (tpp) REVERT: B 3104 MET cc_start: 0.8471 (tmm) cc_final: 0.8245 (tmm) REVERT: B 3109 PHE cc_start: 0.9139 (m-10) cc_final: 0.8913 (m-10) REVERT: B 3131 TYR cc_start: 0.9193 (m-80) cc_final: 0.8819 (m-80) REVERT: B 3162 PHE cc_start: 0.9264 (t80) cc_final: 0.8824 (t80) REVERT: B 3166 PHE cc_start: 0.8853 (t80) cc_final: 0.8615 (t80) REVERT: B 3181 TYR cc_start: 0.8197 (t80) cc_final: 0.7827 (t80) REVERT: B 3245 TYR cc_start: 0.9072 (t80) cc_final: 0.8565 (t80) REVERT: B 3304 GLN cc_start: 0.9267 (tp-100) cc_final: 0.8809 (tp-100) REVERT: B 3819 MET cc_start: 0.7142 (mpp) cc_final: 0.6233 (ptp) REVERT: B 4143 LYS cc_start: 0.8994 (tppt) cc_final: 0.8507 (tppt) REVERT: B 4568 MET cc_start: 0.7662 (mmm) cc_final: 0.7314 (mpp) REVERT: B 4672 MET cc_start: 0.8127 (mtm) cc_final: 0.7621 (mtm) REVERT: C 81 MET cc_start: 0.8873 (tpt) cc_final: 0.8402 (tpt) REVERT: C 895 MET cc_start: 0.8774 (ptp) cc_final: 0.8529 (ppp) REVERT: C 902 TRP cc_start: 0.4247 (t-100) cc_final: 0.3681 (t-100) REVERT: C 935 MET cc_start: 0.8881 (ppp) cc_final: 0.8534 (ppp) REVERT: C 995 MET cc_start: 0.8825 (ttt) cc_final: 0.8600 (ttt) REVERT: C 1165 MET cc_start: 0.8264 (ttt) cc_final: 0.8020 (mtp) REVERT: C 1306 MET cc_start: 0.8809 (mtp) cc_final: 0.8570 (mtm) REVERT: C 1628 MET cc_start: 0.8809 (ttm) cc_final: 0.8554 (ttm) REVERT: C 1729 MET cc_start: 0.7928 (ptt) cc_final: 0.7702 (ptp) REVERT: C 1975 MET cc_start: 0.8867 (tmm) cc_final: 0.8419 (tmm) REVERT: C 2172 MET cc_start: 0.8843 (tpp) cc_final: 0.8470 (tpp) REVERT: C 2214 MET cc_start: 0.9309 (mmm) cc_final: 0.8799 (mmm) REVERT: C 2279 MET cc_start: 0.8290 (tmm) cc_final: 0.8057 (tmm) REVERT: C 2541 HIS cc_start: 0.9104 (m90) cc_final: 0.8778 (m-70) REVERT: C 2584 MET cc_start: 0.8606 (mpp) cc_final: 0.8244 (mpp) REVERT: C 2585 MET cc_start: 0.9066 (mmt) cc_final: 0.8513 (mmt) REVERT: C 2605 MET cc_start: 0.8750 (ttp) cc_final: 0.8219 (tmm) REVERT: C 2689 MET cc_start: 0.5909 (ttt) cc_final: 0.5608 (ttt) REVERT: C 2719 TYR cc_start: 0.8789 (t80) cc_final: 0.7661 (t80) REVERT: C 2782 MET cc_start: 0.9036 (tpt) cc_final: 0.8565 (mmm) REVERT: C 2843 MET cc_start: 0.9062 (ppp) cc_final: 0.8667 (ppp) REVERT: C 2849 HIS cc_start: 0.9338 (t70) cc_final: 0.8840 (t-170) REVERT: C 2874 TYR cc_start: 0.7943 (t80) cc_final: 0.7615 (t80) REVERT: C 2939 TYR cc_start: 0.8948 (m-80) cc_final: 0.8285 (m-10) REVERT: C 2975 PHE cc_start: 0.8900 (m-80) cc_final: 0.8577 (m-80) REVERT: C 2982 PHE cc_start: 0.8786 (m-80) cc_final: 0.8220 (m-80) REVERT: C 3046 MET cc_start: 0.8934 (tpp) cc_final: 0.8627 (tpt) REVERT: C 3109 PHE cc_start: 0.9134 (m-10) cc_final: 0.8906 (m-10) REVERT: C 3131 TYR cc_start: 0.9191 (m-80) cc_final: 0.8538 (m-80) REVERT: C 3162 PHE cc_start: 0.9231 (t80) cc_final: 0.8755 (t80) REVERT: C 3166 PHE cc_start: 0.8794 (t80) cc_final: 0.8548 (t80) REVERT: C 3181 TYR cc_start: 0.8253 (t80) cc_final: 0.7968 (t80) REVERT: C 3245 TYR cc_start: 0.9053 (t80) cc_final: 0.8551 (t80) REVERT: C 3304 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8834 (tp-100) REVERT: C 4274 MET cc_start: 0.6311 (mpp) cc_final: 0.5130 (tmm) REVERT: C 4672 MET cc_start: 0.8135 (mtm) cc_final: 0.7457 (mtm) REVERT: C 4728 MET cc_start: 0.8466 (mmp) cc_final: 0.8219 (mmm) REVERT: C 4809 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8310 (tpp) REVERT: D 81 MET cc_start: 0.8873 (tpt) cc_final: 0.8642 (tpt) REVERT: D 895 MET cc_start: 0.8811 (ptp) cc_final: 0.8560 (ppp) REVERT: D 902 TRP cc_start: 0.4318 (t-100) cc_final: 0.3514 (t-100) REVERT: D 935 MET cc_start: 0.8857 (ppp) cc_final: 0.8489 (ppp) REVERT: D 1165 MET cc_start: 0.8253 (ttt) cc_final: 0.7975 (mtp) REVERT: D 1306 MET cc_start: 0.8823 (mtp) cc_final: 0.8591 (mtm) REVERT: D 1975 MET cc_start: 0.8850 (tmm) cc_final: 0.8379 (tmm) REVERT: D 2172 MET cc_start: 0.8862 (tpp) cc_final: 0.8465 (tpp) REVERT: D 2214 MET cc_start: 0.9334 (mmm) cc_final: 0.8816 (mmm) REVERT: D 2279 MET cc_start: 0.8261 (tmm) cc_final: 0.8020 (tmm) REVERT: D 2541 HIS cc_start: 0.9117 (m90) cc_final: 0.8800 (m-70) REVERT: D 2584 MET cc_start: 0.8627 (mpp) cc_final: 0.8333 (mpp) REVERT: D 2585 MET cc_start: 0.9070 (mmt) cc_final: 0.8435 (mmt) REVERT: D 2605 MET cc_start: 0.8615 (tmm) cc_final: 0.8267 (tmm) REVERT: D 2689 MET cc_start: 0.5887 (ttt) cc_final: 0.5405 (ttt) REVERT: D 2719 TYR cc_start: 0.8688 (t80) cc_final: 0.8049 (t80) REVERT: D 2782 MET cc_start: 0.9050 (tpt) cc_final: 0.8536 (mmm) REVERT: D 2798 MET cc_start: 0.8885 (ppp) cc_final: 0.8644 (ppp) REVERT: D 2843 MET cc_start: 0.9049 (ppp) cc_final: 0.8633 (ppp) REVERT: D 2849 HIS cc_start: 0.9355 (t70) cc_final: 0.8845 (t-170) REVERT: D 2874 TYR cc_start: 0.7998 (t80) cc_final: 0.7670 (t80) REVERT: D 2939 TYR cc_start: 0.8976 (m-80) cc_final: 0.8324 (m-10) REVERT: D 2975 PHE cc_start: 0.8918 (m-80) cc_final: 0.8547 (m-80) REVERT: D 2982 PHE cc_start: 0.8808 (m-80) cc_final: 0.8208 (m-80) REVERT: D 3131 TYR cc_start: 0.9166 (m-80) cc_final: 0.8524 (m-80) REVERT: D 3181 TYR cc_start: 0.8199 (t80) cc_final: 0.7969 (t80) REVERT: D 3245 TYR cc_start: 0.9097 (t80) cc_final: 0.8563 (t80) REVERT: D 3304 GLN cc_start: 0.9295 (tp-100) cc_final: 0.8866 (tp-100) REVERT: D 4672 MET cc_start: 0.8190 (mtm) cc_final: 0.7583 (mtm) outliers start: 53 outliers final: 26 residues processed: 807 average time/residue: 1.1826 time to fit residues: 1702.4200 Evaluate side-chains 783 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 755 time to evaluate : 12.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 2739 ASN Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3073 GLU Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 4012 MET Chi-restraints excluded: chain C residue 4809 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3285 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 872 optimal weight: 7.9990 chunk 487 optimal weight: 10.0000 chunk 1306 optimal weight: 20.0000 chunk 1068 optimal weight: 7.9990 chunk 432 optimal weight: 4.9990 chunk 1572 optimal weight: 7.9990 chunk 1698 optimal weight: 9.9990 chunk 1400 optimal weight: 0.6980 chunk 1558 optimal weight: 5.9990 chunk 535 optimal weight: 4.9990 chunk 1261 optimal weight: 5.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A4620 GLN ** B 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 HIS ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3308 ASN ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 630 HIS ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 HIS ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 141628 Z= 0.282 Angle : 0.616 11.578 191356 Z= 0.316 Chirality : 0.041 0.205 20988 Planarity : 0.005 0.129 24588 Dihedral : 6.486 82.549 19040 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.44 % Favored : 96.47 % Rotamer: Outliers : 0.41 % Allowed : 5.04 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.06), residues: 17212 helix: 1.41 (0.05), residues: 9064 sheet: -0.16 (0.13), residues: 1544 loop : -0.70 (0.08), residues: 6604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A2852 HIS 0.015 0.001 HIS B4055 PHE 0.022 0.001 PHE A2921 TYR 0.034 0.002 TYR A1703 ARG 0.006 0.000 ARG A4503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 854 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 791 time to evaluate : 12.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8793 (tpt) cc_final: 0.8554 (tpt) REVERT: A 349 MET cc_start: 0.7602 (tpt) cc_final: 0.7227 (tpt) REVERT: A 494 MET cc_start: 0.8874 (mmp) cc_final: 0.8613 (mmp) REVERT: A 655 MET cc_start: 0.8577 (mmp) cc_final: 0.8349 (mmp) REVERT: A 899 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8363 (mp0) REVERT: A 902 TRP cc_start: 0.4642 (t-100) cc_final: 0.3775 (t-100) REVERT: A 995 MET cc_start: 0.8843 (ttt) cc_final: 0.8621 (ttt) REVERT: A 1306 MET cc_start: 0.8778 (mtp) cc_final: 0.8540 (mtm) REVERT: A 1975 MET cc_start: 0.8857 (tmm) cc_final: 0.8364 (tmm) REVERT: A 2172 MET cc_start: 0.8745 (tpp) cc_final: 0.8369 (tpp) REVERT: A 2214 MET cc_start: 0.9338 (mmm) cc_final: 0.9058 (mmm) REVERT: A 2234 MET cc_start: 0.8862 (tpt) cc_final: 0.8143 (tmm) REVERT: A 2279 MET cc_start: 0.8259 (tmm) cc_final: 0.8022 (tmm) REVERT: A 2541 HIS cc_start: 0.9127 (m90) cc_final: 0.8789 (m-70) REVERT: A 2584 MET cc_start: 0.8672 (mpp) cc_final: 0.8344 (mpp) REVERT: A 2585 MET cc_start: 0.8404 (mpp) cc_final: 0.8024 (mmt) REVERT: A 2605 MET cc_start: 0.8671 (tmm) cc_final: 0.8343 (tmm) REVERT: A 2719 TYR cc_start: 0.8709 (t80) cc_final: 0.7848 (t80) REVERT: A 2782 MET cc_start: 0.8955 (tpt) cc_final: 0.8534 (mmm) REVERT: A 2785 TRP cc_start: 0.8301 (m100) cc_final: 0.7968 (m-90) REVERT: A 2843 MET cc_start: 0.9013 (ppp) cc_final: 0.8555 (ppp) REVERT: A 2849 HIS cc_start: 0.9244 (t70) cc_final: 0.8410 (t-170) REVERT: A 2877 LEU cc_start: 0.8618 (mt) cc_final: 0.8378 (mt) REVERT: A 2975 PHE cc_start: 0.8891 (m-80) cc_final: 0.8669 (m-80) REVERT: A 2982 PHE cc_start: 0.8796 (m-80) cc_final: 0.8200 (m-80) REVERT: A 3131 TYR cc_start: 0.9188 (m-80) cc_final: 0.8468 (m-80) REVERT: A 3245 TYR cc_start: 0.9068 (t80) cc_final: 0.8658 (t80) REVERT: A 3246 MET cc_start: 0.8944 (mmt) cc_final: 0.8644 (mmt) REVERT: A 3304 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8889 (tp-100) REVERT: A 3605 MET cc_start: 0.4534 (mmm) cc_final: 0.4281 (mmm) REVERT: A 4143 LYS cc_start: 0.8961 (tppt) cc_final: 0.8723 (tppt) REVERT: A 4274 MET cc_start: 0.5722 (mmt) cc_final: 0.5485 (mmt) REVERT: A 4279 MET cc_start: 0.6744 (mtt) cc_final: 0.6194 (ttt) REVERT: A 4292 MET cc_start: 0.8501 (mmm) cc_final: 0.7948 (mmm) REVERT: A 4728 MET cc_start: 0.8356 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: A 4804 MET cc_start: 0.8481 (mmm) cc_final: 0.7947 (mmm) REVERT: A 4809 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8281 (tpp) REVERT: E 101 ASP cc_start: 0.8188 (t70) cc_final: 0.7936 (t0) REVERT: F 4 GLU cc_start: 0.7798 (mp0) cc_final: 0.7297 (mp0) REVERT: F 67 MET cc_start: 0.8559 (mtp) cc_final: 0.8357 (mtp) REVERT: F 101 ASP cc_start: 0.8225 (t70) cc_final: 0.7985 (t0) REVERT: G 4 GLU cc_start: 0.7756 (mp0) cc_final: 0.7246 (mp0) REVERT: G 101 ASP cc_start: 0.8234 (t70) cc_final: 0.7992 (t0) REVERT: H 67 MET cc_start: 0.8555 (mtp) cc_final: 0.8348 (mtp) REVERT: H 101 ASP cc_start: 0.8183 (t70) cc_final: 0.7937 (t0) REVERT: B 81 MET cc_start: 0.8826 (tpt) cc_final: 0.8599 (tpt) REVERT: B 349 MET cc_start: 0.7665 (tpt) cc_final: 0.7278 (tpt) REVERT: B 899 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8273 (mp0) REVERT: B 902 TRP cc_start: 0.4332 (t-100) cc_final: 0.3791 (t-100) REVERT: B 935 MET cc_start: 0.8851 (ppp) cc_final: 0.8522 (ppp) REVERT: B 1306 MET cc_start: 0.8814 (mtp) cc_final: 0.8602 (mtm) REVERT: B 1794 MET cc_start: 0.8930 (mtm) cc_final: 0.8649 (mtp) REVERT: B 1975 MET cc_start: 0.8884 (tmm) cc_final: 0.8395 (tmm) REVERT: B 2234 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8161 (tmm) REVERT: B 2279 MET cc_start: 0.8298 (tmm) cc_final: 0.8033 (tmm) REVERT: B 2541 HIS cc_start: 0.9096 (m90) cc_final: 0.8758 (m-70) REVERT: B 2584 MET cc_start: 0.8556 (mpp) cc_final: 0.8312 (mpp) REVERT: B 2585 MET cc_start: 0.9010 (mmt) cc_final: 0.8401 (mmm) REVERT: B 2605 MET cc_start: 0.8575 (tmm) cc_final: 0.8227 (tmm) REVERT: B 2689 MET cc_start: 0.6034 (ttt) cc_final: 0.5743 (ttt) REVERT: B 2719 TYR cc_start: 0.8682 (t80) cc_final: 0.8015 (t80) REVERT: B 2732 TRP cc_start: 0.8995 (t60) cc_final: 0.8794 (t60) REVERT: B 2782 MET cc_start: 0.9059 (tpt) cc_final: 0.8605 (mmm) REVERT: B 2798 MET cc_start: 0.8883 (ppp) cc_final: 0.8678 (ppp) REVERT: B 2840 MET cc_start: 0.8047 (mtt) cc_final: 0.7534 (mtt) REVERT: B 2843 MET cc_start: 0.9092 (ppp) cc_final: 0.8710 (ppp) REVERT: B 2849 HIS cc_start: 0.9299 (t70) cc_final: 0.8752 (t-170) REVERT: B 2874 TYR cc_start: 0.8053 (t80) cc_final: 0.7665 (t80) REVERT: B 2939 TYR cc_start: 0.8947 (m-80) cc_final: 0.8346 (m-10) REVERT: B 2975 PHE cc_start: 0.8842 (m-80) cc_final: 0.8634 (m-80) REVERT: B 2982 PHE cc_start: 0.8755 (m-80) cc_final: 0.8156 (m-80) REVERT: B 3046 MET cc_start: 0.8894 (tpp) cc_final: 0.8614 (tpt) REVERT: B 3104 MET cc_start: 0.8477 (tmm) cc_final: 0.8192 (tmm) REVERT: B 3109 PHE cc_start: 0.9107 (m-10) cc_final: 0.8896 (m-10) REVERT: B 3131 TYR cc_start: 0.9198 (m-80) cc_final: 0.8758 (m-80) REVERT: B 3181 TYR cc_start: 0.8230 (t80) cc_final: 0.7893 (t80) REVERT: B 3304 GLN cc_start: 0.9253 (tp-100) cc_final: 0.8791 (tp-100) REVERT: B 3819 MET cc_start: 0.7119 (mpp) cc_final: 0.6289 (ptp) REVERT: B 4143 LYS cc_start: 0.8950 (tppt) cc_final: 0.8726 (tppt) REVERT: B 4279 MET cc_start: 0.6594 (mtt) cc_final: 0.6180 (ttt) REVERT: B 4568 MET cc_start: 0.7673 (mmm) cc_final: 0.7294 (mpp) REVERT: B 4672 MET cc_start: 0.8141 (mtm) cc_final: 0.7422 (mtm) REVERT: C 81 MET cc_start: 0.8856 (tpt) cc_final: 0.8371 (tpt) REVERT: C 349 MET cc_start: 0.7472 (tpt) cc_final: 0.7015 (tpt) REVERT: C 655 MET cc_start: 0.8670 (mmp) cc_final: 0.8432 (mmp) REVERT: C 895 MET cc_start: 0.8757 (ptp) cc_final: 0.8536 (ppp) REVERT: C 902 TRP cc_start: 0.4297 (t-100) cc_final: 0.3714 (t-100) REVERT: C 935 MET cc_start: 0.8844 (ppp) cc_final: 0.8596 (ppp) REVERT: C 995 MET cc_start: 0.8834 (ttt) cc_final: 0.8595 (ttt) REVERT: C 1165 MET cc_start: 0.8059 (ttt) cc_final: 0.7759 (mtp) REVERT: C 1306 MET cc_start: 0.8806 (mtp) cc_final: 0.8590 (mtm) REVERT: C 1628 MET cc_start: 0.8804 (ttm) cc_final: 0.8550 (ttm) REVERT: C 1794 MET cc_start: 0.8948 (mtm) cc_final: 0.8657 (mtp) REVERT: C 1975 MET cc_start: 0.8879 (tmm) cc_final: 0.8388 (tmm) REVERT: C 2279 MET cc_start: 0.8323 (tmm) cc_final: 0.8097 (tmm) REVERT: C 2541 HIS cc_start: 0.9105 (m90) cc_final: 0.8766 (m-70) REVERT: C 2584 MET cc_start: 0.8536 (mpp) cc_final: 0.8313 (mpp) REVERT: C 2585 MET cc_start: 0.9026 (mmt) cc_final: 0.8432 (mmm) REVERT: C 2605 MET cc_start: 0.8740 (ttp) cc_final: 0.8220 (tmm) REVERT: C 2688 MET cc_start: 0.8532 (tpt) cc_final: 0.8265 (tpp) REVERT: C 2689 MET cc_start: 0.5887 (ttt) cc_final: 0.5529 (ttt) REVERT: C 2719 TYR cc_start: 0.8747 (t80) cc_final: 0.8122 (t80) REVERT: C 2782 MET cc_start: 0.9029 (tpt) cc_final: 0.8561 (mmm) REVERT: C 2798 MET cc_start: 0.8930 (ppp) cc_final: 0.8706 (ppp) REVERT: C 2843 MET cc_start: 0.9065 (ppp) cc_final: 0.8659 (ppp) REVERT: C 2849 HIS cc_start: 0.9285 (t70) cc_final: 0.8759 (t-170) REVERT: C 2874 TYR cc_start: 0.7992 (t80) cc_final: 0.7652 (t80) REVERT: C 2939 TYR cc_start: 0.8952 (m-80) cc_final: 0.8360 (m-10) REVERT: C 2982 PHE cc_start: 0.8771 (m-80) cc_final: 0.8203 (m-80) REVERT: C 3046 MET cc_start: 0.8884 (tpp) cc_final: 0.8615 (tpp) REVERT: C 3131 TYR cc_start: 0.9184 (m-80) cc_final: 0.8742 (m-80) REVERT: C 3181 TYR cc_start: 0.8239 (t80) cc_final: 0.7982 (t80) REVERT: C 3245 TYR cc_start: 0.9029 (t80) cc_final: 0.8586 (t80) REVERT: C 3304 GLN cc_start: 0.9236 (tp-100) cc_final: 0.8775 (tp-100) REVERT: C 4274 MET cc_start: 0.6332 (mpp) cc_final: 0.6041 (mpp) REVERT: C 4279 MET cc_start: 0.6583 (mtt) cc_final: 0.6149 (ttt) REVERT: C 4672 MET cc_start: 0.8120 (mtm) cc_final: 0.7439 (mtm) REVERT: C 4728 MET cc_start: 0.8463 (mmp) cc_final: 0.8220 (mmm) REVERT: D 81 MET cc_start: 0.8866 (tpt) cc_final: 0.8623 (tpt) REVERT: D 655 MET cc_start: 0.8670 (mmp) cc_final: 0.8431 (mmp) REVERT: D 895 MET cc_start: 0.8746 (ptp) cc_final: 0.8533 (ppp) REVERT: D 902 TRP cc_start: 0.4401 (t-100) cc_final: 0.3533 (t-100) REVERT: D 935 MET cc_start: 0.8830 (ppp) cc_final: 0.8503 (ppp) REVERT: D 1165 MET cc_start: 0.8100 (ttt) cc_final: 0.7798 (mtp) REVERT: D 1306 MET cc_start: 0.8781 (mtp) cc_final: 0.8549 (mtm) REVERT: D 1975 MET cc_start: 0.8862 (tmm) cc_final: 0.8355 (tmm) REVERT: D 2234 MET cc_start: 0.8887 (tpt) cc_final: 0.8657 (tpt) REVERT: D 2279 MET cc_start: 0.8275 (tmm) cc_final: 0.8040 (tmm) REVERT: D 2541 HIS cc_start: 0.9114 (m90) cc_final: 0.8793 (m-70) REVERT: D 2585 MET cc_start: 0.9051 (mmt) cc_final: 0.8460 (mmm) REVERT: D 2605 MET cc_start: 0.8581 (tmm) cc_final: 0.8247 (tmm) REVERT: D 2689 MET cc_start: 0.5664 (ttt) cc_final: 0.5456 (ttt) REVERT: D 2719 TYR cc_start: 0.8692 (t80) cc_final: 0.8031 (t80) REVERT: D 2782 MET cc_start: 0.9047 (tpt) cc_final: 0.8578 (mmm) REVERT: D 2843 MET cc_start: 0.9073 (ppp) cc_final: 0.8641 (ppp) REVERT: D 2849 HIS cc_start: 0.9298 (t70) cc_final: 0.8707 (t-170) REVERT: D 2874 TYR cc_start: 0.8048 (t80) cc_final: 0.7627 (t80) REVERT: D 2886 ARG cc_start: 0.9301 (mpt-90) cc_final: 0.8918 (mtt-85) REVERT: D 2939 TYR cc_start: 0.8969 (m-80) cc_final: 0.8394 (m-10) REVERT: D 2982 PHE cc_start: 0.8790 (m-80) cc_final: 0.8181 (m-80) REVERT: D 3131 TYR cc_start: 0.9158 (m-80) cc_final: 0.8709 (m-80) REVERT: D 3181 TYR cc_start: 0.8226 (t80) cc_final: 0.8019 (t80) REVERT: D 3299 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9238 (pp) REVERT: D 4279 MET cc_start: 0.6602 (mtt) cc_final: 0.6166 (ttt) REVERT: D 4672 MET cc_start: 0.8187 (mtm) cc_final: 0.7555 (mtm) REVERT: D 4809 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8277 (ttt) outliers start: 63 outliers final: 36 residues processed: 816 average time/residue: 1.1828 time to fit residues: 1716.1113 Evaluate side-chains 810 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 767 time to evaluate : 12.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4012 MET Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain A residue 4809 MET Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2234 MET Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3299 LEU Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1553 optimal weight: 8.9990 chunk 1181 optimal weight: 10.0000 chunk 815 optimal weight: 40.0000 chunk 174 optimal weight: 10.0000 chunk 750 optimal weight: 8.9990 chunk 1055 optimal weight: 20.0000 chunk 1577 optimal weight: 20.0000 chunk 1670 optimal weight: 0.9990 chunk 824 optimal weight: 10.0000 chunk 1495 optimal weight: 9.9990 chunk 450 optimal weight: 7.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3308 ASN ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 ASN ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 ASN C1615 GLN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 398 HIS ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1046 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2890 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 141628 Z= 0.426 Angle : 0.659 13.798 191356 Z= 0.340 Chirality : 0.042 0.186 20988 Planarity : 0.005 0.127 24588 Dihedral : 6.442 83.380 19037 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 0.63 % Allowed : 6.35 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.06), residues: 17212 helix: 1.41 (0.05), residues: 9096 sheet: -0.24 (0.13), residues: 1492 loop : -0.73 (0.08), residues: 6624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A2852 HIS 0.013 0.001 HIS B4055 PHE 0.024 0.002 PHE B2720 TYR 0.036 0.002 TYR A1703 ARG 0.008 0.001 ARG A 801 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 789 time to evaluate : 12.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8811 (tpt) cc_final: 0.8323 (tpt) REVERT: A 349 MET cc_start: 0.7782 (tpt) cc_final: 0.7339 (tpt) REVERT: A 494 MET cc_start: 0.8833 (mmp) cc_final: 0.8590 (mmp) REVERT: A 902 TRP cc_start: 0.5241 (t-100) cc_final: 0.4332 (t-100) REVERT: A 995 MET cc_start: 0.8904 (ttt) cc_final: 0.8691 (ttt) REVERT: A 1306 MET cc_start: 0.8826 (mtp) cc_final: 0.8586 (mtm) REVERT: A 1421 MET cc_start: 0.8479 (mmp) cc_final: 0.8180 (mmp) REVERT: A 1975 MET cc_start: 0.8859 (tmm) cc_final: 0.8321 (tmm) REVERT: A 2162 MET cc_start: 0.8817 (mmp) cc_final: 0.8560 (mmp) REVERT: A 2172 MET cc_start: 0.8776 (tpp) cc_final: 0.8461 (tpp) REVERT: A 2214 MET cc_start: 0.9311 (mmm) cc_final: 0.9066 (tpp) REVERT: A 2234 MET cc_start: 0.8892 (tpt) cc_final: 0.8645 (tpt) REVERT: A 2279 MET cc_start: 0.8328 (tmm) cc_final: 0.8099 (tmm) REVERT: A 2541 HIS cc_start: 0.9174 (m90) cc_final: 0.8828 (m-70) REVERT: A 2584 MET cc_start: 0.8699 (mpp) cc_final: 0.8348 (mpp) REVERT: A 2585 MET cc_start: 0.8539 (mpp) cc_final: 0.8105 (mmt) REVERT: A 2605 MET cc_start: 0.8682 (tmm) cc_final: 0.8356 (tmm) REVERT: A 2689 MET cc_start: 0.5577 (ttt) cc_final: 0.5277 (ttt) REVERT: A 2719 TYR cc_start: 0.8888 (t80) cc_final: 0.8446 (t80) REVERT: A 2782 MET cc_start: 0.9099 (tpt) cc_final: 0.8700 (mmm) REVERT: A 2785 TRP cc_start: 0.8295 (m100) cc_final: 0.7827 (m100) REVERT: A 2798 MET cc_start: 0.9133 (tmm) cc_final: 0.8487 (mmt) REVERT: A 2835 ARG cc_start: 0.9276 (mmm160) cc_final: 0.8895 (mmp80) REVERT: A 2843 MET cc_start: 0.9100 (ppp) cc_final: 0.8544 (ppp) REVERT: A 2849 HIS cc_start: 0.9309 (t70) cc_final: 0.8863 (t70) REVERT: A 2975 PHE cc_start: 0.8889 (m-80) cc_final: 0.8688 (m-80) REVERT: A 2982 PHE cc_start: 0.8842 (m-80) cc_final: 0.8267 (m-80) REVERT: A 3245 TYR cc_start: 0.9048 (t80) cc_final: 0.8604 (t80) REVERT: A 3246 MET cc_start: 0.8933 (mmt) cc_final: 0.8649 (mmt) REVERT: A 3304 GLN cc_start: 0.9292 (tp-100) cc_final: 0.8906 (tp-100) REVERT: A 3981 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8168 (ttp) REVERT: A 4143 LYS cc_start: 0.9036 (tppt) cc_final: 0.8629 (tppt) REVERT: A 4279 MET cc_start: 0.6678 (mtt) cc_final: 0.6187 (ttt) REVERT: A 4728 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8156 (mmm) REVERT: A 4804 MET cc_start: 0.8376 (mmm) cc_final: 0.7771 (mmm) REVERT: A 4809 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.8296 (tpp) REVERT: E 101 ASP cc_start: 0.8234 (t70) cc_final: 0.8029 (t0) REVERT: F 54 GLN cc_start: 0.8656 (mp10) cc_final: 0.8419 (mp10) REVERT: F 101 ASP cc_start: 0.8283 (t70) cc_final: 0.8060 (t0) REVERT: G 54 GLN cc_start: 0.8667 (mp10) cc_final: 0.8463 (mp10) REVERT: G 101 ASP cc_start: 0.8275 (t70) cc_final: 0.8066 (t0) REVERT: H 101 ASP cc_start: 0.8226 (t70) cc_final: 0.8018 (t0) REVERT: B 81 MET cc_start: 0.8845 (tpt) cc_final: 0.8627 (tpt) REVERT: B 349 MET cc_start: 0.7818 (tpt) cc_final: 0.7353 (tpt) REVERT: B 902 TRP cc_start: 0.4871 (t-100) cc_final: 0.4186 (t-100) REVERT: B 935 MET cc_start: 0.8890 (ppp) cc_final: 0.8622 (ppp) REVERT: B 1306 MET cc_start: 0.8812 (mtp) cc_final: 0.8560 (mtm) REVERT: B 1794 MET cc_start: 0.8997 (mtm) cc_final: 0.8679 (mtp) REVERT: B 1975 MET cc_start: 0.8867 (tmm) cc_final: 0.8329 (tmm) REVERT: B 2234 MET cc_start: 0.8939 (tpp) cc_final: 0.8180 (tmm) REVERT: B 2279 MET cc_start: 0.8342 (tmm) cc_final: 0.8101 (tmm) REVERT: B 2541 HIS cc_start: 0.9149 (m90) cc_final: 0.8808 (m-70) REVERT: B 2584 MET cc_start: 0.8604 (mpp) cc_final: 0.8387 (mpp) REVERT: B 2585 MET cc_start: 0.9047 (mmt) cc_final: 0.8453 (mmm) REVERT: B 2605 MET cc_start: 0.8597 (tmm) cc_final: 0.8249 (tmm) REVERT: B 2719 TYR cc_start: 0.8725 (t80) cc_final: 0.8088 (t80) REVERT: B 2732 TRP cc_start: 0.9032 (t60) cc_final: 0.8816 (t60) REVERT: B 2782 MET cc_start: 0.9109 (tpt) cc_final: 0.8728 (mmm) REVERT: B 2843 MET cc_start: 0.9089 (ppp) cc_final: 0.8719 (ppp) REVERT: B 2848 TYR cc_start: 0.9460 (OUTLIER) cc_final: 0.8896 (m-80) REVERT: B 2849 HIS cc_start: 0.9263 (t70) cc_final: 0.8722 (t-170) REVERT: B 2874 TYR cc_start: 0.8150 (t80) cc_final: 0.7789 (t80) REVERT: B 2939 TYR cc_start: 0.8983 (m-80) cc_final: 0.8400 (m-10) REVERT: B 2982 PHE cc_start: 0.8790 (m-80) cc_final: 0.8195 (m-80) REVERT: B 3046 MET cc_start: 0.8948 (tpp) cc_final: 0.8690 (tpt) REVERT: B 3131 TYR cc_start: 0.9269 (m-80) cc_final: 0.8739 (m-80) REVERT: B 3181 TYR cc_start: 0.8311 (t80) cc_final: 0.8050 (t80) REVERT: B 3245 TYR cc_start: 0.9106 (t80) cc_final: 0.8754 (t80) REVERT: B 3304 GLN cc_start: 0.9203 (tp-100) cc_final: 0.8743 (tp-100) REVERT: B 4143 LYS cc_start: 0.9012 (tppt) cc_final: 0.8753 (tppt) REVERT: B 4279 MET cc_start: 0.6606 (mtt) cc_final: 0.6184 (ttt) REVERT: B 4568 MET cc_start: 0.7681 (mmm) cc_final: 0.7319 (mpp) REVERT: B 4672 MET cc_start: 0.8198 (mtm) cc_final: 0.7564 (mtm) REVERT: C 81 MET cc_start: 0.8865 (tpt) cc_final: 0.8400 (tpt) REVERT: C 349 MET cc_start: 0.7604 (tpt) cc_final: 0.7151 (tpt) REVERT: C 895 MET cc_start: 0.8733 (ptp) cc_final: 0.8457 (ppp) REVERT: C 902 TRP cc_start: 0.4776 (t-100) cc_final: 0.4060 (t-100) REVERT: C 935 MET cc_start: 0.8913 (ppp) cc_final: 0.8657 (ppp) REVERT: C 995 MET cc_start: 0.8920 (ttt) cc_final: 0.8668 (ttt) REVERT: C 1165 MET cc_start: 0.8269 (ttt) cc_final: 0.7831 (mtp) REVERT: C 1306 MET cc_start: 0.8817 (mtp) cc_final: 0.8563 (mtm) REVERT: C 1628 MET cc_start: 0.8805 (ttm) cc_final: 0.8524 (ttm) REVERT: C 1794 MET cc_start: 0.8971 (mtm) cc_final: 0.8653 (mtp) REVERT: C 1975 MET cc_start: 0.8865 (tmm) cc_final: 0.8327 (tmm) REVERT: C 2162 MET cc_start: 0.8791 (mmp) cc_final: 0.8576 (mmp) REVERT: C 2167 MET cc_start: 0.8888 (ptp) cc_final: 0.8233 (ptp) REVERT: C 2214 MET cc_start: 0.9328 (mmm) cc_final: 0.9107 (tpp) REVERT: C 2234 MET cc_start: 0.8939 (tpp) cc_final: 0.8648 (mmm) REVERT: C 2279 MET cc_start: 0.8368 (tmm) cc_final: 0.8145 (tmm) REVERT: C 2541 HIS cc_start: 0.9160 (m90) cc_final: 0.8830 (m-70) REVERT: C 2585 MET cc_start: 0.9052 (mmt) cc_final: 0.8476 (mmm) REVERT: C 2605 MET cc_start: 0.8757 (ttp) cc_final: 0.8243 (tmm) REVERT: C 2688 MET cc_start: 0.8435 (tpt) cc_final: 0.8210 (mmm) REVERT: C 2719 TYR cc_start: 0.8801 (t80) cc_final: 0.8181 (t80) REVERT: C 2782 MET cc_start: 0.9097 (tpt) cc_final: 0.8705 (mmm) REVERT: C 2785 TRP cc_start: 0.8542 (m-90) cc_final: 0.8264 (m100) REVERT: C 2798 MET cc_start: 0.8934 (ppp) cc_final: 0.8726 (ppp) REVERT: C 2843 MET cc_start: 0.9082 (ppp) cc_final: 0.8582 (ppp) REVERT: C 2848 TYR cc_start: 0.9454 (OUTLIER) cc_final: 0.8901 (m-80) REVERT: C 2849 HIS cc_start: 0.9248 (t70) cc_final: 0.8716 (t-170) REVERT: C 2874 TYR cc_start: 0.8091 (t80) cc_final: 0.7766 (t80) REVERT: C 2939 TYR cc_start: 0.8986 (m-80) cc_final: 0.8413 (m-10) REVERT: C 2982 PHE cc_start: 0.8913 (m-80) cc_final: 0.8177 (m-80) REVERT: C 3003 MET cc_start: 0.8628 (ptm) cc_final: 0.8197 (ptp) REVERT: C 3046 MET cc_start: 0.8938 (tpp) cc_final: 0.8686 (tpt) REVERT: C 3131 TYR cc_start: 0.9260 (m-80) cc_final: 0.8734 (m-80) REVERT: C 3215 MET cc_start: 0.9533 (mpp) cc_final: 0.9307 (pmm) REVERT: C 3304 GLN cc_start: 0.9198 (tp-100) cc_final: 0.8756 (tp-100) REVERT: C 4274 MET cc_start: 0.6098 (mpp) cc_final: 0.5861 (mpp) REVERT: C 4279 MET cc_start: 0.6605 (mtt) cc_final: 0.6154 (ttt) REVERT: C 4672 MET cc_start: 0.8174 (mtm) cc_final: 0.7520 (mtm) REVERT: D 81 MET cc_start: 0.8871 (tpt) cc_final: 0.8643 (tpt) REVERT: D 895 MET cc_start: 0.8802 (ptp) cc_final: 0.8494 (ppp) REVERT: D 902 TRP cc_start: 0.4970 (t-100) cc_final: 0.4072 (t-100) REVERT: D 935 MET cc_start: 0.8901 (ppp) cc_final: 0.8641 (ppp) REVERT: D 1165 MET cc_start: 0.8237 (ttt) cc_final: 0.7761 (mtp) REVERT: D 1306 MET cc_start: 0.8808 (mtp) cc_final: 0.8557 (mtm) REVERT: D 1975 MET cc_start: 0.8851 (tmm) cc_final: 0.8300 (tmm) REVERT: D 2214 MET cc_start: 0.9367 (tpp) cc_final: 0.8921 (mmm) REVERT: D 2234 MET cc_start: 0.8904 (tpt) cc_final: 0.8650 (mmm) REVERT: D 2279 MET cc_start: 0.8328 (tmm) cc_final: 0.8115 (tmm) REVERT: D 2541 HIS cc_start: 0.9153 (m90) cc_final: 0.8851 (m-70) REVERT: D 2585 MET cc_start: 0.8991 (mmt) cc_final: 0.8604 (mmm) REVERT: D 2605 MET cc_start: 0.8615 (tmm) cc_final: 0.8275 (tmm) REVERT: D 2689 MET cc_start: 0.5878 (ttt) cc_final: 0.5561 (ttt) REVERT: D 2719 TYR cc_start: 0.8895 (t80) cc_final: 0.8281 (t80) REVERT: D 2782 MET cc_start: 0.9112 (tpt) cc_final: 0.8718 (mmm) REVERT: D 2785 TRP cc_start: 0.8541 (m-90) cc_final: 0.8256 (m100) REVERT: D 2798 MET cc_start: 0.9030 (ppp) cc_final: 0.8783 (ppp) REVERT: D 2843 MET cc_start: 0.9090 (ppp) cc_final: 0.8580 (ppp) REVERT: D 2849 HIS cc_start: 0.9290 (t70) cc_final: 0.8629 (t-170) REVERT: D 2874 TYR cc_start: 0.8162 (t80) cc_final: 0.7746 (t80) REVERT: D 2939 TYR cc_start: 0.9002 (m-80) cc_final: 0.8426 (m-10) REVERT: D 2982 PHE cc_start: 0.8917 (m-80) cc_final: 0.8159 (m-80) REVERT: D 3003 MET cc_start: 0.8684 (ptm) cc_final: 0.8271 (ptp) REVERT: D 3131 TYR cc_start: 0.9229 (m-80) cc_final: 0.8702 (m-80) REVERT: D 3215 MET cc_start: 0.9537 (mpp) cc_final: 0.9291 (pmm) REVERT: D 3245 TYR cc_start: 0.9044 (t80) cc_final: 0.8720 (t80) REVERT: D 3981 MET cc_start: 0.8534 (ttm) cc_final: 0.8274 (ttp) REVERT: D 4279 MET cc_start: 0.6500 (mtt) cc_final: 0.6097 (ttt) REVERT: D 4672 MET cc_start: 0.8211 (mtm) cc_final: 0.7599 (mtm) REVERT: D 4809 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8328 (ttt) outliers start: 96 outliers final: 56 residues processed: 847 average time/residue: 1.1755 time to fit residues: 1778.9254 Evaluate side-chains 833 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 771 time to evaluate : 13.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 MET Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1721 MET Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 3981 MET Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain A residue 4809 MET Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 309 MET Chi-restraints excluded: chain C residue 317 MET Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 317 MET Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1391 optimal weight: 10.0000 chunk 948 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 1243 optimal weight: 2.9990 chunk 689 optimal weight: 30.0000 chunk 1425 optimal weight: 6.9990 chunk 1154 optimal weight: 50.0000 chunk 1 optimal weight: 9.9990 chunk 852 optimal weight: 9.9990 chunk 1499 optimal weight: 20.0000 chunk 421 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 ASN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2890 GLN ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2890 GLN ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2890 GLN ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 934 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2890 GLN ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 141628 Z= 0.348 Angle : 0.630 13.142 191356 Z= 0.322 Chirality : 0.041 0.201 20988 Planarity : 0.005 0.125 24588 Dihedral : 6.396 84.160 19037 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 0.76 % Allowed : 7.03 % Favored : 92.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.06), residues: 17212 helix: 1.50 (0.05), residues: 9076 sheet: -0.33 (0.13), residues: 1544 loop : -0.67 (0.08), residues: 6592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D2852 HIS 0.014 0.001 HIS B4055 PHE 0.026 0.002 PHE D3166 TYR 0.040 0.002 TYR C2760 ARG 0.009 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 783 time to evaluate : 12.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8810 (tpt) cc_final: 0.8579 (tpt) REVERT: A 349 MET cc_start: 0.7750 (tpt) cc_final: 0.7325 (tpt) REVERT: A 393 MET cc_start: 0.7927 (mmm) cc_final: 0.7617 (mmm) REVERT: A 399 MET cc_start: 0.7927 (tmm) cc_final: 0.7692 (tmm) REVERT: A 895 MET cc_start: 0.9158 (ptm) cc_final: 0.8871 (ppp) REVERT: A 902 TRP cc_start: 0.5456 (t-100) cc_final: 0.4511 (t-100) REVERT: A 995 MET cc_start: 0.8900 (ttt) cc_final: 0.8673 (ttt) REVERT: A 1173 MET cc_start: 0.8726 (mtm) cc_final: 0.8389 (mtp) REVERT: A 1306 MET cc_start: 0.8793 (mtp) cc_final: 0.8553 (mtm) REVERT: A 1421 MET cc_start: 0.8521 (mmp) cc_final: 0.8194 (mmp) REVERT: A 1975 MET cc_start: 0.8839 (tmm) cc_final: 0.8267 (tmm) REVERT: A 2162 MET cc_start: 0.8850 (mmp) cc_final: 0.8638 (mmp) REVERT: A 2279 MET cc_start: 0.8330 (tmm) cc_final: 0.8105 (tmm) REVERT: A 2496 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9109 (tt) REVERT: A 2541 HIS cc_start: 0.9169 (m90) cc_final: 0.8806 (m-70) REVERT: A 2580 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.7094 (tp) REVERT: A 2584 MET cc_start: 0.8659 (mpp) cc_final: 0.8369 (mpp) REVERT: A 2585 MET cc_start: 0.8543 (mpp) cc_final: 0.7827 (mmm) REVERT: A 2605 MET cc_start: 0.8684 (tmm) cc_final: 0.8345 (tmm) REVERT: A 2689 MET cc_start: 0.5758 (ttt) cc_final: 0.5486 (ttt) REVERT: A 2719 TYR cc_start: 0.8875 (t80) cc_final: 0.8428 (t80) REVERT: A 2785 TRP cc_start: 0.8303 (m100) cc_final: 0.7837 (m100) REVERT: A 2798 MET cc_start: 0.9154 (tmm) cc_final: 0.8554 (mmt) REVERT: A 2843 MET cc_start: 0.9109 (ppp) cc_final: 0.8587 (ppp) REVERT: A 2849 HIS cc_start: 0.9286 (t70) cc_final: 0.8819 (t70) REVERT: A 2982 PHE cc_start: 0.8824 (m-80) cc_final: 0.8244 (m-80) REVERT: A 3104 MET cc_start: 0.8682 (tmm) cc_final: 0.8413 (tmm) REVERT: A 3131 TYR cc_start: 0.9290 (m-80) cc_final: 0.8702 (m-80) REVERT: A 3245 TYR cc_start: 0.9000 (t80) cc_final: 0.8519 (t80) REVERT: A 3246 MET cc_start: 0.8967 (mmt) cc_final: 0.8583 (mmt) REVERT: A 3304 GLN cc_start: 0.9243 (tp-100) cc_final: 0.8837 (tp-100) REVERT: A 4143 LYS cc_start: 0.9079 (tppt) cc_final: 0.8692 (tppt) REVERT: A 4279 MET cc_start: 0.6681 (mtt) cc_final: 0.6152 (ttt) REVERT: A 4728 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8145 (mmm) REVERT: A 4809 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8341 (tpp) REVERT: E 67 MET cc_start: 0.8492 (mtp) cc_final: 0.8212 (mtp) REVERT: F 4 GLU cc_start: 0.7619 (mp0) cc_final: 0.7233 (mp0) REVERT: F 54 GLN cc_start: 0.8638 (mp10) cc_final: 0.8327 (mp10) REVERT: G 54 GLN cc_start: 0.8679 (mp10) cc_final: 0.8374 (mp10) REVERT: B 81 MET cc_start: 0.8835 (tpt) cc_final: 0.8613 (tpt) REVERT: B 349 MET cc_start: 0.7761 (tpt) cc_final: 0.7327 (tpt) REVERT: B 895 MET cc_start: 0.9056 (ptm) cc_final: 0.8678 (ppp) REVERT: B 902 TRP cc_start: 0.5121 (t-100) cc_final: 0.4395 (t-100) REVERT: B 935 MET cc_start: 0.8886 (ppp) cc_final: 0.8624 (ppp) REVERT: B 1173 MET cc_start: 0.8730 (mtm) cc_final: 0.8386 (mtp) REVERT: B 1306 MET cc_start: 0.8794 (mtp) cc_final: 0.8572 (mtm) REVERT: B 1721 MET cc_start: 0.7946 (mtm) cc_final: 0.7744 (mtm) REVERT: B 1975 MET cc_start: 0.8871 (tmm) cc_final: 0.8310 (tmm) REVERT: B 2214 MET cc_start: 0.9320 (mmm) cc_final: 0.9101 (tpp) REVERT: B 2234 MET cc_start: 0.8937 (tpp) cc_final: 0.8629 (mmm) REVERT: B 2279 MET cc_start: 0.8343 (tmm) cc_final: 0.8094 (tmm) REVERT: B 2496 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9105 (tt) REVERT: B 2541 HIS cc_start: 0.9152 (m90) cc_final: 0.8795 (m-70) REVERT: B 2585 MET cc_start: 0.9013 (mmt) cc_final: 0.8484 (mmm) REVERT: B 2605 MET cc_start: 0.8604 (tmm) cc_final: 0.8251 (tmm) REVERT: B 2719 TYR cc_start: 0.8871 (t80) cc_final: 0.8243 (t80) REVERT: B 2732 TRP cc_start: 0.9031 (t60) cc_final: 0.8804 (t60) REVERT: B 2782 MET cc_start: 0.9141 (tpt) cc_final: 0.8750 (mmm) REVERT: B 2798 MET cc_start: 0.9020 (ppp) cc_final: 0.8739 (ppp) REVERT: B 2843 MET cc_start: 0.9086 (ppp) cc_final: 0.8716 (ppp) REVERT: B 2848 TYR cc_start: 0.9467 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: B 2849 HIS cc_start: 0.9246 (t70) cc_final: 0.8731 (t-170) REVERT: B 2874 TYR cc_start: 0.8140 (t80) cc_final: 0.7799 (t80) REVERT: B 2939 TYR cc_start: 0.8967 (m-80) cc_final: 0.8381 (m-10) REVERT: B 2982 PHE cc_start: 0.8902 (m-80) cc_final: 0.8124 (m-80) REVERT: B 3046 MET cc_start: 0.8931 (tpp) cc_final: 0.8694 (tpt) REVERT: B 3131 TYR cc_start: 0.9268 (m-80) cc_final: 0.8715 (m-80) REVERT: B 3181 TYR cc_start: 0.8351 (t80) cc_final: 0.8140 (t80) REVERT: B 3245 TYR cc_start: 0.9056 (t80) cc_final: 0.8770 (t80) REVERT: B 3304 GLN cc_start: 0.9180 (tp-100) cc_final: 0.8719 (tp-100) REVERT: B 4143 LYS cc_start: 0.9044 (tppt) cc_final: 0.8639 (tppt) REVERT: B 4279 MET cc_start: 0.6609 (mtt) cc_final: 0.6184 (ttt) REVERT: B 4568 MET cc_start: 0.7657 (mmm) cc_final: 0.7300 (mpp) REVERT: B 4672 MET cc_start: 0.8194 (mtm) cc_final: 0.7535 (mtm) REVERT: C 81 MET cc_start: 0.8858 (tpt) cc_final: 0.8381 (tpt) REVERT: C 349 MET cc_start: 0.7600 (tpt) cc_final: 0.7186 (tpt) REVERT: C 902 TRP cc_start: 0.5048 (t-100) cc_final: 0.4381 (t-100) REVERT: C 935 MET cc_start: 0.8906 (ppp) cc_final: 0.8657 (ppp) REVERT: C 995 MET cc_start: 0.8900 (ttt) cc_final: 0.8647 (ttt) REVERT: C 1165 MET cc_start: 0.8150 (ttt) cc_final: 0.7702 (mtp) REVERT: C 1306 MET cc_start: 0.8799 (mtp) cc_final: 0.8553 (mtm) REVERT: C 1628 MET cc_start: 0.8797 (ttm) cc_final: 0.8488 (ttm) REVERT: C 1975 MET cc_start: 0.8852 (tmm) cc_final: 0.8301 (tmm) REVERT: C 2214 MET cc_start: 0.9307 (mmm) cc_final: 0.9079 (tpp) REVERT: C 2234 MET cc_start: 0.8923 (tpp) cc_final: 0.8622 (mmm) REVERT: C 2279 MET cc_start: 0.8366 (tmm) cc_final: 0.8131 (tmm) REVERT: C 2496 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9117 (tt) REVERT: C 2541 HIS cc_start: 0.9153 (m90) cc_final: 0.8831 (m-70) REVERT: C 2585 MET cc_start: 0.8973 (mmt) cc_final: 0.8578 (mmm) REVERT: C 2605 MET cc_start: 0.8739 (ttp) cc_final: 0.8235 (tmm) REVERT: C 2688 MET cc_start: 0.8482 (tpt) cc_final: 0.8279 (tpp) REVERT: C 2719 TYR cc_start: 0.8785 (t80) cc_final: 0.8160 (t80) REVERT: C 2782 MET cc_start: 0.9104 (tpt) cc_final: 0.8712 (mmm) REVERT: C 2843 MET cc_start: 0.9056 (ppp) cc_final: 0.8652 (ppp) REVERT: C 2848 TYR cc_start: 0.9460 (OUTLIER) cc_final: 0.8926 (m-80) REVERT: C 2849 HIS cc_start: 0.9229 (t70) cc_final: 0.8729 (t-170) REVERT: C 2874 TYR cc_start: 0.8073 (t80) cc_final: 0.7774 (t80) REVERT: C 2939 TYR cc_start: 0.8971 (m-80) cc_final: 0.8395 (m-10) REVERT: C 2982 PHE cc_start: 0.8893 (m-80) cc_final: 0.8140 (m-80) REVERT: C 3046 MET cc_start: 0.8928 (tpp) cc_final: 0.8683 (tpt) REVERT: C 3109 PHE cc_start: 0.9129 (m-10) cc_final: 0.8900 (m-10) REVERT: C 3131 TYR cc_start: 0.9269 (m-80) cc_final: 0.8707 (m-80) REVERT: C 3245 TYR cc_start: 0.9058 (t80) cc_final: 0.8776 (t80) REVERT: C 3304 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8712 (tp-100) REVERT: C 4274 MET cc_start: 0.6033 (mpp) cc_final: 0.5775 (mpp) REVERT: C 4279 MET cc_start: 0.6602 (mtt) cc_final: 0.6175 (ttt) REVERT: C 4672 MET cc_start: 0.8212 (mtm) cc_final: 0.7596 (mtm) REVERT: D 81 MET cc_start: 0.8853 (tpt) cc_final: 0.8370 (tpt) REVERT: D 899 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: D 902 TRP cc_start: 0.5229 (t-100) cc_final: 0.4300 (t-100) REVERT: D 935 MET cc_start: 0.8869 (ppp) cc_final: 0.8628 (ppp) REVERT: D 1165 MET cc_start: 0.8119 (ttt) cc_final: 0.7680 (mtp) REVERT: D 1306 MET cc_start: 0.8799 (mtp) cc_final: 0.8561 (mtm) REVERT: D 1721 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: D 1975 MET cc_start: 0.8846 (tmm) cc_final: 0.8278 (tmm) REVERT: D 2150 MET cc_start: 0.8533 (mtm) cc_final: 0.8292 (mtt) REVERT: D 2214 MET cc_start: 0.9376 (tpp) cc_final: 0.8892 (mmm) REVERT: D 2234 MET cc_start: 0.8881 (tpt) cc_final: 0.8626 (tpt) REVERT: D 2279 MET cc_start: 0.8338 (tmm) cc_final: 0.8109 (tmm) REVERT: D 2496 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9103 (tt) REVERT: D 2541 HIS cc_start: 0.9152 (m90) cc_final: 0.8828 (m-70) REVERT: D 2585 MET cc_start: 0.8992 (mmt) cc_final: 0.8678 (mmm) REVERT: D 2605 MET cc_start: 0.8638 (tmm) cc_final: 0.8281 (tmm) REVERT: D 2689 MET cc_start: 0.6081 (ttt) cc_final: 0.5719 (ttt) REVERT: D 2719 TYR cc_start: 0.8852 (t80) cc_final: 0.8214 (t80) REVERT: D 2782 MET cc_start: 0.9146 (tpt) cc_final: 0.8758 (mmm) REVERT: D 2785 TRP cc_start: 0.8576 (m-90) cc_final: 0.8296 (m100) REVERT: D 2798 MET cc_start: 0.9001 (ppp) cc_final: 0.8760 (ppp) REVERT: D 2843 MET cc_start: 0.9097 (ppp) cc_final: 0.8579 (ppp) REVERT: D 2849 HIS cc_start: 0.9235 (t70) cc_final: 0.8548 (t-170) REVERT: D 2874 TYR cc_start: 0.8204 (t80) cc_final: 0.7791 (t80) REVERT: D 2939 TYR cc_start: 0.8997 (m-80) cc_final: 0.8421 (m-10) REVERT: D 2982 PHE cc_start: 0.8897 (m-80) cc_final: 0.8118 (m-80) REVERT: D 3109 PHE cc_start: 0.9112 (m-10) cc_final: 0.8912 (m-10) REVERT: D 3131 TYR cc_start: 0.9247 (m-80) cc_final: 0.8681 (m-80) REVERT: D 3166 PHE cc_start: 0.8583 (t80) cc_final: 0.8371 (t80) REVERT: D 3245 TYR cc_start: 0.9015 (t80) cc_final: 0.8729 (t80) REVERT: D 4279 MET cc_start: 0.6451 (mtt) cc_final: 0.6067 (ttt) REVERT: D 4672 MET cc_start: 0.8213 (mtm) cc_final: 0.7622 (mtm) REVERT: D 4809 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8262 (ttt) outliers start: 116 outliers final: 73 residues processed: 849 average time/residue: 1.1748 time to fit residues: 1778.5737 Evaluate side-chains 850 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 765 time to evaluate : 10.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1300 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2496 LEU Chi-restraints excluded: chain A residue 2512 MET Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4492 LEU Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain A residue 4809 MET Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 899 GLU Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2496 LEU Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3201 VAL Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4012 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2496 LEU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4492 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1721 MET Chi-restraints excluded: chain D residue 2496 LEU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 4492 LEU Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 561 optimal weight: 9.9990 chunk 1504 optimal weight: 7.9990 chunk 330 optimal weight: 30.0000 chunk 980 optimal weight: 8.9990 chunk 412 optimal weight: 7.9990 chunk 1671 optimal weight: 8.9990 chunk 1387 optimal weight: 0.9990 chunk 774 optimal weight: 5.9990 chunk 139 optimal weight: 4.9990 chunk 553 optimal weight: 20.0000 chunk 877 optimal weight: 0.9980 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 GLN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3727 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 934 GLN ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 934 GLN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 934 GLN ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 141628 Z= 0.263 Angle : 0.605 15.795 191356 Z= 0.307 Chirality : 0.040 0.187 20988 Planarity : 0.005 0.122 24588 Dihedral : 6.278 85.175 19028 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 0.90 % Allowed : 7.47 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.07), residues: 17212 helix: 1.60 (0.06), residues: 9068 sheet: -0.30 (0.13), residues: 1504 loop : -0.61 (0.08), residues: 6640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D2852 HIS 0.013 0.001 HIS B4055 PHE 0.023 0.001 PHE A3166 TYR 0.027 0.001 TYR C1703 ARG 0.007 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 781 time to evaluate : 12.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8806 (tpt) cc_final: 0.8562 (tpt) REVERT: A 349 MET cc_start: 0.7700 (tpt) cc_final: 0.7273 (tpt) REVERT: A 399 MET cc_start: 0.7969 (tmm) cc_final: 0.7757 (tmm) REVERT: A 895 MET cc_start: 0.9155 (ptm) cc_final: 0.8861 (ppp) REVERT: A 902 TRP cc_start: 0.5496 (t-100) cc_final: 0.4636 (t-100) REVERT: A 995 MET cc_start: 0.8896 (ttt) cc_final: 0.8647 (ttt) REVERT: A 1173 MET cc_start: 0.8740 (mtm) cc_final: 0.8423 (mtp) REVERT: A 1306 MET cc_start: 0.8791 (mtp) cc_final: 0.8584 (mtm) REVERT: A 1421 MET cc_start: 0.8512 (mmp) cc_final: 0.8189 (mmp) REVERT: A 1975 MET cc_start: 0.8846 (tmm) cc_final: 0.8270 (tmm) REVERT: A 2150 MET cc_start: 0.8451 (mtm) cc_final: 0.8209 (mtt) REVERT: A 2162 MET cc_start: 0.8757 (mmp) cc_final: 0.8473 (mmp) REVERT: A 2167 MET cc_start: 0.8886 (ptp) cc_final: 0.7692 (ptp) REVERT: A 2214 MET cc_start: 0.9320 (tpp) cc_final: 0.9074 (mmm) REVERT: A 2234 MET cc_start: 0.9033 (tpt) cc_final: 0.8775 (mmm) REVERT: A 2279 MET cc_start: 0.8325 (tmm) cc_final: 0.8075 (tmm) REVERT: A 2496 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9094 (tt) REVERT: A 2541 HIS cc_start: 0.9141 (m90) cc_final: 0.8781 (m-70) REVERT: A 2580 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7061 (tp) REVERT: A 2584 MET cc_start: 0.8625 (mpp) cc_final: 0.8345 (mpp) REVERT: A 2585 MET cc_start: 0.8557 (mpp) cc_final: 0.7814 (mmm) REVERT: A 2605 MET cc_start: 0.8679 (tmm) cc_final: 0.8302 (tmm) REVERT: A 2689 MET cc_start: 0.5879 (ttt) cc_final: 0.5632 (ttt) REVERT: A 2719 TYR cc_start: 0.8874 (t80) cc_final: 0.8429 (t80) REVERT: A 2785 TRP cc_start: 0.8277 (m100) cc_final: 0.7624 (m100) REVERT: A 2798 MET cc_start: 0.9124 (tmm) cc_final: 0.8544 (mmt) REVERT: A 2835 ARG cc_start: 0.9231 (mmm160) cc_final: 0.8910 (mmp80) REVERT: A 2849 HIS cc_start: 0.9296 (t70) cc_final: 0.8921 (t70) REVERT: A 2982 PHE cc_start: 0.8870 (m-80) cc_final: 0.8093 (m-80) REVERT: A 3104 MET cc_start: 0.8677 (tmm) cc_final: 0.8414 (tmm) REVERT: A 3131 TYR cc_start: 0.9285 (m-80) cc_final: 0.8686 (m-80) REVERT: A 3245 TYR cc_start: 0.8977 (t80) cc_final: 0.8501 (t80) REVERT: A 3246 MET cc_start: 0.8926 (mmt) cc_final: 0.8583 (mmt) REVERT: A 3304 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8809 (tp-100) REVERT: A 3819 MET cc_start: 0.7440 (mpp) cc_final: 0.6465 (ptt) REVERT: A 4035 TYR cc_start: 0.8100 (m-80) cc_final: 0.7867 (m-80) REVERT: A 4052 MET cc_start: 0.7765 (ppp) cc_final: 0.7298 (ppp) REVERT: A 4143 LYS cc_start: 0.9100 (tppt) cc_final: 0.8442 (tppt) REVERT: A 4256 MET cc_start: 0.8235 (mmt) cc_final: 0.8016 (mmp) REVERT: A 4279 MET cc_start: 0.6690 (mtt) cc_final: 0.6185 (ttt) REVERT: A 4292 MET cc_start: 0.8427 (mmt) cc_final: 0.7888 (mmm) REVERT: A 4728 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8135 (mmm) REVERT: E 67 MET cc_start: 0.8453 (mtp) cc_final: 0.8179 (mtp) REVERT: F 4 GLU cc_start: 0.7660 (mp0) cc_final: 0.7225 (mp0) REVERT: F 54 GLN cc_start: 0.8666 (mp10) cc_final: 0.8311 (mp10) REVERT: G 4 GLU cc_start: 0.7591 (mp0) cc_final: 0.7181 (mp0) REVERT: G 54 GLN cc_start: 0.8674 (mp10) cc_final: 0.8309 (mp10) REVERT: H 58 LYS cc_start: 0.8957 (pttm) cc_final: 0.8540 (pttm) REVERT: H 62 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8410 (mm-30) REVERT: B 81 MET cc_start: 0.8828 (tpt) cc_final: 0.8601 (tpt) REVERT: B 349 MET cc_start: 0.7725 (tpt) cc_final: 0.7301 (tpt) REVERT: B 895 MET cc_start: 0.9058 (ptm) cc_final: 0.8392 (ppp) REVERT: B 902 TRP cc_start: 0.5235 (t-100) cc_final: 0.4545 (t-100) REVERT: B 935 MET cc_start: 0.8844 (ppp) cc_final: 0.8524 (ppp) REVERT: B 1173 MET cc_start: 0.8770 (mtm) cc_final: 0.8448 (mtp) REVERT: B 1306 MET cc_start: 0.8800 (mtp) cc_final: 0.8592 (mtm) REVERT: B 1975 MET cc_start: 0.8858 (tmm) cc_final: 0.8305 (tmm) REVERT: B 2162 MET cc_start: 0.8822 (mmp) cc_final: 0.8503 (mmp) REVERT: B 2167 MET cc_start: 0.8457 (ptp) cc_final: 0.8174 (pmm) REVERT: B 2214 MET cc_start: 0.9317 (mmm) cc_final: 0.9103 (tpp) REVERT: B 2234 MET cc_start: 0.8876 (tpp) cc_final: 0.8550 (mmm) REVERT: B 2279 MET cc_start: 0.8335 (tmm) cc_final: 0.8083 (tmm) REVERT: B 2496 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9081 (tt) REVERT: B 2541 HIS cc_start: 0.9131 (m90) cc_final: 0.8783 (m-70) REVERT: B 2585 MET cc_start: 0.8950 (mmt) cc_final: 0.8564 (mmm) REVERT: B 2605 MET cc_start: 0.8592 (tmm) cc_final: 0.8229 (tmm) REVERT: B 2719 TYR cc_start: 0.8876 (t80) cc_final: 0.8236 (t80) REVERT: B 2732 TRP cc_start: 0.9023 (t60) cc_final: 0.8782 (t60) REVERT: B 2782 MET cc_start: 0.9131 (tpt) cc_final: 0.8768 (mmm) REVERT: B 2785 TRP cc_start: 0.8241 (m-90) cc_final: 0.7758 (m100) REVERT: B 2798 MET cc_start: 0.8991 (ppp) cc_final: 0.8721 (ppp) REVERT: B 2843 MET cc_start: 0.9102 (ppp) cc_final: 0.8589 (ppp) REVERT: B 2848 TYR cc_start: 0.9472 (OUTLIER) cc_final: 0.8939 (m-80) REVERT: B 2849 HIS cc_start: 0.9214 (t70) cc_final: 0.8581 (t-170) REVERT: B 2874 TYR cc_start: 0.8140 (t80) cc_final: 0.7815 (t80) REVERT: B 2939 TYR cc_start: 0.8942 (m-80) cc_final: 0.8361 (m-10) REVERT: B 2982 PHE cc_start: 0.8853 (m-80) cc_final: 0.8074 (m-80) REVERT: B 3046 MET cc_start: 0.8911 (tpp) cc_final: 0.8670 (tpt) REVERT: B 3131 TYR cc_start: 0.9283 (m-80) cc_final: 0.8719 (m-80) REVERT: B 3181 TYR cc_start: 0.8387 (t80) cc_final: 0.8122 (t80) REVERT: B 3245 TYR cc_start: 0.9037 (t80) cc_final: 0.8743 (t80) REVERT: B 3250 TRP cc_start: 0.9080 (t-100) cc_final: 0.8525 (t-100) REVERT: B 3302 PHE cc_start: 0.9170 (m-80) cc_final: 0.8251 (t80) REVERT: B 3304 GLN cc_start: 0.9133 (tp-100) cc_final: 0.8684 (tp-100) REVERT: B 3819 MET cc_start: 0.7146 (mpp) cc_final: 0.6266 (ptt) REVERT: B 4143 LYS cc_start: 0.9081 (tppt) cc_final: 0.8453 (tppt) REVERT: B 4279 MET cc_start: 0.6583 (mtt) cc_final: 0.6154 (ttt) REVERT: B 4568 MET cc_start: 0.7667 (mmm) cc_final: 0.7291 (mpp) REVERT: B 4672 MET cc_start: 0.8200 (mtm) cc_final: 0.7579 (mtm) REVERT: C 81 MET cc_start: 0.8843 (tpt) cc_final: 0.8368 (tpt) REVERT: C 349 MET cc_start: 0.7592 (tpt) cc_final: 0.7173 (tpt) REVERT: C 902 TRP cc_start: 0.5151 (t-100) cc_final: 0.4476 (t-100) REVERT: C 935 MET cc_start: 0.8873 (ppp) cc_final: 0.8632 (ppp) REVERT: C 995 MET cc_start: 0.8882 (ttt) cc_final: 0.8628 (ttt) REVERT: C 1165 MET cc_start: 0.8019 (ttt) cc_final: 0.7596 (mtp) REVERT: C 1306 MET cc_start: 0.8782 (mtp) cc_final: 0.8582 (mtm) REVERT: C 1628 MET cc_start: 0.8779 (ttm) cc_final: 0.8467 (ttm) REVERT: C 1975 MET cc_start: 0.8852 (tmm) cc_final: 0.8300 (tmm) REVERT: C 2214 MET cc_start: 0.9327 (mmm) cc_final: 0.9104 (tpp) REVERT: C 2234 MET cc_start: 0.8846 (tpp) cc_final: 0.8521 (mmm) REVERT: C 2279 MET cc_start: 0.8356 (tmm) cc_final: 0.8118 (tmm) REVERT: C 2496 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9092 (tt) REVERT: C 2541 HIS cc_start: 0.9129 (m90) cc_final: 0.8816 (m-70) REVERT: C 2585 MET cc_start: 0.8940 (mmt) cc_final: 0.8597 (mmm) REVERT: C 2605 MET cc_start: 0.8730 (ttp) cc_final: 0.8214 (tmm) REVERT: C 2688 MET cc_start: 0.8517 (tpt) cc_final: 0.8315 (tpp) REVERT: C 2719 TYR cc_start: 0.8904 (t80) cc_final: 0.8289 (t80) REVERT: C 2782 MET cc_start: 0.9106 (tpt) cc_final: 0.8711 (mmm) REVERT: C 2828 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6970 (mtp) REVERT: C 2843 MET cc_start: 0.9089 (ppp) cc_final: 0.8685 (ppp) REVERT: C 2848 TYR cc_start: 0.9472 (OUTLIER) cc_final: 0.8946 (m-80) REVERT: C 2849 HIS cc_start: 0.9188 (t70) cc_final: 0.8582 (t-170) REVERT: C 2874 TYR cc_start: 0.8102 (t80) cc_final: 0.7804 (t80) REVERT: C 2939 TYR cc_start: 0.8955 (m-80) cc_final: 0.8370 (m-10) REVERT: C 2982 PHE cc_start: 0.8856 (m-80) cc_final: 0.8094 (m-80) REVERT: C 3046 MET cc_start: 0.8904 (tpp) cc_final: 0.8654 (tpt) REVERT: C 3109 PHE cc_start: 0.9124 (m-10) cc_final: 0.8861 (m-10) REVERT: C 3131 TYR cc_start: 0.9268 (m-80) cc_final: 0.8714 (m-80) REVERT: C 3245 TYR cc_start: 0.9032 (t80) cc_final: 0.8775 (t80) REVERT: C 3250 TRP cc_start: 0.9095 (t-100) cc_final: 0.8669 (t-100) REVERT: C 3304 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8679 (tp-100) REVERT: C 3819 MET cc_start: 0.7313 (mpp) cc_final: 0.6389 (ptt) REVERT: C 3985 MET cc_start: 0.9232 (mmm) cc_final: 0.8838 (mmm) REVERT: C 4274 MET cc_start: 0.5941 (mpp) cc_final: 0.5691 (mpp) REVERT: C 4279 MET cc_start: 0.6577 (mtt) cc_final: 0.6129 (ttt) REVERT: C 4672 MET cc_start: 0.8217 (mtm) cc_final: 0.7573 (mtm) REVERT: D 81 MET cc_start: 0.8836 (tpt) cc_final: 0.8602 (tpt) REVERT: D 902 TRP cc_start: 0.5408 (t-100) cc_final: 0.4520 (t-100) REVERT: D 935 MET cc_start: 0.8846 (ppp) cc_final: 0.8524 (ppp) REVERT: D 1165 MET cc_start: 0.8030 (ttt) cc_final: 0.7579 (mtp) REVERT: D 1173 MET cc_start: 0.8512 (mtp) cc_final: 0.8298 (mtp) REVERT: D 1306 MET cc_start: 0.8768 (mtp) cc_final: 0.8531 (mtm) REVERT: D 1975 MET cc_start: 0.8845 (tmm) cc_final: 0.8277 (tmm) REVERT: D 2214 MET cc_start: 0.9355 (tpp) cc_final: 0.8810 (mmm) REVERT: D 2234 MET cc_start: 0.8849 (tpt) cc_final: 0.8564 (mmm) REVERT: D 2279 MET cc_start: 0.8327 (tmm) cc_final: 0.8088 (tmm) REVERT: D 2496 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9073 (tt) REVERT: D 2541 HIS cc_start: 0.9138 (m90) cc_final: 0.8797 (m-70) REVERT: D 2585 MET cc_start: 0.8990 (mmt) cc_final: 0.8721 (mmm) REVERT: D 2605 MET cc_start: 0.8626 (tmm) cc_final: 0.8264 (tmm) REVERT: D 2719 TYR cc_start: 0.8822 (t80) cc_final: 0.8170 (t80) REVERT: D 2782 MET cc_start: 0.9099 (tpt) cc_final: 0.8707 (mmm) REVERT: D 2798 MET cc_start: 0.8962 (ppp) cc_final: 0.8725 (ppp) REVERT: D 2828 MET cc_start: 0.7321 (OUTLIER) cc_final: 0.6942 (mtp) REVERT: D 2843 MET cc_start: 0.9100 (ppp) cc_final: 0.8680 (ppp) REVERT: D 2874 TYR cc_start: 0.8199 (t80) cc_final: 0.7732 (t80) REVERT: D 2939 TYR cc_start: 0.8979 (m-80) cc_final: 0.8399 (m-10) REVERT: D 2982 PHE cc_start: 0.8860 (m-80) cc_final: 0.8082 (m-80) REVERT: D 3109 PHE cc_start: 0.9118 (m-10) cc_final: 0.8862 (m-10) REVERT: D 3131 TYR cc_start: 0.9240 (m-80) cc_final: 0.8655 (m-80) REVERT: D 3245 TYR cc_start: 0.8994 (t80) cc_final: 0.8736 (t80) REVERT: D 3250 TRP cc_start: 0.9105 (t-100) cc_final: 0.8647 (t-100) REVERT: D 3819 MET cc_start: 0.7363 (mpp) cc_final: 0.6453 (ptt) REVERT: D 4052 MET cc_start: 0.7683 (ppp) cc_final: 0.7338 (ppp) REVERT: D 4279 MET cc_start: 0.6522 (mtt) cc_final: 0.6100 (ttt) REVERT: D 4672 MET cc_start: 0.8234 (mtm) cc_final: 0.7615 (mtm) REVERT: D 4809 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8209 (tpt) outliers start: 137 outliers final: 82 residues processed: 871 average time/residue: 1.2407 time to fit residues: 1953.1629 Evaluate side-chains 863 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 770 time to evaluate : 12.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1721 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2496 LEU Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4492 LEU Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2496 LEU Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4239 LEU Chi-restraints excluded: chain B residue 4492 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2496 LEU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2828 MET Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4239 LEU Chi-restraints excluded: chain C residue 4492 LEU Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2496 LEU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2828 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3719 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4492 LEU Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1611 optimal weight: 7.9990 chunk 188 optimal weight: 6.9990 chunk 952 optimal weight: 9.9990 chunk 1220 optimal weight: 9.9990 chunk 945 optimal weight: 10.0000 chunk 1407 optimal weight: 6.9990 chunk 933 optimal weight: 1.9990 chunk 1665 optimal weight: 2.9990 chunk 1042 optimal weight: 10.0000 chunk 1015 optimal weight: 6.9990 chunk 768 optimal weight: 40.0000 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 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1978 ASN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C4620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D4620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 141628 Z= 0.313 Angle : 0.624 12.957 191356 Z= 0.316 Chirality : 0.041 0.191 20988 Planarity : 0.005 0.122 24588 Dihedral : 6.257 86.183 19028 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.78 % Allowed : 7.84 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.07), residues: 17212 helix: 1.61 (0.05), residues: 9084 sheet: -0.36 (0.13), residues: 1480 loop : -0.66 (0.08), residues: 6648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C2852 HIS 0.017 0.001 HIS A3034 PHE 0.024 0.001 PHE A3109 TYR 0.026 0.001 TYR C1703 ARG 0.007 0.000 ARG D 801 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 775 time to evaluate : 12.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8821 (tpt) cc_final: 0.8586 (tpt) REVERT: A 349 MET cc_start: 0.7745 (tpt) cc_final: 0.7304 (tpt) REVERT: A 393 MET cc_start: 0.7816 (mmm) cc_final: 0.7479 (mmm) REVERT: A 399 MET cc_start: 0.7994 (tmm) cc_final: 0.7790 (tmm) REVERT: A 895 MET cc_start: 0.9166 (ptm) cc_final: 0.8881 (ppp) REVERT: A 902 TRP cc_start: 0.5693 (t-100) cc_final: 0.4764 (t-100) REVERT: A 995 MET cc_start: 0.8918 (ttt) cc_final: 0.8662 (ttt) REVERT: A 1173 MET cc_start: 0.8729 (mtm) cc_final: 0.8472 (mtm) REVERT: A 1300 MET cc_start: 0.8566 (mtp) cc_final: 0.8286 (mtp) REVERT: A 1306 MET cc_start: 0.8775 (mtp) cc_final: 0.8533 (mtm) REVERT: A 1421 MET cc_start: 0.8496 (mmp) cc_final: 0.8174 (mmp) REVERT: A 1975 MET cc_start: 0.8847 (tmm) cc_final: 0.8265 (tmm) REVERT: A 2150 MET cc_start: 0.8462 (mtm) cc_final: 0.8214 (mtt) REVERT: A 2214 MET cc_start: 0.9339 (tpp) cc_final: 0.9015 (mmm) REVERT: A 2234 MET cc_start: 0.9063 (tpt) cc_final: 0.8745 (mmm) REVERT: A 2279 MET cc_start: 0.8345 (tmm) cc_final: 0.8103 (tmm) REVERT: A 2496 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9097 (tt) REVERT: A 2541 HIS cc_start: 0.9150 (m90) cc_final: 0.8795 (m-70) REVERT: A 2580 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 2584 MET cc_start: 0.8621 (mpp) cc_final: 0.8366 (mpp) REVERT: A 2585 MET cc_start: 0.8576 (mpp) cc_final: 0.7814 (mmm) REVERT: A 2605 MET cc_start: 0.8684 (tmm) cc_final: 0.8303 (tmm) REVERT: A 2689 MET cc_start: 0.5955 (ttt) cc_final: 0.5718 (ttt) REVERT: A 2719 TYR cc_start: 0.8890 (t80) cc_final: 0.8455 (t80) REVERT: A 2785 TRP cc_start: 0.8346 (m100) cc_final: 0.7684 (m100) REVERT: A 2798 MET cc_start: 0.9129 (tmm) cc_final: 0.8555 (mmt) REVERT: A 2828 MET cc_start: 0.7027 (mtp) cc_final: 0.6783 (mtp) REVERT: A 2835 ARG cc_start: 0.9246 (mmm160) cc_final: 0.8929 (mmp80) REVERT: A 2849 HIS cc_start: 0.9315 (t70) cc_final: 0.9008 (t70) REVERT: A 2982 PHE cc_start: 0.8898 (m-80) cc_final: 0.8118 (m-80) REVERT: A 3215 MET cc_start: 0.9512 (mpp) cc_final: 0.9213 (pmm) REVERT: A 3245 TYR cc_start: 0.8926 (t80) cc_final: 0.8447 (t80) REVERT: A 3246 MET cc_start: 0.8877 (mmt) cc_final: 0.8506 (mmt) REVERT: A 3319 PHE cc_start: 0.8016 (m-80) cc_final: 0.7439 (m-80) REVERT: A 3819 MET cc_start: 0.7455 (mpp) cc_final: 0.6441 (ptt) REVERT: A 4035 TYR cc_start: 0.8132 (m-80) cc_final: 0.7892 (m-80) REVERT: A 4052 MET cc_start: 0.7796 (ppp) cc_final: 0.7354 (ppp) REVERT: A 4143 LYS cc_start: 0.9110 (tppt) cc_final: 0.8484 (tppt) REVERT: A 4279 MET cc_start: 0.6708 (mtt) cc_final: 0.6195 (ttt) REVERT: A 4728 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8133 (mmm) REVERT: E 58 LYS cc_start: 0.8967 (pttm) cc_final: 0.8644 (pttm) REVERT: E 62 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8453 (mm-30) REVERT: E 67 MET cc_start: 0.8459 (mtp) cc_final: 0.8216 (mtp) REVERT: F 4 GLU cc_start: 0.7674 (mp0) cc_final: 0.7213 (mp0) REVERT: F 54 GLN cc_start: 0.8670 (mp10) cc_final: 0.8302 (mp10) REVERT: G 54 GLN cc_start: 0.8687 (mp10) cc_final: 0.8292 (mp10) REVERT: H 62 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8412 (mm-30) REVERT: B 81 MET cc_start: 0.8827 (tpt) cc_final: 0.8603 (tpt) REVERT: B 349 MET cc_start: 0.7753 (tpt) cc_final: 0.7325 (tpt) REVERT: B 393 MET cc_start: 0.7793 (mmm) cc_final: 0.7497 (mmm) REVERT: B 895 MET cc_start: 0.8993 (ptm) cc_final: 0.8625 (ppp) REVERT: B 902 TRP cc_start: 0.5398 (t-100) cc_final: 0.4639 (t-100) REVERT: B 1173 MET cc_start: 0.8754 (mtm) cc_final: 0.8428 (mtp) REVERT: B 1306 MET cc_start: 0.8813 (mtp) cc_final: 0.8603 (mtm) REVERT: B 1975 MET cc_start: 0.8857 (tmm) cc_final: 0.8300 (tmm) REVERT: B 2214 MET cc_start: 0.9308 (mmm) cc_final: 0.9103 (tpp) REVERT: B 2234 MET cc_start: 0.8845 (tpp) cc_final: 0.8499 (mmm) REVERT: B 2279 MET cc_start: 0.8362 (tmm) cc_final: 0.8109 (tmm) REVERT: B 2496 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9097 (tt) REVERT: B 2541 HIS cc_start: 0.9147 (m90) cc_final: 0.8787 (m-70) REVERT: B 2585 MET cc_start: 0.8962 (mmt) cc_final: 0.8653 (mmm) REVERT: B 2605 MET cc_start: 0.8598 (tmm) cc_final: 0.8231 (tmm) REVERT: B 2681 MET cc_start: 0.9191 (tpp) cc_final: 0.8845 (tpp) REVERT: B 2719 TYR cc_start: 0.8886 (t80) cc_final: 0.8246 (t80) REVERT: B 2732 TRP cc_start: 0.9040 (t60) cc_final: 0.8796 (t60) REVERT: B 2782 MET cc_start: 0.9165 (tpt) cc_final: 0.8774 (mmm) REVERT: B 2798 MET cc_start: 0.8990 (ppp) cc_final: 0.8735 (ppp) REVERT: B 2843 MET cc_start: 0.9091 (ppp) cc_final: 0.8686 (ppp) REVERT: B 2848 TYR cc_start: 0.9490 (OUTLIER) cc_final: 0.8972 (m-80) REVERT: B 2849 HIS cc_start: 0.9173 (t70) cc_final: 0.8636 (t-170) REVERT: B 2874 TYR cc_start: 0.8151 (t80) cc_final: 0.7872 (t80) REVERT: B 2939 TYR cc_start: 0.8944 (m-80) cc_final: 0.8364 (m-10) REVERT: B 2982 PHE cc_start: 0.8846 (m-80) cc_final: 0.8085 (m-80) REVERT: B 3003 MET cc_start: 0.8618 (ptm) cc_final: 0.8183 (ptp) REVERT: B 3046 MET cc_start: 0.8908 (tpp) cc_final: 0.8671 (tpt) REVERT: B 3166 PHE cc_start: 0.8602 (t80) cc_final: 0.8335 (t80) REVERT: B 3181 TYR cc_start: 0.8432 (t80) cc_final: 0.8186 (t80) REVERT: B 3245 TYR cc_start: 0.9011 (t80) cc_final: 0.8729 (t80) REVERT: B 3250 TRP cc_start: 0.9112 (t-100) cc_final: 0.8553 (t-100) REVERT: B 3302 PHE cc_start: 0.9185 (m-80) cc_final: 0.8272 (t80) REVERT: B 3304 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8683 (tp-100) REVERT: B 3319 PHE cc_start: 0.8082 (m-80) cc_final: 0.7385 (m-80) REVERT: B 3689 MET cc_start: 0.8590 (mmp) cc_final: 0.8370 (mmp) REVERT: B 3819 MET cc_start: 0.7179 (mpp) cc_final: 0.6307 (ptt) REVERT: B 4143 LYS cc_start: 0.9102 (tppt) cc_final: 0.8518 (tppt) REVERT: B 4279 MET cc_start: 0.6591 (mtt) cc_final: 0.6153 (ttt) REVERT: B 4568 MET cc_start: 0.7669 (mmm) cc_final: 0.7288 (mpp) REVERT: B 4672 MET cc_start: 0.8214 (mtm) cc_final: 0.7617 (mtm) REVERT: C 81 MET cc_start: 0.8849 (tpt) cc_final: 0.8385 (tpt) REVERT: C 128 MET cc_start: 0.9060 (mtm) cc_final: 0.8855 (mtm) REVERT: C 349 MET cc_start: 0.7629 (tpt) cc_final: 0.7217 (tpt) REVERT: C 902 TRP cc_start: 0.5416 (t-100) cc_final: 0.4656 (t-100) REVERT: C 935 MET cc_start: 0.8899 (ppp) cc_final: 0.8646 (ppp) REVERT: C 995 MET cc_start: 0.8894 (ttt) cc_final: 0.8648 (ttt) REVERT: C 1165 MET cc_start: 0.8112 (ttt) cc_final: 0.7623 (mtp) REVERT: C 1306 MET cc_start: 0.8791 (mtp) cc_final: 0.8552 (mtm) REVERT: C 1628 MET cc_start: 0.8787 (ttm) cc_final: 0.8524 (ttm) REVERT: C 1975 MET cc_start: 0.8849 (tmm) cc_final: 0.8281 (tmm) REVERT: C 2214 MET cc_start: 0.9330 (mmm) cc_final: 0.9107 (tpp) REVERT: C 2234 MET cc_start: 0.8838 (tpp) cc_final: 0.8049 (tmm) REVERT: C 2279 MET cc_start: 0.8370 (tmm) cc_final: 0.8133 (tmm) REVERT: C 2496 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9101 (tt) REVERT: C 2541 HIS cc_start: 0.9156 (m90) cc_final: 0.8831 (m-70) REVERT: C 2585 MET cc_start: 0.8937 (mmt) cc_final: 0.8644 (mmm) REVERT: C 2605 MET cc_start: 0.8755 (ttp) cc_final: 0.8199 (tmm) REVERT: C 2719 TYR cc_start: 0.8957 (t80) cc_final: 0.8340 (t80) REVERT: C 2782 MET cc_start: 0.9149 (tpt) cc_final: 0.8825 (mmm) REVERT: C 2785 TRP cc_start: 0.8227 (m-90) cc_final: 0.7554 (m-90) REVERT: C 2828 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7038 (mtp) REVERT: C 2835 ARG cc_start: 0.9240 (mmm160) cc_final: 0.8835 (mmp80) REVERT: C 2843 MET cc_start: 0.9089 (ppp) cc_final: 0.8626 (ppp) REVERT: C 2848 TYR cc_start: 0.9496 (OUTLIER) cc_final: 0.8988 (m-80) REVERT: C 2849 HIS cc_start: 0.9156 (t70) cc_final: 0.8628 (t-170) REVERT: C 2874 TYR cc_start: 0.8087 (t80) cc_final: 0.7822 (t80) REVERT: C 2939 TYR cc_start: 0.8961 (m-80) cc_final: 0.8379 (m-10) REVERT: C 2982 PHE cc_start: 0.8853 (m-80) cc_final: 0.8104 (m-80) REVERT: C 3003 MET cc_start: 0.8629 (ptm) cc_final: 0.8198 (ptp) REVERT: C 3046 MET cc_start: 0.8906 (tpp) cc_final: 0.8665 (tpt) REVERT: C 3109 PHE cc_start: 0.9122 (m-10) cc_final: 0.8855 (m-10) REVERT: C 3215 MET cc_start: 0.9542 (mpp) cc_final: 0.9314 (pmm) REVERT: C 3245 TYR cc_start: 0.9000 (t80) cc_final: 0.8733 (t80) REVERT: C 3250 TRP cc_start: 0.9113 (t-100) cc_final: 0.8625 (t-100) REVERT: C 3302 PHE cc_start: 0.9177 (m-80) cc_final: 0.8268 (t80) REVERT: C 3304 GLN cc_start: 0.9114 (tp-100) cc_final: 0.8678 (tp-100) REVERT: C 3319 PHE cc_start: 0.8098 (m-80) cc_final: 0.7434 (m-80) REVERT: C 3819 MET cc_start: 0.7324 (mpp) cc_final: 0.6378 (ptt) REVERT: C 3985 MET cc_start: 0.9241 (mmm) cc_final: 0.8857 (mmm) REVERT: C 4274 MET cc_start: 0.5936 (mpp) cc_final: 0.5685 (mpp) REVERT: C 4279 MET cc_start: 0.6590 (mtt) cc_final: 0.6135 (ttt) REVERT: C 4672 MET cc_start: 0.8222 (mtm) cc_final: 0.7612 (mtm) REVERT: C 4809 MET cc_start: 0.8797 (tpp) cc_final: 0.7968 (tpp) REVERT: D 81 MET cc_start: 0.8835 (tpt) cc_final: 0.8607 (tpt) REVERT: D 895 MET cc_start: 0.8906 (mtm) cc_final: 0.8699 (ppp) REVERT: D 899 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: D 902 TRP cc_start: 0.5555 (t-100) cc_final: 0.4595 (t-100) REVERT: D 1165 MET cc_start: 0.8114 (ttt) cc_final: 0.7609 (mtp) REVERT: D 1173 MET cc_start: 0.8547 (mtp) cc_final: 0.8330 (mtp) REVERT: D 1306 MET cc_start: 0.8772 (mtp) cc_final: 0.8531 (mtm) REVERT: D 1975 MET cc_start: 0.8838 (tmm) cc_final: 0.8253 (tmm) REVERT: D 2150 MET cc_start: 0.8495 (mtm) cc_final: 0.8248 (mtt) REVERT: D 2214 MET cc_start: 0.9350 (tpp) cc_final: 0.8783 (mmm) REVERT: D 2234 MET cc_start: 0.8845 (tpt) cc_final: 0.8519 (mmm) REVERT: D 2279 MET cc_start: 0.8345 (tmm) cc_final: 0.8117 (tmm) REVERT: D 2496 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.9077 (tt) REVERT: D 2541 HIS cc_start: 0.9147 (m90) cc_final: 0.8806 (m-70) REVERT: D 2585 MET cc_start: 0.8993 (mmt) cc_final: 0.8747 (mmm) REVERT: D 2605 MET cc_start: 0.8634 (tmm) cc_final: 0.8266 (tmm) REVERT: D 2719 TYR cc_start: 0.8834 (t80) cc_final: 0.8179 (t80) REVERT: D 2798 MET cc_start: 0.8970 (ppp) cc_final: 0.8739 (ppp) REVERT: D 2828 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6940 (mtp) REVERT: D 2843 MET cc_start: 0.9123 (ppp) cc_final: 0.8695 (ppp) REVERT: D 2849 HIS cc_start: 0.9191 (t70) cc_final: 0.8452 (t-170) REVERT: D 2874 TYR cc_start: 0.8216 (t80) cc_final: 0.7829 (t80) REVERT: D 2939 TYR cc_start: 0.8981 (m-80) cc_final: 0.8408 (m-10) REVERT: D 2982 PHE cc_start: 0.8862 (m-80) cc_final: 0.8101 (m-80) REVERT: D 3109 PHE cc_start: 0.9116 (m-10) cc_final: 0.8856 (m-10) REVERT: D 3215 MET cc_start: 0.9551 (mpp) cc_final: 0.9289 (pmm) REVERT: D 3245 TYR cc_start: 0.8982 (t80) cc_final: 0.8718 (t80) REVERT: D 3250 TRP cc_start: 0.9137 (t-100) cc_final: 0.8666 (t-100) REVERT: D 3319 PHE cc_start: 0.8127 (m-80) cc_final: 0.7440 (m-80) REVERT: D 3819 MET cc_start: 0.7364 (mpp) cc_final: 0.6439 (ptt) REVERT: D 4052 MET cc_start: 0.7696 (ppp) cc_final: 0.7388 (ppp) REVERT: D 4279 MET cc_start: 0.6523 (mtt) cc_final: 0.6106 (ttt) REVERT: D 4672 MET cc_start: 0.8229 (mtm) cc_final: 0.7632 (mtm) REVERT: D 4809 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8229 (tpt) outliers start: 119 outliers final: 87 residues processed: 852 average time/residue: 1.1772 time to fit residues: 1794.0641 Evaluate side-chains 867 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 768 time to evaluate : 12.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 1721 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2241 ASP Chi-restraints excluded: chain A residue 2496 LEU Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 3719 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4492 LEU Chi-restraints excluded: chain A residue 4728 MET Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2496 LEU Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4239 LEU Chi-restraints excluded: chain B residue 4492 LEU Chi-restraints excluded: chain C residue 240 HIS Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 993 GLU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2241 ASP Chi-restraints excluded: chain C residue 2496 LEU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2828 MET Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain C residue 3739 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4492 LEU Chi-restraints excluded: chain C residue 4817 MET Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2496 LEU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2828 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3719 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain D residue 4492 LEU Chi-restraints excluded: chain D residue 4809 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1030 optimal weight: 10.0000 chunk 665 optimal weight: 10.0000 chunk 994 optimal weight: 10.0000 chunk 501 optimal weight: 9.9990 chunk 327 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 1058 optimal weight: 10.0000 chunk 1134 optimal weight: 30.0000 chunk 823 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 1309 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1169 ASN ** A2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3031 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3727 GLN A3953 HIS ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3727 GLN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2059 GLN ** C2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN C3953 HIS ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C4620 GLN D 240 HIS ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1169 ASN ** D2464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3727 GLN D3953 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 141628 Z= 0.180 Angle : 0.589 13.939 191356 Z= 0.296 Chirality : 0.040 0.193 20988 Planarity : 0.004 0.120 24588 Dihedral : 6.174 87.298 19028 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 0.72 % Allowed : 8.03 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.07), residues: 17212 helix: 1.67 (0.06), residues: 9100 sheet: -0.25 (0.13), residues: 1508 loop : -0.56 (0.08), residues: 6604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP D2852 HIS 0.013 0.001 HIS B4055 PHE 0.024 0.001 PHE C3166 TYR 0.019 0.001 TYR C1703 ARG 0.006 0.000 ARG D 520 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 784 time to evaluate : 12.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8797 (tpt) cc_final: 0.8292 (tpt) REVERT: A 349 MET cc_start: 0.7646 (tpt) cc_final: 0.7269 (tpt) REVERT: A 393 MET cc_start: 0.7790 (mmm) cc_final: 0.7370 (mmm) REVERT: A 895 MET cc_start: 0.9180 (ptm) cc_final: 0.8861 (ppp) REVERT: A 902 TRP cc_start: 0.5602 (t-100) cc_final: 0.4753 (t-100) REVERT: A 995 MET cc_start: 0.8856 (ttt) cc_final: 0.8585 (ttt) REVERT: A 1165 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7594 (mtp) REVERT: A 1173 MET cc_start: 0.8760 (mtm) cc_final: 0.8453 (mtp) REVERT: A 1300 MET cc_start: 0.8512 (mtp) cc_final: 0.8236 (mtp) REVERT: A 1421 MET cc_start: 0.8489 (mmp) cc_final: 0.8180 (mmp) REVERT: A 1975 MET cc_start: 0.8842 (tmm) cc_final: 0.8231 (tmm) REVERT: A 2214 MET cc_start: 0.9266 (tpp) cc_final: 0.8951 (mmm) REVERT: A 2234 MET cc_start: 0.9004 (tpt) cc_final: 0.8735 (mmm) REVERT: A 2279 MET cc_start: 0.8326 (tmm) cc_final: 0.8077 (tmm) REVERT: A 2496 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9046 (tt) REVERT: A 2541 HIS cc_start: 0.9111 (m90) cc_final: 0.8738 (m-70) REVERT: A 2584 MET cc_start: 0.8544 (mpp) cc_final: 0.8298 (mpp) REVERT: A 2585 MET cc_start: 0.8547 (mpp) cc_final: 0.8087 (mmt) REVERT: A 2605 MET cc_start: 0.8661 (tmm) cc_final: 0.8279 (tmm) REVERT: A 2689 MET cc_start: 0.6030 (ttt) cc_final: 0.5779 (ttt) REVERT: A 2719 TYR cc_start: 0.8873 (t80) cc_final: 0.8435 (t80) REVERT: A 2785 TRP cc_start: 0.8300 (m100) cc_final: 0.7642 (m100) REVERT: A 2798 MET cc_start: 0.9107 (tmm) cc_final: 0.8552 (mmt) REVERT: A 2828 MET cc_start: 0.7045 (mtp) cc_final: 0.6811 (mtp) REVERT: A 2835 ARG cc_start: 0.9209 (mmm160) cc_final: 0.8859 (mmp80) REVERT: A 2982 PHE cc_start: 0.8825 (m-80) cc_final: 0.8042 (m-80) REVERT: A 3104 MET cc_start: 0.8683 (tmm) cc_final: 0.8390 (tmm) REVERT: A 3215 MET cc_start: 0.9483 (mpp) cc_final: 0.9185 (pmm) REVERT: A 3245 TYR cc_start: 0.8941 (t80) cc_final: 0.8474 (t80) REVERT: A 3246 MET cc_start: 0.8941 (mmt) cc_final: 0.8613 (mmt) REVERT: A 3273 MET cc_start: 0.8203 (pmm) cc_final: 0.7999 (pmm) REVERT: A 3304 GLN cc_start: 0.9166 (tp-100) cc_final: 0.8771 (tp-100) REVERT: A 3319 PHE cc_start: 0.7979 (m-80) cc_final: 0.7407 (m-80) REVERT: A 3819 MET cc_start: 0.7347 (mpp) cc_final: 0.6417 (ptt) REVERT: A 4035 TYR cc_start: 0.8086 (m-80) cc_final: 0.7835 (m-80) REVERT: A 4052 MET cc_start: 0.7806 (ppp) cc_final: 0.7394 (ppp) REVERT: A 4143 LYS cc_start: 0.9124 (tppt) cc_final: 0.8497 (tppt) REVERT: A 4186 MET cc_start: 0.8377 (mmm) cc_final: 0.7805 (mmm) REVERT: A 4279 MET cc_start: 0.6722 (mtt) cc_final: 0.6227 (ttt) REVERT: A 4292 MET cc_start: 0.8434 (mmt) cc_final: 0.7877 (mmm) REVERT: A 4884 MET cc_start: 0.8313 (mmm) cc_final: 0.7948 (mmm) REVERT: E 58 LYS cc_start: 0.8934 (pttm) cc_final: 0.8525 (pttm) REVERT: E 62 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8424 (mm-30) REVERT: E 67 MET cc_start: 0.8394 (mtp) cc_final: 0.8188 (mtp) REVERT: F 54 GLN cc_start: 0.8666 (mp10) cc_final: 0.8274 (mp10) REVERT: G 4 GLU cc_start: 0.7572 (mp0) cc_final: 0.7140 (mp0) REVERT: G 54 GLN cc_start: 0.8724 (mp10) cc_final: 0.8307 (mp10) REVERT: H 54 GLN cc_start: 0.8553 (mp10) cc_final: 0.8189 (mp10) REVERT: H 58 LYS cc_start: 0.8934 (pttm) cc_final: 0.8474 (pttm) REVERT: H 62 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 81 MET cc_start: 0.8812 (tpt) cc_final: 0.8581 (tpt) REVERT: B 349 MET cc_start: 0.7674 (tpt) cc_final: 0.7289 (tpt) REVERT: B 895 MET cc_start: 0.8987 (ptm) cc_final: 0.8766 (ppp) REVERT: B 902 TRP cc_start: 0.5290 (t-100) cc_final: 0.4623 (t-100) REVERT: B 935 MET cc_start: 0.8820 (ppp) cc_final: 0.8521 (ppp) REVERT: B 1165 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7646 (mtp) REVERT: B 1173 MET cc_start: 0.8775 (mtm) cc_final: 0.8463 (mtp) REVERT: B 1306 MET cc_start: 0.8775 (mtp) cc_final: 0.8564 (mtm) REVERT: B 1975 MET cc_start: 0.8853 (tmm) cc_final: 0.8264 (tmm) REVERT: B 2167 MET cc_start: 0.8852 (pmm) cc_final: 0.8037 (ptp) REVERT: B 2214 MET cc_start: 0.9317 (mmm) cc_final: 0.9075 (tpp) REVERT: B 2234 MET cc_start: 0.8766 (tpp) cc_final: 0.7952 (tmm) REVERT: B 2279 MET cc_start: 0.8336 (tmm) cc_final: 0.8071 (tmm) REVERT: B 2496 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9049 (tt) REVERT: B 2541 HIS cc_start: 0.9089 (m90) cc_final: 0.8708 (m-70) REVERT: B 2585 MET cc_start: 0.8912 (mmt) cc_final: 0.8691 (mmm) REVERT: B 2605 MET cc_start: 0.8573 (tmm) cc_final: 0.8196 (tmm) REVERT: B 2681 MET cc_start: 0.9133 (tpp) cc_final: 0.8808 (tpp) REVERT: B 2719 TYR cc_start: 0.8852 (t80) cc_final: 0.8186 (t80) REVERT: B 2732 TRP cc_start: 0.9025 (t60) cc_final: 0.8769 (t60) REVERT: B 2782 MET cc_start: 0.9126 (tpt) cc_final: 0.8730 (mmm) REVERT: B 2798 MET cc_start: 0.8956 (ppp) cc_final: 0.8695 (ppp) REVERT: B 2843 MET cc_start: 0.9101 (ppp) cc_final: 0.8675 (ppp) REVERT: B 2848 TYR cc_start: 0.9483 (OUTLIER) cc_final: 0.8963 (m-80) REVERT: B 2849 HIS cc_start: 0.9135 (t70) cc_final: 0.8620 (t-170) REVERT: B 2874 TYR cc_start: 0.8152 (t80) cc_final: 0.7851 (t80) REVERT: B 2939 TYR cc_start: 0.8900 (m-80) cc_final: 0.8307 (m-10) REVERT: B 2982 PHE cc_start: 0.8799 (m-80) cc_final: 0.8029 (m-80) REVERT: B 3003 MET cc_start: 0.8615 (ptm) cc_final: 0.8175 (ptp) REVERT: B 3046 MET cc_start: 0.8853 (tpp) cc_final: 0.8595 (tpt) REVERT: B 3166 PHE cc_start: 0.8664 (t80) cc_final: 0.8400 (t80) REVERT: B 3181 TYR cc_start: 0.8422 (t80) cc_final: 0.8111 (t80) REVERT: B 3215 MET cc_start: 0.9519 (pmm) cc_final: 0.9274 (pmm) REVERT: B 3245 TYR cc_start: 0.8992 (t80) cc_final: 0.8703 (t80) REVERT: B 3250 TRP cc_start: 0.9048 (t-100) cc_final: 0.8458 (t-100) REVERT: B 3302 PHE cc_start: 0.9130 (m-80) cc_final: 0.8269 (t80) REVERT: B 3304 GLN cc_start: 0.9098 (tp-100) cc_final: 0.8648 (tp-100) REVERT: B 3319 PHE cc_start: 0.8053 (m-80) cc_final: 0.7350 (m-80) REVERT: B 3819 MET cc_start: 0.7045 (mpp) cc_final: 0.6214 (ptt) REVERT: B 3999 MET cc_start: 0.8797 (tpp) cc_final: 0.8553 (ttm) REVERT: B 4035 TYR cc_start: 0.8165 (m-80) cc_final: 0.7950 (m-10) REVERT: B 4143 LYS cc_start: 0.9117 (tppt) cc_final: 0.8488 (tppt) REVERT: B 4186 MET cc_start: 0.8354 (mmm) cc_final: 0.7780 (mmm) REVERT: B 4279 MET cc_start: 0.6713 (mtt) cc_final: 0.6276 (ttt) REVERT: B 4568 MET cc_start: 0.7672 (mmm) cc_final: 0.7293 (mpp) REVERT: B 4672 MET cc_start: 0.8192 (mtm) cc_final: 0.7708 (mtp) REVERT: B 4809 MET cc_start: 0.8814 (tpp) cc_final: 0.8031 (tpp) REVERT: C 81 MET cc_start: 0.8827 (tpt) cc_final: 0.8344 (tpt) REVERT: C 241 MET cc_start: 0.7640 (mmp) cc_final: 0.7425 (mmp) REVERT: C 349 MET cc_start: 0.7504 (tpt) cc_final: 0.7148 (tpt) REVERT: C 902 TRP cc_start: 0.5369 (t-100) cc_final: 0.4694 (t-100) REVERT: C 935 MET cc_start: 0.8842 (ppp) cc_final: 0.8520 (ppp) REVERT: C 995 MET cc_start: 0.8861 (ttt) cc_final: 0.8594 (ttt) REVERT: C 1165 MET cc_start: 0.7921 (ttt) cc_final: 0.7512 (mtp) REVERT: C 1300 MET cc_start: 0.8520 (mtp) cc_final: 0.8294 (mtp) REVERT: C 1306 MET cc_start: 0.8752 (mtp) cc_final: 0.8550 (mtm) REVERT: C 1975 MET cc_start: 0.8837 (tmm) cc_final: 0.8237 (tmm) REVERT: C 2214 MET cc_start: 0.9333 (mmm) cc_final: 0.9076 (tpp) REVERT: C 2234 MET cc_start: 0.8763 (tpp) cc_final: 0.7949 (tmm) REVERT: C 2279 MET cc_start: 0.8344 (tmm) cc_final: 0.8109 (tmm) REVERT: C 2496 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9071 (tt) REVERT: C 2541 HIS cc_start: 0.9117 (m90) cc_final: 0.8779 (m-70) REVERT: C 2585 MET cc_start: 0.8900 (mmt) cc_final: 0.8688 (mmm) REVERT: C 2605 MET cc_start: 0.8721 (ttp) cc_final: 0.8150 (tmm) REVERT: C 2719 TYR cc_start: 0.8945 (t80) cc_final: 0.8308 (t80) REVERT: C 2782 MET cc_start: 0.9121 (tpt) cc_final: 0.8742 (mmm) REVERT: C 2828 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6944 (mtp) REVERT: C 2835 ARG cc_start: 0.9218 (mmm160) cc_final: 0.8827 (mmp80) REVERT: C 2843 MET cc_start: 0.9071 (ppp) cc_final: 0.8641 (ppp) REVERT: C 2848 TYR cc_start: 0.9476 (OUTLIER) cc_final: 0.8954 (m-80) REVERT: C 2849 HIS cc_start: 0.9108 (t70) cc_final: 0.8582 (t-170) REVERT: C 2874 TYR cc_start: 0.8059 (t80) cc_final: 0.7813 (t80) REVERT: C 2939 TYR cc_start: 0.8919 (m-80) cc_final: 0.8340 (m-10) REVERT: C 2982 PHE cc_start: 0.8804 (m-80) cc_final: 0.8052 (m-80) REVERT: C 3003 MET cc_start: 0.8634 (ptm) cc_final: 0.8195 (ptp) REVERT: C 3046 MET cc_start: 0.8854 (tpp) cc_final: 0.8598 (tpt) REVERT: C 3215 MET cc_start: 0.9500 (mpp) cc_final: 0.9281 (pmm) REVERT: C 3245 TYR cc_start: 0.8957 (t80) cc_final: 0.8697 (t80) REVERT: C 3302 PHE cc_start: 0.9130 (m-80) cc_final: 0.8233 (t80) REVERT: C 3304 GLN cc_start: 0.9088 (tp-100) cc_final: 0.8645 (tp-100) REVERT: C 3319 PHE cc_start: 0.8077 (m-80) cc_final: 0.7392 (m-80) REVERT: C 3689 MET cc_start: 0.8528 (mmp) cc_final: 0.8256 (mmp) REVERT: C 3819 MET cc_start: 0.7235 (mpp) cc_final: 0.6307 (ptt) REVERT: C 3985 MET cc_start: 0.9220 (mmm) cc_final: 0.8820 (mmm) REVERT: C 3999 MET cc_start: 0.8819 (tpp) cc_final: 0.8525 (tpp) REVERT: C 4035 TYR cc_start: 0.8128 (m-80) cc_final: 0.7918 (m-10) REVERT: C 4186 MET cc_start: 0.8360 (mmm) cc_final: 0.7782 (mmm) REVERT: C 4274 MET cc_start: 0.5925 (mpp) cc_final: 0.5659 (mpp) REVERT: C 4279 MET cc_start: 0.6703 (mtt) cc_final: 0.6249 (ttt) REVERT: C 4672 MET cc_start: 0.8195 (mtm) cc_final: 0.7750 (mtp) REVERT: C 4809 MET cc_start: 0.8832 (tpp) cc_final: 0.8126 (tpp) REVERT: D 81 MET cc_start: 0.8819 (tpt) cc_final: 0.8582 (tpt) REVERT: D 895 MET cc_start: 0.8928 (mtm) cc_final: 0.8686 (ppp) REVERT: D 899 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8244 (mp0) REVERT: D 902 TRP cc_start: 0.5463 (t-100) cc_final: 0.4583 (t-100) REVERT: D 935 MET cc_start: 0.8811 (ppp) cc_final: 0.8487 (ppp) REVERT: D 1165 MET cc_start: 0.7893 (ttt) cc_final: 0.7482 (mtp) REVERT: D 1173 MET cc_start: 0.8521 (mtp) cc_final: 0.8297 (mtp) REVERT: D 1306 MET cc_start: 0.8744 (mtp) cc_final: 0.8507 (mtm) REVERT: D 1975 MET cc_start: 0.8828 (tmm) cc_final: 0.8219 (tmm) REVERT: D 2214 MET cc_start: 0.9309 (tpp) cc_final: 0.8754 (mmm) REVERT: D 2234 MET cc_start: 0.8781 (tpt) cc_final: 0.8487 (mmm) REVERT: D 2279 MET cc_start: 0.8320 (tmm) cc_final: 0.8088 (tmm) REVERT: D 2496 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9043 (tt) REVERT: D 2541 HIS cc_start: 0.9097 (m90) cc_final: 0.8739 (m-70) REVERT: D 2585 MET cc_start: 0.8951 (mmt) cc_final: 0.8737 (mmm) REVERT: D 2605 MET cc_start: 0.8606 (tmm) cc_final: 0.8226 (tmm) REVERT: D 2719 TYR cc_start: 0.8796 (t80) cc_final: 0.8122 (t80) REVERT: D 2782 MET cc_start: 0.8923 (tpp) cc_final: 0.8547 (mmm) REVERT: D 2785 TRP cc_start: 0.8215 (m-90) cc_final: 0.7721 (m100) REVERT: D 2798 MET cc_start: 0.8938 (ppp) cc_final: 0.8704 (ppp) REVERT: D 2828 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6875 (mtp) REVERT: D 2843 MET cc_start: 0.9113 (ppp) cc_final: 0.8583 (ppp) REVERT: D 2849 HIS cc_start: 0.9116 (t70) cc_final: 0.8444 (t-170) REVERT: D 2874 TYR cc_start: 0.8165 (t80) cc_final: 0.7793 (t80) REVERT: D 2939 TYR cc_start: 0.8942 (m-80) cc_final: 0.8364 (m-10) REVERT: D 2982 PHE cc_start: 0.8815 (m-80) cc_final: 0.8049 (m-80) REVERT: D 3003 MET cc_start: 0.8686 (ptm) cc_final: 0.8276 (ptp) REVERT: D 3109 PHE cc_start: 0.9116 (m-10) cc_final: 0.8840 (m-10) REVERT: D 3215 MET cc_start: 0.9508 (mpp) cc_final: 0.9251 (pmm) REVERT: D 3245 TYR cc_start: 0.8929 (t80) cc_final: 0.8669 (t80) REVERT: D 3250 TRP cc_start: 0.9041 (t-100) cc_final: 0.8508 (t-100) REVERT: D 3319 PHE cc_start: 0.8082 (m-80) cc_final: 0.7403 (m-80) REVERT: D 3819 MET cc_start: 0.7290 (mpp) cc_final: 0.6357 (ptt) REVERT: D 3985 MET cc_start: 0.9235 (mmm) cc_final: 0.8816 (mmm) REVERT: D 4052 MET cc_start: 0.7655 (ppp) cc_final: 0.7349 (ppp) REVERT: D 4186 MET cc_start: 0.8325 (mmm) cc_final: 0.7737 (mmm) REVERT: D 4279 MET cc_start: 0.6663 (mtt) cc_final: 0.6228 (ttt) REVERT: D 4672 MET cc_start: 0.8207 (mtm) cc_final: 0.7788 (mtp) REVERT: D 4884 MET cc_start: 0.8308 (mmm) cc_final: 0.7946 (mmm) outliers start: 109 outliers final: 78 residues processed: 855 average time/residue: 1.1950 time to fit residues: 1823.0421 Evaluate side-chains 865 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 776 time to evaluate : 12.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2496 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4492 LEU Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2496 LEU Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4239 LEU Chi-restraints excluded: chain B residue 4492 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 993 GLU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2496 LEU Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2828 MET Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain C residue 4239 LEU Chi-restraints excluded: chain C residue 4492 LEU Chi-restraints excluded: chain C residue 4817 MET Chi-restraints excluded: chain D residue 240 HIS Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2496 LEU Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2828 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3719 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1515 optimal weight: 0.0050 chunk 1595 optimal weight: 40.0000 chunk 1455 optimal weight: 4.9990 chunk 1552 optimal weight: 50.0000 chunk 934 optimal weight: 9.9990 chunk 676 optimal weight: 0.9990 chunk 1218 optimal weight: 10.0000 chunk 476 optimal weight: 3.9990 chunk 1402 optimal weight: 9.9990 chunk 1467 optimal weight: 4.9990 chunk 1546 optimal weight: 0.0000 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1978 ASN A2059 GLN A2464 HIS ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3031 ASN ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3727 GLN ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1169 ASN ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2059 GLN B2464 HIS ** B2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B4620 GLN ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2464 HIS ** C2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2059 GLN D2464 HIS ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3727 GLN D4620 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 141628 Z= 0.177 Angle : 0.587 16.089 191356 Z= 0.293 Chirality : 0.039 0.192 20988 Planarity : 0.004 0.119 24588 Dihedral : 6.086 88.097 19028 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Rotamer: Outliers : 0.68 % Allowed : 8.25 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.23 % 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: 1.00 (0.07), residues: 17212 helix: 1.70 (0.06), residues: 9112 sheet: -0.19 (0.13), residues: 1536 loop : -0.56 (0.08), residues: 6564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A2852 HIS 0.029 0.001 HIS D 240 PHE 0.035 0.001 PHE D3302 TYR 0.019 0.001 TYR C1703 ARG 0.005 0.000 ARG D2835 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 893 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 790 time to evaluate : 12.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8800 (tpt) cc_final: 0.8295 (tpt) REVERT: A 349 MET cc_start: 0.7691 (tpt) cc_final: 0.7323 (tpt) REVERT: A 393 MET cc_start: 0.7758 (mmm) cc_final: 0.7329 (mmm) REVERT: A 895 MET cc_start: 0.9173 (ptm) cc_final: 0.8850 (ppp) REVERT: A 902 TRP cc_start: 0.5575 (t-100) cc_final: 0.4687 (t-100) REVERT: A 995 MET cc_start: 0.8847 (ttt) cc_final: 0.8572 (ttt) REVERT: A 1165 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7621 (mtp) REVERT: A 1173 MET cc_start: 0.8782 (mtm) cc_final: 0.8475 (mtp) REVERT: A 1300 MET cc_start: 0.8521 (mtp) cc_final: 0.8245 (mtp) REVERT: A 1421 MET cc_start: 0.8475 (mmp) cc_final: 0.8169 (mmp) REVERT: A 1975 MET cc_start: 0.8841 (tmm) cc_final: 0.8229 (tmm) REVERT: A 2214 MET cc_start: 0.9241 (tpp) cc_final: 0.9014 (mmm) REVERT: A 2234 MET cc_start: 0.9011 (tpt) cc_final: 0.8757 (mmm) REVERT: A 2279 MET cc_start: 0.8329 (tmm) cc_final: 0.8096 (tmm) REVERT: A 2496 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9034 (tt) REVERT: A 2541 HIS cc_start: 0.9090 (m90) cc_final: 0.8720 (m-70) REVERT: A 2580 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.7003 (tp) REVERT: A 2585 MET cc_start: 0.8566 (mpp) cc_final: 0.7828 (mmm) REVERT: A 2605 MET cc_start: 0.8657 (tmm) cc_final: 0.8271 (tmm) REVERT: A 2689 MET cc_start: 0.6097 (ttt) cc_final: 0.5801 (ttt) REVERT: A 2719 TYR cc_start: 0.8871 (t80) cc_final: 0.8438 (t80) REVERT: A 2785 TRP cc_start: 0.8338 (m100) cc_final: 0.7421 (m100) REVERT: A 2798 MET cc_start: 0.9108 (tmm) cc_final: 0.8547 (mmt) REVERT: A 2828 MET cc_start: 0.7037 (mtp) cc_final: 0.6822 (mtp) REVERT: A 2835 ARG cc_start: 0.9187 (mmm160) cc_final: 0.8826 (mmp80) REVERT: A 2982 PHE cc_start: 0.8818 (m-80) cc_final: 0.8047 (m-80) REVERT: A 3245 TYR cc_start: 0.8956 (t80) cc_final: 0.8493 (t80) REVERT: A 3246 MET cc_start: 0.8912 (mmt) cc_final: 0.8496 (mmt) REVERT: A 3304 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8758 (tp-100) REVERT: A 3319 PHE cc_start: 0.8002 (m-80) cc_final: 0.7418 (m-80) REVERT: A 3819 MET cc_start: 0.7342 (mpp) cc_final: 0.6407 (ptt) REVERT: A 4002 MET cc_start: 0.8645 (tmm) cc_final: 0.8427 (tmm) REVERT: A 4035 TYR cc_start: 0.8073 (m-80) cc_final: 0.7823 (m-80) REVERT: A 4052 MET cc_start: 0.7798 (ppp) cc_final: 0.7388 (ppp) REVERT: A 4143 LYS cc_start: 0.9133 (tppt) cc_final: 0.8495 (tppt) REVERT: A 4186 MET cc_start: 0.8376 (mmm) cc_final: 0.7774 (mmm) REVERT: A 4279 MET cc_start: 0.6796 (mtt) cc_final: 0.6368 (ttt) REVERT: F 54 GLN cc_start: 0.8663 (mp10) cc_final: 0.8254 (mp10) REVERT: G 54 GLN cc_start: 0.8722 (mp10) cc_final: 0.8281 (mp10) REVERT: H 54 GLN cc_start: 0.8547 (mp10) cc_final: 0.8167 (mp10) REVERT: B 81 MET cc_start: 0.8811 (tpt) cc_final: 0.8583 (tpt) REVERT: B 128 MET cc_start: 0.9036 (mtm) cc_final: 0.8823 (mtp) REVERT: B 349 MET cc_start: 0.7693 (tpt) cc_final: 0.7292 (tpt) REVERT: B 895 MET cc_start: 0.8998 (ptm) cc_final: 0.8759 (ppp) REVERT: B 902 TRP cc_start: 0.5331 (t-100) cc_final: 0.4641 (t-100) REVERT: B 935 MET cc_start: 0.8835 (ppp) cc_final: 0.8545 (ppp) REVERT: B 995 MET cc_start: 0.8755 (ttt) cc_final: 0.8160 (ptm) REVERT: B 1165 MET cc_start: 0.8313 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: B 1173 MET cc_start: 0.8776 (mtm) cc_final: 0.8457 (mtp) REVERT: B 1306 MET cc_start: 0.8761 (mtp) cc_final: 0.8546 (mtm) REVERT: B 1794 MET cc_start: 0.8945 (mtm) cc_final: 0.8655 (mtp) REVERT: B 1975 MET cc_start: 0.8845 (tmm) cc_final: 0.8256 (tmm) REVERT: B 2234 MET cc_start: 0.8768 (tpp) cc_final: 0.7907 (tmm) REVERT: B 2279 MET cc_start: 0.8345 (tmm) cc_final: 0.8104 (tmm) REVERT: B 2496 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9042 (tt) REVERT: B 2541 HIS cc_start: 0.9082 (m90) cc_final: 0.8697 (m-70) REVERT: B 2605 MET cc_start: 0.8574 (tmm) cc_final: 0.8196 (tmm) REVERT: B 2681 MET cc_start: 0.9123 (tpp) cc_final: 0.8793 (tpp) REVERT: B 2719 TYR cc_start: 0.8865 (t80) cc_final: 0.8190 (t80) REVERT: B 2732 TRP cc_start: 0.9027 (t60) cc_final: 0.8771 (t60) REVERT: B 2798 MET cc_start: 0.8957 (ppp) cc_final: 0.8701 (ppp) REVERT: B 2843 MET cc_start: 0.9112 (ppp) cc_final: 0.8694 (ppp) REVERT: B 2848 TYR cc_start: 0.9483 (OUTLIER) cc_final: 0.8959 (m-80) REVERT: B 2849 HIS cc_start: 0.9127 (t70) cc_final: 0.8624 (t-170) REVERT: B 2874 TYR cc_start: 0.8118 (t80) cc_final: 0.7842 (t80) REVERT: B 2939 TYR cc_start: 0.8918 (m-80) cc_final: 0.8345 (m-10) REVERT: B 2982 PHE cc_start: 0.8791 (m-80) cc_final: 0.8013 (m-80) REVERT: B 3003 MET cc_start: 0.8630 (ptm) cc_final: 0.8196 (ptp) REVERT: B 3046 MET cc_start: 0.8839 (tpp) cc_final: 0.8581 (tpt) REVERT: B 3166 PHE cc_start: 0.8694 (t80) cc_final: 0.8405 (t80) REVERT: B 3181 TYR cc_start: 0.8438 (t80) cc_final: 0.8031 (t80) REVERT: B 3215 MET cc_start: 0.9512 (pmm) cc_final: 0.9272 (pmm) REVERT: B 3245 TYR cc_start: 0.8998 (t80) cc_final: 0.8709 (t80) REVERT: B 3250 TRP cc_start: 0.9008 (t-100) cc_final: 0.8379 (t-100) REVERT: B 3302 PHE cc_start: 0.9128 (m-80) cc_final: 0.8266 (t80) REVERT: B 3304 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8635 (tp-100) REVERT: B 3319 PHE cc_start: 0.8058 (m-80) cc_final: 0.7337 (m-80) REVERT: B 3689 MET cc_start: 0.8548 (mmp) cc_final: 0.8324 (mmp) REVERT: B 3819 MET cc_start: 0.7002 (mpp) cc_final: 0.6140 (ptp) REVERT: B 4035 TYR cc_start: 0.8146 (m-80) cc_final: 0.7930 (m-10) REVERT: B 4143 LYS cc_start: 0.9129 (tppt) cc_final: 0.8498 (tppt) REVERT: B 4186 MET cc_start: 0.8390 (mmm) cc_final: 0.7786 (mmm) REVERT: B 4274 MET cc_start: 0.6020 (mpp) cc_final: 0.4727 (tmm) REVERT: B 4279 MET cc_start: 0.6710 (mtt) cc_final: 0.6356 (ttt) REVERT: B 4568 MET cc_start: 0.7672 (mmm) cc_final: 0.7283 (mpp) REVERT: B 4672 MET cc_start: 0.8188 (mtm) cc_final: 0.7766 (mtp) REVERT: B 4809 MET cc_start: 0.8840 (tpp) cc_final: 0.8093 (tpp) REVERT: C 81 MET cc_start: 0.8821 (tpt) cc_final: 0.8591 (tpt) REVERT: C 241 MET cc_start: 0.7652 (mmp) cc_final: 0.7450 (mmp) REVERT: C 349 MET cc_start: 0.7526 (tpt) cc_final: 0.7159 (tpt) REVERT: C 902 TRP cc_start: 0.5394 (t-100) cc_final: 0.4701 (t-100) REVERT: C 935 MET cc_start: 0.8856 (ppp) cc_final: 0.8545 (ppp) REVERT: C 995 MET cc_start: 0.8868 (ttt) cc_final: 0.8606 (ttt) REVERT: C 1165 MET cc_start: 0.7944 (ttt) cc_final: 0.7502 (mtp) REVERT: C 1300 MET cc_start: 0.8543 (mtp) cc_final: 0.8303 (mtp) REVERT: C 1306 MET cc_start: 0.8736 (mtp) cc_final: 0.8531 (mtm) REVERT: C 1794 MET cc_start: 0.8936 (mtm) cc_final: 0.8671 (mtp) REVERT: C 1975 MET cc_start: 0.8845 (tmm) cc_final: 0.8234 (tmm) REVERT: C 2279 MET cc_start: 0.8350 (tmm) cc_final: 0.8129 (tmm) REVERT: C 2496 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9058 (tt) REVERT: C 2541 HIS cc_start: 0.9086 (m90) cc_final: 0.8738 (m-70) REVERT: C 2605 MET cc_start: 0.8721 (ttp) cc_final: 0.8153 (tmm) REVERT: C 2719 TYR cc_start: 0.8957 (t80) cc_final: 0.8321 (t80) REVERT: C 2828 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: C 2835 ARG cc_start: 0.9195 (mmm160) cc_final: 0.8785 (mmp80) REVERT: C 2843 MET cc_start: 0.9083 (ppp) cc_final: 0.8649 (ppp) REVERT: C 2848 TYR cc_start: 0.9470 (OUTLIER) cc_final: 0.8949 (m-80) REVERT: C 2849 HIS cc_start: 0.9099 (t70) cc_final: 0.8378 (t-170) REVERT: C 2874 TYR cc_start: 0.8065 (t80) cc_final: 0.7804 (t80) REVERT: C 2877 LEU cc_start: 0.8764 (mt) cc_final: 0.8463 (mt) REVERT: C 2939 TYR cc_start: 0.8922 (m-80) cc_final: 0.8363 (m-10) REVERT: C 2982 PHE cc_start: 0.8803 (m-80) cc_final: 0.8055 (m-80) REVERT: C 3003 MET cc_start: 0.8632 (ptm) cc_final: 0.8196 (ptp) REVERT: C 3215 MET cc_start: 0.9498 (mpp) cc_final: 0.9195 (pmm) REVERT: C 3245 TYR cc_start: 0.8947 (t80) cc_final: 0.8677 (t80) REVERT: C 3250 TRP cc_start: 0.8887 (t-100) cc_final: 0.8141 (t-100) REVERT: C 3302 PHE cc_start: 0.9131 (m-80) cc_final: 0.8231 (t80) REVERT: C 3304 GLN cc_start: 0.9073 (tp-100) cc_final: 0.8628 (tp-100) REVERT: C 3319 PHE cc_start: 0.8064 (m-80) cc_final: 0.7376 (m-80) REVERT: C 3689 MET cc_start: 0.8535 (mmp) cc_final: 0.8269 (mmp) REVERT: C 3819 MET cc_start: 0.7212 (mpp) cc_final: 0.6294 (ptt) REVERT: C 3985 MET cc_start: 0.9227 (mmm) cc_final: 0.8838 (mmm) REVERT: C 3999 MET cc_start: 0.8833 (tpp) cc_final: 0.8174 (tpp) REVERT: C 4002 MET cc_start: 0.8671 (tmm) cc_final: 0.8426 (tmm) REVERT: C 4035 TYR cc_start: 0.8117 (m-80) cc_final: 0.7911 (m-10) REVERT: C 4186 MET cc_start: 0.8386 (mmm) cc_final: 0.7758 (mmm) REVERT: C 4279 MET cc_start: 0.6707 (mtt) cc_final: 0.6271 (ttt) REVERT: C 4672 MET cc_start: 0.8176 (mtm) cc_final: 0.7773 (mtp) REVERT: C 4809 MET cc_start: 0.8848 (tpp) cc_final: 0.8175 (tpp) REVERT: D 81 MET cc_start: 0.8819 (tpt) cc_final: 0.8583 (tpt) REVERT: D 895 MET cc_start: 0.8934 (mtm) cc_final: 0.8686 (ppp) REVERT: D 899 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8246 (mp0) REVERT: D 902 TRP cc_start: 0.5487 (t-100) cc_final: 0.4575 (t-100) REVERT: D 935 MET cc_start: 0.8814 (ppp) cc_final: 0.8465 (ppp) REVERT: D 995 MET cc_start: 0.8770 (ttt) cc_final: 0.8203 (ptm) REVERT: D 1165 MET cc_start: 0.7934 (ttt) cc_final: 0.7487 (mtp) REVERT: D 1173 MET cc_start: 0.8517 (mtp) cc_final: 0.8292 (mtp) REVERT: D 1306 MET cc_start: 0.8739 (mtp) cc_final: 0.8496 (mtm) REVERT: D 1975 MET cc_start: 0.8840 (tmm) cc_final: 0.8214 (tmm) REVERT: D 2150 MET cc_start: 0.8474 (mtm) cc_final: 0.8231 (mtt) REVERT: D 2214 MET cc_start: 0.9295 (tpp) cc_final: 0.8766 (mmm) REVERT: D 2279 MET cc_start: 0.8331 (tmm) cc_final: 0.8095 (tmm) REVERT: D 2496 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9029 (tt) REVERT: D 2541 HIS cc_start: 0.9076 (m90) cc_final: 0.8720 (m-70) REVERT: D 2605 MET cc_start: 0.8594 (tmm) cc_final: 0.8215 (tmm) REVERT: D 2719 TYR cc_start: 0.8806 (t80) cc_final: 0.8122 (t80) REVERT: D 2782 MET cc_start: 0.8915 (tpp) cc_final: 0.8527 (mmm) REVERT: D 2785 TRP cc_start: 0.8209 (m-90) cc_final: 0.7696 (m100) REVERT: D 2798 MET cc_start: 0.8935 (ppp) cc_final: 0.8704 (ppp) REVERT: D 2828 MET cc_start: 0.7239 (OUTLIER) cc_final: 0.6861 (mtp) REVERT: D 2843 MET cc_start: 0.9130 (ppp) cc_final: 0.8592 (ppp) REVERT: D 2849 HIS cc_start: 0.9109 (t70) cc_final: 0.8274 (t-170) REVERT: D 2874 TYR cc_start: 0.8151 (t80) cc_final: 0.7817 (t80) REVERT: D 2877 LEU cc_start: 0.8776 (mt) cc_final: 0.8416 (mt) REVERT: D 2939 TYR cc_start: 0.8949 (m-80) cc_final: 0.8397 (m-10) REVERT: D 2982 PHE cc_start: 0.8802 (m-80) cc_final: 0.8047 (m-80) REVERT: D 3003 MET cc_start: 0.8670 (ptm) cc_final: 0.8262 (ptp) REVERT: D 3109 PHE cc_start: 0.9118 (m-10) cc_final: 0.8844 (m-10) REVERT: D 3215 MET cc_start: 0.9508 (mpp) cc_final: 0.9170 (pmm) REVERT: D 3245 TYR cc_start: 0.8955 (t80) cc_final: 0.8700 (t80) REVERT: D 3250 TRP cc_start: 0.9013 (t-100) cc_final: 0.8429 (t-100) REVERT: D 3304 GLN cc_start: 0.9109 (tp-100) cc_final: 0.8664 (tp-100) REVERT: D 3319 PHE cc_start: 0.8085 (m-80) cc_final: 0.7377 (m-80) REVERT: D 3819 MET cc_start: 0.7293 (mpp) cc_final: 0.6376 (ptt) REVERT: D 3985 MET cc_start: 0.9248 (mmm) cc_final: 0.8838 (mmm) REVERT: D 4052 MET cc_start: 0.7665 (ppp) cc_final: 0.7371 (ppp) REVERT: D 4186 MET cc_start: 0.8346 (mmm) cc_final: 0.7741 (mmm) REVERT: D 4279 MET cc_start: 0.6694 (mtt) cc_final: 0.6254 (ttt) REVERT: D 4672 MET cc_start: 0.8180 (mtm) cc_final: 0.7780 (mtp) REVERT: D 4884 MET cc_start: 0.8315 (mmm) cc_final: 0.7916 (mmm) outliers start: 103 outliers final: 85 residues processed: 855 average time/residue: 1.1837 time to fit residues: 1807.6804 Evaluate side-chains 877 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 780 time to evaluate : 12.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 HIS Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 956 HIS Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2496 LEU Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2732 TRP Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 3719 MET Chi-restraints excluded: chain A residue 4019 MET Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4492 LEU Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 956 HIS Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2496 LEU Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4239 LEU Chi-restraints excluded: chain B residue 4492 LEU Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 956 HIS Chi-restraints excluded: chain C residue 993 GLU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2496 LEU Chi-restraints excluded: chain C residue 2732 TRP Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2828 MET Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4239 LEU Chi-restraints excluded: chain C residue 4492 LEU Chi-restraints excluded: chain C residue 4817 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 956 HIS Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 1720 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2496 LEU Chi-restraints excluded: chain D residue 2732 TRP Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2828 MET Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3719 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain D residue 4492 LEU Chi-restraints excluded: chain D residue 4817 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1019 optimal weight: 0.5980 chunk 1641 optimal weight: 5.9990 chunk 1001 optimal weight: 1.9990 chunk 778 optimal weight: 4.9990 chunk 1140 optimal weight: 20.0000 chunk 1721 optimal weight: 0.0370 chunk 1584 optimal weight: 8.9990 chunk 1370 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 1058 optimal weight: 10.0000 chunk 840 optimal weight: 0.6980 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A3727 GLN ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3727 GLN ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1169 ASN ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 240 HIS ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1615 GLN ** D2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3727 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 141628 Z= 0.148 Angle : 0.584 14.662 191356 Z= 0.291 Chirality : 0.039 0.193 20988 Planarity : 0.004 0.118 24588 Dihedral : 5.982 89.241 19028 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 0.60 % Allowed : 8.42 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.07), residues: 17212 helix: 1.71 (0.06), residues: 9128 sheet: -0.02 (0.13), residues: 1564 loop : -0.55 (0.08), residues: 6520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP A2852 HIS 0.012 0.001 HIS B4055 PHE 0.042 0.001 PHE D3302 TYR 0.020 0.001 TYR D1060 ARG 0.007 0.000 ARG D2581 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 34424 Ramachandran restraints generated. 17212 Oldfield, 0 Emsley, 17212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 791 time to evaluate : 12.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 MET cc_start: 0.8793 (tpt) cc_final: 0.8556 (tpt) REVERT: A 349 MET cc_start: 0.7624 (tpt) cc_final: 0.7284 (tpt) REVERT: A 399 MET cc_start: 0.7981 (tmm) cc_final: 0.7712 (tmm) REVERT: A 895 MET cc_start: 0.9160 (ptm) cc_final: 0.8839 (ppp) REVERT: A 902 TRP cc_start: 0.5503 (t-100) cc_final: 0.4632 (t-100) REVERT: A 935 MET cc_start: 0.8827 (ppp) cc_final: 0.8592 (ppp) REVERT: A 995 MET cc_start: 0.8830 (ttt) cc_final: 0.8536 (ttt) REVERT: A 1165 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: A 1173 MET cc_start: 0.8792 (mtm) cc_final: 0.8471 (mtp) REVERT: A 1300 MET cc_start: 0.8476 (mtp) cc_final: 0.8203 (mtp) REVERT: A 1421 MET cc_start: 0.8495 (mmp) cc_final: 0.8198 (mmp) REVERT: A 1975 MET cc_start: 0.8844 (tmm) cc_final: 0.8230 (tmm) REVERT: A 2279 MET cc_start: 0.8316 (tmm) cc_final: 0.8078 (tmm) REVERT: A 2541 HIS cc_start: 0.9069 (m90) cc_final: 0.8707 (m-70) REVERT: A 2580 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.7929 (tp) REVERT: A 2585 MET cc_start: 0.8304 (mpp) cc_final: 0.7861 (mmm) REVERT: A 2605 MET cc_start: 0.8636 (tmm) cc_final: 0.8237 (tmm) REVERT: A 2689 MET cc_start: 0.6135 (ttt) cc_final: 0.5691 (ttt) REVERT: A 2719 TYR cc_start: 0.8838 (t80) cc_final: 0.8392 (t80) REVERT: A 2785 TRP cc_start: 0.8312 (m100) cc_final: 0.7450 (m100) REVERT: A 2798 MET cc_start: 0.9087 (tmm) cc_final: 0.8525 (mmt) REVERT: A 2835 ARG cc_start: 0.9170 (mmm160) cc_final: 0.8795 (mmp80) REVERT: A 2982 PHE cc_start: 0.8768 (m-80) cc_final: 0.7994 (m-80) REVERT: A 3215 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.9126 (pmm) REVERT: A 3245 TYR cc_start: 0.8961 (t80) cc_final: 0.8486 (t80) REVERT: A 3246 MET cc_start: 0.8896 (mmt) cc_final: 0.8273 (mmt) REVERT: A 3304 GLN cc_start: 0.9136 (tp-100) cc_final: 0.8735 (tp-100) REVERT: A 3319 PHE cc_start: 0.7982 (m-80) cc_final: 0.7400 (m-80) REVERT: A 3819 MET cc_start: 0.7261 (mpp) cc_final: 0.6280 (ptt) REVERT: A 4002 MET cc_start: 0.8607 (tmm) cc_final: 0.8376 (tmm) REVERT: A 4035 TYR cc_start: 0.7988 (m-80) cc_final: 0.7729 (m-80) REVERT: A 4052 MET cc_start: 0.7816 (ppp) cc_final: 0.7427 (ppp) REVERT: A 4143 LYS cc_start: 0.9140 (tppt) cc_final: 0.8506 (tppt) REVERT: A 4186 MET cc_start: 0.8300 (mmm) cc_final: 0.7807 (mmm) REVERT: A 4279 MET cc_start: 0.6962 (mtt) cc_final: 0.6516 (ttt) REVERT: F 54 GLN cc_start: 0.8627 (mp10) cc_final: 0.8226 (mp10) REVERT: G 54 GLN cc_start: 0.8714 (mp10) cc_final: 0.8276 (mp10) REVERT: H 54 GLN cc_start: 0.8542 (mp10) cc_final: 0.8151 (mp10) REVERT: H 67 MET cc_start: 0.8570 (mtp) cc_final: 0.8339 (mtp) REVERT: B 81 MET cc_start: 0.8806 (tpt) cc_final: 0.8578 (tpt) REVERT: B 349 MET cc_start: 0.7636 (tpt) cc_final: 0.7272 (tpt) REVERT: B 895 MET cc_start: 0.8985 (ptm) cc_final: 0.8746 (ppp) REVERT: B 902 TRP cc_start: 0.5227 (t-100) cc_final: 0.4614 (t-100) REVERT: B 935 MET cc_start: 0.8831 (ppp) cc_final: 0.8545 (ppp) REVERT: B 995 MET cc_start: 0.8741 (ttt) cc_final: 0.8170 (ptm) REVERT: B 1165 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7577 (mtp) REVERT: B 1173 MET cc_start: 0.8798 (mtm) cc_final: 0.8477 (mtp) REVERT: B 1306 MET cc_start: 0.8734 (mtp) cc_final: 0.8514 (mtm) REVERT: B 1794 MET cc_start: 0.8889 (mtm) cc_final: 0.8607 (mtp) REVERT: B 1975 MET cc_start: 0.8854 (tmm) cc_final: 0.8264 (tmm) REVERT: B 2279 MET cc_start: 0.8334 (tmm) cc_final: 0.8090 (tmm) REVERT: B 2541 HIS cc_start: 0.9036 (m90) cc_final: 0.8626 (m-70) REVERT: B 2605 MET cc_start: 0.8594 (tmm) cc_final: 0.8203 (tmm) REVERT: B 2681 MET cc_start: 0.9053 (tpp) cc_final: 0.8749 (tpp) REVERT: B 2719 TYR cc_start: 0.8852 (t80) cc_final: 0.8168 (t80) REVERT: B 2732 TRP cc_start: 0.9021 (t60) cc_final: 0.8767 (t60) REVERT: B 2782 MET cc_start: 0.8914 (tpp) cc_final: 0.8498 (mmm) REVERT: B 2798 MET cc_start: 0.8919 (ppp) cc_final: 0.8657 (ppp) REVERT: B 2843 MET cc_start: 0.9112 (ppp) cc_final: 0.8690 (ppp) REVERT: B 2848 TYR cc_start: 0.9488 (OUTLIER) cc_final: 0.8967 (m-80) REVERT: B 2849 HIS cc_start: 0.9100 (t70) cc_final: 0.8396 (t-170) REVERT: B 2874 TYR cc_start: 0.8071 (t80) cc_final: 0.7618 (t80) REVERT: B 2877 LEU cc_start: 0.8821 (mt) cc_final: 0.8525 (mt) REVERT: B 2939 TYR cc_start: 0.8904 (m-80) cc_final: 0.8349 (m-10) REVERT: B 2982 PHE cc_start: 0.8760 (m-80) cc_final: 0.7982 (m-80) REVERT: B 3003 MET cc_start: 0.8624 (ptm) cc_final: 0.8185 (ptp) REVERT: B 3046 MET cc_start: 0.8794 (tpp) cc_final: 0.8537 (tpt) REVERT: B 3166 PHE cc_start: 0.8714 (t80) cc_final: 0.8430 (t80) REVERT: B 3181 TYR cc_start: 0.8461 (t80) cc_final: 0.8106 (t80) REVERT: B 3215 MET cc_start: 0.9495 (pmm) cc_final: 0.9245 (pmm) REVERT: B 3245 TYR cc_start: 0.8994 (t80) cc_final: 0.8713 (t80) REVERT: B 3250 TRP cc_start: 0.8908 (t-100) cc_final: 0.8235 (t-100) REVERT: B 3302 PHE cc_start: 0.9104 (m-80) cc_final: 0.8262 (t80) REVERT: B 3304 GLN cc_start: 0.9071 (tp-100) cc_final: 0.8610 (tp-100) REVERT: B 3319 PHE cc_start: 0.8019 (m-80) cc_final: 0.7358 (m-80) REVERT: B 3689 MET cc_start: 0.8486 (mmp) cc_final: 0.8192 (mmp) REVERT: B 3819 MET cc_start: 0.6884 (mpp) cc_final: 0.6026 (ptp) REVERT: B 3981 MET cc_start: 0.8852 (tmm) cc_final: 0.8318 (ttm) REVERT: B 4035 TYR cc_start: 0.8119 (m-80) cc_final: 0.7905 (m-10) REVERT: B 4143 LYS cc_start: 0.9138 (tppt) cc_final: 0.8515 (tppt) REVERT: B 4186 MET cc_start: 0.8277 (mmm) cc_final: 0.7766 (mmm) REVERT: B 4274 MET cc_start: 0.5967 (mpp) cc_final: 0.4657 (tmm) REVERT: B 4279 MET cc_start: 0.6863 (mtt) cc_final: 0.6474 (ttt) REVERT: B 4568 MET cc_start: 0.7696 (mmm) cc_final: 0.7282 (mpp) REVERT: B 4672 MET cc_start: 0.8160 (mtm) cc_final: 0.7726 (mtp) REVERT: B 4748 MET cc_start: 0.7310 (mpp) cc_final: 0.6731 (mpp) REVERT: B 4804 MET cc_start: 0.8516 (mmm) cc_final: 0.8269 (mmm) REVERT: B 4809 MET cc_start: 0.8871 (tpp) cc_final: 0.8220 (tpp) REVERT: C 81 MET cc_start: 0.8818 (tpt) cc_final: 0.8591 (tpt) REVERT: C 241 MET cc_start: 0.7616 (mmp) cc_final: 0.7415 (mmp) REVERT: C 349 MET cc_start: 0.7481 (tpt) cc_final: 0.7141 (tpt) REVERT: C 899 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: C 902 TRP cc_start: 0.5308 (t-100) cc_final: 0.4618 (t-100) REVERT: C 935 MET cc_start: 0.8830 (ppp) cc_final: 0.8527 (ppp) REVERT: C 995 MET cc_start: 0.8869 (ttt) cc_final: 0.8578 (ttt) REVERT: C 1165 MET cc_start: 0.7821 (ttt) cc_final: 0.7399 (mtp) REVERT: C 1300 MET cc_start: 0.8536 (mtp) cc_final: 0.8336 (mtp) REVERT: C 1306 MET cc_start: 0.8707 (mtp) cc_final: 0.8504 (mtm) REVERT: C 1794 MET cc_start: 0.8894 (mtm) cc_final: 0.8642 (mtp) REVERT: C 1975 MET cc_start: 0.8843 (tmm) cc_final: 0.8253 (tmm) REVERT: C 2172 MET cc_start: 0.8729 (tpp) cc_final: 0.8517 (mpp) REVERT: C 2234 MET cc_start: 0.8946 (mmm) cc_final: 0.8634 (tpt) REVERT: C 2279 MET cc_start: 0.8333 (tmm) cc_final: 0.8113 (tmm) REVERT: C 2541 HIS cc_start: 0.9050 (m90) cc_final: 0.8665 (m-70) REVERT: C 2605 MET cc_start: 0.8739 (ttp) cc_final: 0.8136 (tmm) REVERT: C 2719 TYR cc_start: 0.8956 (t80) cc_final: 0.8320 (t80) REVERT: C 2782 MET cc_start: 0.8882 (tpp) cc_final: 0.8474 (mmm) REVERT: C 2835 ARG cc_start: 0.9170 (mmm160) cc_final: 0.8717 (mmp80) REVERT: C 2843 MET cc_start: 0.9060 (ppp) cc_final: 0.8611 (ppp) REVERT: C 2848 TYR cc_start: 0.9475 (OUTLIER) cc_final: 0.8952 (m-80) REVERT: C 2849 HIS cc_start: 0.9076 (t70) cc_final: 0.8363 (t-170) REVERT: C 2874 TYR cc_start: 0.8003 (t80) cc_final: 0.7778 (t80) REVERT: C 2877 LEU cc_start: 0.8793 (mt) cc_final: 0.8524 (mt) REVERT: C 2939 TYR cc_start: 0.8911 (m-80) cc_final: 0.8367 (m-10) REVERT: C 2982 PHE cc_start: 0.8766 (m-80) cc_final: 0.8027 (m-80) REVERT: C 3003 MET cc_start: 0.8655 (ptm) cc_final: 0.8236 (ptp) REVERT: C 3215 MET cc_start: 0.9492 (mpp) cc_final: 0.9160 (pmm) REVERT: C 3245 TYR cc_start: 0.8925 (t80) cc_final: 0.8658 (t80) REVERT: C 3250 TRP cc_start: 0.8818 (t-100) cc_final: 0.8084 (t-100) REVERT: C 3302 PHE cc_start: 0.9107 (m-80) cc_final: 0.8217 (t80) REVERT: C 3304 GLN cc_start: 0.9046 (tp-100) cc_final: 0.8587 (tp-100) REVERT: C 3319 PHE cc_start: 0.8067 (m-80) cc_final: 0.7374 (m-80) REVERT: C 3689 MET cc_start: 0.8534 (mmp) cc_final: 0.8249 (mmp) REVERT: C 3819 MET cc_start: 0.7089 (mpp) cc_final: 0.6166 (ptp) REVERT: C 3985 MET cc_start: 0.9219 (mmm) cc_final: 0.8913 (mmm) REVERT: C 3999 MET cc_start: 0.8775 (tpp) cc_final: 0.8236 (ttm) REVERT: C 4002 MET cc_start: 0.8631 (tmm) cc_final: 0.8367 (tmm) REVERT: C 4035 TYR cc_start: 0.8041 (m-80) cc_final: 0.7824 (m-10) REVERT: C 4186 MET cc_start: 0.8269 (mmm) cc_final: 0.7759 (mmm) REVERT: C 4274 MET cc_start: 0.5959 (mpp) cc_final: 0.4667 (tmm) REVERT: C 4279 MET cc_start: 0.6864 (mtt) cc_final: 0.6463 (ttt) REVERT: C 4672 MET cc_start: 0.8131 (mtm) cc_final: 0.7748 (mtp) REVERT: C 4748 MET cc_start: 0.7288 (mpp) cc_final: 0.6749 (mpp) REVERT: C 4809 MET cc_start: 0.8860 (tpp) cc_final: 0.8273 (tpp) REVERT: D 81 MET cc_start: 0.8825 (tpt) cc_final: 0.8594 (tpt) REVERT: D 895 MET cc_start: 0.8959 (mtm) cc_final: 0.8690 (ppp) REVERT: D 899 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8252 (mp0) REVERT: D 902 TRP cc_start: 0.5370 (t-100) cc_final: 0.4503 (t-100) REVERT: D 935 MET cc_start: 0.8799 (ppp) cc_final: 0.8464 (ppp) REVERT: D 995 MET cc_start: 0.8742 (ttt) cc_final: 0.8186 (ptp) REVERT: D 1165 MET cc_start: 0.7820 (ttt) cc_final: 0.7401 (mtp) REVERT: D 1306 MET cc_start: 0.8711 (mtp) cc_final: 0.8473 (mtm) REVERT: D 1794 MET cc_start: 0.8866 (mtm) cc_final: 0.8598 (mtp) REVERT: D 1975 MET cc_start: 0.8842 (tmm) cc_final: 0.8237 (tmm) REVERT: D 2214 MET cc_start: 0.9264 (tpp) cc_final: 0.8747 (mmm) REVERT: D 2234 MET cc_start: 0.8717 (mmt) cc_final: 0.8483 (mmm) REVERT: D 2279 MET cc_start: 0.8333 (tmm) cc_final: 0.8111 (tmm) REVERT: D 2541 HIS cc_start: 0.9033 (m90) cc_final: 0.8661 (m-70) REVERT: D 2605 MET cc_start: 0.8596 (tmm) cc_final: 0.8216 (tmm) REVERT: D 2719 TYR cc_start: 0.8794 (t80) cc_final: 0.8096 (t80) REVERT: D 2782 MET cc_start: 0.8873 (tpp) cc_final: 0.8490 (mmm) REVERT: D 2785 TRP cc_start: 0.8181 (m-90) cc_final: 0.7657 (m100) REVERT: D 2798 MET cc_start: 0.8919 (ppp) cc_final: 0.8689 (ppp) REVERT: D 2843 MET cc_start: 0.9143 (ppp) cc_final: 0.8614 (ppp) REVERT: D 2849 HIS cc_start: 0.9092 (t70) cc_final: 0.8282 (t-170) REVERT: D 2874 TYR cc_start: 0.8102 (t80) cc_final: 0.7799 (t80) REVERT: D 2877 LEU cc_start: 0.8811 (mt) cc_final: 0.8441 (mt) REVERT: D 2939 TYR cc_start: 0.8931 (m-80) cc_final: 0.8399 (m-10) REVERT: D 2982 PHE cc_start: 0.8767 (m-80) cc_final: 0.8017 (m-80) REVERT: D 3003 MET cc_start: 0.8678 (ptm) cc_final: 0.8272 (ptp) REVERT: D 3109 PHE cc_start: 0.9105 (m-10) cc_final: 0.8901 (m-10) REVERT: D 3215 MET cc_start: 0.9502 (mpp) cc_final: 0.9152 (pmm) REVERT: D 3245 TYR cc_start: 0.8970 (t80) cc_final: 0.8729 (t80) REVERT: D 3250 TRP cc_start: 0.8903 (t-100) cc_final: 0.8333 (t-100) REVERT: D 3302 PHE cc_start: 0.9114 (m-80) cc_final: 0.8231 (t80) REVERT: D 3304 GLN cc_start: 0.9099 (tp-100) cc_final: 0.8645 (tp-100) REVERT: D 3319 PHE cc_start: 0.8054 (m-80) cc_final: 0.7367 (m-80) REVERT: D 3819 MET cc_start: 0.7149 (mpp) cc_final: 0.6214 (ptp) REVERT: D 3985 MET cc_start: 0.9249 (mmm) cc_final: 0.8899 (mmm) REVERT: D 4052 MET cc_start: 0.7660 (ppp) cc_final: 0.7369 (ppp) REVERT: D 4186 MET cc_start: 0.8263 (mmm) cc_final: 0.7745 (mmm) REVERT: D 4274 MET cc_start: 0.5948 (mpp) cc_final: 0.4592 (tmm) REVERT: D 4279 MET cc_start: 0.6860 (mtt) cc_final: 0.6468 (ttt) REVERT: D 4672 MET cc_start: 0.8161 (mtm) cc_final: 0.7774 (mtp) REVERT: D 4884 MET cc_start: 0.8290 (mmm) cc_final: 0.8067 (mmm) outliers start: 91 outliers final: 70 residues processed: 853 average time/residue: 1.1833 time to fit residues: 1800.0308 Evaluate side-chains 863 residues out of total 15188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 785 time to evaluate : 12.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 993 GLU Chi-restraints excluded: chain A residue 1162 VAL Chi-restraints excluded: chain A residue 1165 MET Chi-restraints excluded: chain A residue 1720 MET Chi-restraints excluded: chain A residue 2134 MET Chi-restraints excluded: chain A residue 2580 LEU Chi-restraints excluded: chain A residue 2801 TYR Chi-restraints excluded: chain A residue 2956 TYR Chi-restraints excluded: chain A residue 3002 GLU Chi-restraints excluded: chain A residue 3060 PHE Chi-restraints excluded: chain A residue 3069 GLU Chi-restraints excluded: chain A residue 3077 GLN Chi-restraints excluded: chain A residue 3215 MET Chi-restraints excluded: chain A residue 3285 TYR Chi-restraints excluded: chain A residue 4239 LEU Chi-restraints excluded: chain A residue 4817 MET Chi-restraints excluded: chain E residue 26 HIS Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain H residue 26 HIS Chi-restraints excluded: chain H residue 56 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 993 GLU Chi-restraints excluded: chain B residue 1162 VAL Chi-restraints excluded: chain B residue 1165 MET Chi-restraints excluded: chain B residue 1300 MET Chi-restraints excluded: chain B residue 2801 TYR Chi-restraints excluded: chain B residue 2848 TYR Chi-restraints excluded: chain B residue 2956 TYR Chi-restraints excluded: chain B residue 3002 GLU Chi-restraints excluded: chain B residue 3060 PHE Chi-restraints excluded: chain B residue 3069 GLU Chi-restraints excluded: chain B residue 3077 GLN Chi-restraints excluded: chain B residue 3285 TYR Chi-restraints excluded: chain B residue 3719 MET Chi-restraints excluded: chain B residue 4019 MET Chi-restraints excluded: chain B residue 4492 LEU Chi-restraints excluded: chain B residue 4817 MET Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 899 GLU Chi-restraints excluded: chain C residue 993 GLU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 2134 MET Chi-restraints excluded: chain C residue 2801 TYR Chi-restraints excluded: chain C residue 2848 TYR Chi-restraints excluded: chain C residue 2956 TYR Chi-restraints excluded: chain C residue 3002 GLU Chi-restraints excluded: chain C residue 3060 PHE Chi-restraints excluded: chain C residue 3069 GLU Chi-restraints excluded: chain C residue 3077 GLN Chi-restraints excluded: chain C residue 3285 TYR Chi-restraints excluded: chain C residue 3719 MET Chi-restraints excluded: chain C residue 4019 MET Chi-restraints excluded: chain C residue 4239 LEU Chi-restraints excluded: chain C residue 4817 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 899 GLU Chi-restraints excluded: chain D residue 993 GLU Chi-restraints excluded: chain D residue 1162 VAL Chi-restraints excluded: chain D residue 1300 MET Chi-restraints excluded: chain D residue 2134 MET Chi-restraints excluded: chain D residue 2167 MET Chi-restraints excluded: chain D residue 2801 TYR Chi-restraints excluded: chain D residue 2956 TYR Chi-restraints excluded: chain D residue 3002 GLU Chi-restraints excluded: chain D residue 3060 PHE Chi-restraints excluded: chain D residue 3069 GLU Chi-restraints excluded: chain D residue 3077 GLN Chi-restraints excluded: chain D residue 3285 TYR Chi-restraints excluded: chain D residue 3719 MET Chi-restraints excluded: chain D residue 4019 MET Chi-restraints excluded: chain D residue 4239 LEU Chi-restraints excluded: chain D residue 4817 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1728 random chunks: chunk 1088 optimal weight: 2.9990 chunk 1460 optimal weight: 6.9990 chunk 419 optimal weight: 8.9990 chunk 1264 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 380 optimal weight: 10.0000 chunk 1373 optimal weight: 10.0000 chunk 574 optimal weight: 5.9990 chunk 1409 optimal weight: 0.0060 chunk 173 optimal weight: 10.0000 chunk 252 optimal weight: 8.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN ** A2586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1978 ASN ** B2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2838 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3727 GLN ** C4055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2868 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D3287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3727 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.041808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.031043 restraints weight = 1646419.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.032350 restraints weight = 660018.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.033041 restraints weight = 383215.144| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 141628 Z= 0.219 Angle : 0.596 17.847 191356 Z= 0.296 Chirality : 0.040 0.230 20988 Planarity : 0.004 0.171 24588 Dihedral : 5.939 89.679 19028 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 0.53 % Allowed : 8.70 % Favored : 90.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 1.07 (0.07), residues: 17212 helix: 1.75 (0.06), residues: 9124 sheet: -0.06 (0.13), residues: 1500 loop : -0.55 (0.08), residues: 6588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A2852 HIS 0.011 0.001 HIS C4055 PHE 0.026 0.001 PHE C3166 TYR 0.018 0.001 TYR B1703 ARG 0.014 0.000 ARG D2793 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 36425.03 seconds wall clock time: 639 minutes 7.52 seconds (38347.52 seconds total)